/***************************************************************************** # Copyright (C) 1994-2008 by David Gordon. # All rights reserved. # # This software is part of a beta-test version of the Consed/Autofinish # package. It should not be redistributed or # used for any commercial purpose, including commercially funded # sequencing, without written permission from the author and the # University of Washington. # # This software is provided ``AS IS'' and any express or implied # warranties, including, but not limited to, the implied warranties of # merchantability and fitness for a particular purpose, are disclaimed. # In no event shall the authors or the University of Washington be # liable for any direct, indirect, incidental, special, exemplary, or # consequential damages (including, but not limited to, procurement of # substitute goods or services; loss of use, data, or profits; or # business interruption) however caused and on any theory of liability, # whether in contract, strict liability, or tort (including negligence # or otherwise) arising in any way out of the use of this software, even # if advised of the possibility of such damage. # # Building Consed from source is error prone and not simple which is # why I provide executables. Due to time limitations I cannot # provide any assistance in building Consed. Even if you do not # modify the source, you may introduce errors due to using a # different version of the compiler, a different version of motif, # different versions of other libraries than I used, etc. For this # reason, if you discover Consed bugs, I can only offer help with # those bugs if you first reproduce those bugs with an executable # provided by me--not an executable you have built. # # Modifying Consed is also difficult. Although Consed is modular, # some modules are used by many other modules. Thus making a change # in one place can have unforeseen effects on many other features. # It may takes months for you to notice these other side-effects # which may not seen connected at all. It is not feasable for me to # provide help with modifying Consed sources because of the # potentially huge amount of time involved. # #*****************************************************************************/ #include "guiEditResources.h" #include #include #include #include #include #include #include #include #include "bIsNumericMaybeWithWhitespace.h" #include "popupErrorMessage.h" #include "bIsNumericDouble.h" #include "consedResources.h" #include "guiapp.h" #include "handleWindowManagerDelete2.h" #include "hp_exception_kludge.h" #include "consedParameters.h" #include "guiapp.h" #include "assert.h" #include #include "please_wait.h" #include "textbox.h" #include #include #include "waitUntilDialogIsVisible.h" #include "popupInfoMessage.h" #include "guiTopWindow.h" #include #include "defaultResources.h" class helpCallbackInfo { public: RWCString soResource_; guiEditResources* pGuiEditResources_; }; #define makeWidgetTypeDouble( RESOURCE, PARAMETER_WITHOUT_PREFIX ) \ \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## Form = XtVaCreateManagedWidget( \ "form1", \ xmFormWidgetClass, \ widRowCol, \ XmNshadowThickness, 0, /* otherwise black line segments*/ \ NULL ); \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## Label = XtVaCreateManagedWidget( \ #RESOURCE , \ xmLabelWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_FORM, \ XmNrightAttachment, XmATTACH_FORM, \ XmNtopAttachment, XmATTACH_FORM, \ XmNtopOffset, 20, \ XmNalignment, XmALIGNMENT_BEGINNING, \ NULL ); \ \ getColors( resources_.d ## PARAMETER_WITHOUT_PREFIX ## _ , \ CONDEF->d ## PARAMETER_WITHOUT_PREFIX ## _, \ pixForeground, \ pixBackground ); \ \ wid ## PARAMETER_WITHOUT_PREFIX ## _ = XtVaCreateManagedWidget( \ #RESOURCE "Input", \ xmTextFieldWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_FORM, \ XmNtopAttachment, XmATTACH_WIDGET, \ XmNtopWidget, wid ## PARAMETER_WITHOUT_PREFIX ## Label , \ XmNbottomAttachment, XmATTACH_FORM, \ XmNvalue, RWCString( resources_.d ## PARAMETER_WITHOUT_PREFIX ## _ ).data(), \ XmNforeground, pixForeground, \ XmNbackground, pixBackground, \ NULL ); \ \ XtAddCallback( wid ## PARAMETER_WITHOUT_PREFIX ## _ , \ XmNlosingFocusCallback, \ cb ## PARAMETER_WITHOUT_PREFIX , \ this ); \ \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## Default = XtVaCreateManagedWidget( \ #RESOURCE "Default", \ xmTextFieldWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, 50, \ XmNtopAttachment, XmATTACH_WIDGET, \ XmNtopWidget, wid ## PARAMETER_WITHOUT_PREFIX ## Label , \ XmNbottomAttachment, XmATTACH_FORM, \ XmNvalue, RWCString( CONDEF->d ## PARAMETER_WITHOUT_PREFIX ## _ ).data(), \ XmNeditable, False, \ XmNcursorPositionVisible, False, \ XmNtraversalOn, False, \ NULL ); \ \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## HelpButton = XtVaCreateManagedWidget( \ "?", \ xmPushButtonWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, 46, \ XmNrightPosition, 49, \ XmNtopAttachment, XmATTACH_WIDGET, \ XmNtopWidget, wid ## PARAMETER_WITHOUT_PREFIX ## Label , \ XmNbottomAttachment, XmATTACH_FORM, \ XmNtraversalOn, False, \ NULL ); \ \ \ pHelp = new helpCallbackInfo();\ pHelp->soResource_ = #RESOURCE ;\ pHelp->pGuiEditResources_ = this;\ \ XtAddCallback( wid ## PARAMETER_WITHOUT_PREFIX ## HelpButton,\ XmNactivateCallback,\ cbUserPushedHelp,\ pHelp );\ // This will translate to this: // Widget widResourceForm = XtVaCreateManagedWidget( // "form", // xmFormWidgetClass, // widRowCol, // XmNshadowThickness, 0, // otherwise black line segments // NULL ); // Widget widLabel1 = XtVaCreateManagedWidget( // "consed.autoFinishMinNumberOfErrorsFixedByAnExp", // xmLabelWidgetClass, // widResourceForm1, // XmNleftAttachment, XmATTACH_FORM, // XmNrightAttachment, XmATTACH_FORM, // XmNtopAttachment, XmATTACH_FORM, // XmNtopOffset, 20, // XmNalignment, XmALIGNMENT_BEGINNING, // NULL ); // getColors( resources_.dAutoFinishMinNumberOfErrorsFixedByAnExp_, // CONDEF->dAutoFinishMinNumberOfErrorsFixedByAnExp_, // pixForeground, // pixBackground ); // widAutoFinishMinNumberOfErrorsFixedByAnExp_ = XtVaCreateManagedWidget( // "consed.autoFinishMinNumberOfErrorsFixedByAnExpInput", // xmTextFieldWidgetClass, // widResourceForm1, // XmNleftAttachment, XmATTACH_FORM, // XmNtopAttachment, XmATTACH_WIDGET, // XmNtopWidget, widLabel1, // XmNbottomAttachment, XmATTACH_FORM, // XmNvalue, RWCString( resources_dAutoFinishMinNumberOfErrorsFixedByAnExp_ ).data(), // XmNforeground, pixForeground, // XmNbackground, pixBackground, // NULL ); // XtAddCallback( widAutoFinishMinNumberOfErrorsFixedByAnExp_, // XmNlosingFocusCallback, // cbAutoFinishMinNumberOfErrorsFixedByAnExp, // this ); // Widget widDefault1 = XtVaCreateManagedWidget( // "consed.autoFinishMinNumberOfErrorsFixedByAnExpDefault", // xmTextFieldWidgetClass, // widResourceForm1, // XmNleftAttachment, XmATTACH_POSITION, // XmNleftPosition, 50, // XmNtopAttachment, XmATTACH_WIDGET, // XmNtopWidget, widLabel1, // XmNbottomAttachment, XmATTACH_FORM, // XmNvalue, RWCString( consedResources::pDefaultResources_->dAutoFinishMinNumberOfErrorsFixedByAnExp_ ).data(), // XmNeditable, False, // XmNcursorPositionVisible, False, // XmNtraversalOn, False, // NULL ); #define makeWidgetTypeInt( RESOURCE, PARAMETER_WITHOUT_PREFIX ) \ \ getColors( resources_.n ## PARAMETER_WITHOUT_PREFIX ## _ , \ CONDEF->n ## PARAMETER_WITHOUT_PREFIX ## _ , \ pixForeground, \ pixBackground ); \ \ \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## Form = XtVaCreateManagedWidget( \ "form", \ xmFormWidgetClass, \ widRowCol, \ XmNshadowThickness, 0, /* otherwise black line segments*/ \ NULL ); \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## Label = XtVaCreateManagedWidget( \ #RESOURCE , \ xmLabelWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_FORM, \ XmNrightAttachment, XmATTACH_FORM, \ XmNtopAttachment, XmATTACH_FORM, \ XmNtopOffset, 20, \ XmNalignment, XmALIGNMENT_BEGINNING, \ NULL ); \ \ \ wid ## PARAMETER_WITHOUT_PREFIX ## _ = XtVaCreateManagedWidget( \ #RESOURCE "Input", \ xmTextFieldWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_FORM, \ XmNtopAttachment, XmATTACH_WIDGET, \ XmNtopWidget, wid ## PARAMETER_WITHOUT_PREFIX ## Label, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNvalue, RWCString( (long) resources_.n ## PARAMETER_WITHOUT_PREFIX ## _ ).data(), \ XmNforeground, pixForeground, \ XmNbackground, pixBackground, \ NULL ); \ \ \ XtAddCallback( wid ## PARAMETER_WITHOUT_PREFIX ## _, \ XmNlosingFocusCallback, \ cb ## PARAMETER_WITHOUT_PREFIX, \ this ); \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## Default = XtVaCreateManagedWidget( \ #RESOURCE "Default", \ xmTextFieldWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, 50, \ XmNtopAttachment, XmATTACH_WIDGET, \ XmNtopWidget, wid ## PARAMETER_WITHOUT_PREFIX ## Label, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNvalue, RWCString( (long) CONDEF->n ## PARAMETER_WITHOUT_PREFIX ## _ ).data(), \ XmNeditable, False, \ XmNcursorPositionVisible, False, \ XmNtraversalOn, False, \ NULL ); \ \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## HelpButton = XtVaCreateManagedWidget( \ "?", \ xmPushButtonWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, 46, \ XmNrightPosition, 49, \ XmNtopAttachment, XmATTACH_WIDGET, \ XmNtopWidget, wid ## PARAMETER_WITHOUT_PREFIX ## Label , \ XmNbottomAttachment, XmATTACH_FORM, \ XmNtraversalOn, False, \ NULL ); \ \ \ pHelp = new helpCallbackInfo(); \ pHelp->soResource_ = #RESOURCE ; \ pHelp->pGuiEditResources_ = this; \ \ XtAddCallback( wid ## PARAMETER_WITHOUT_PREFIX ## HelpButton, \ XmNactivateCallback, \ cbUserPushedHelp, \ pHelp ); \ // will convert to this: // consed.autoFinishAverageInsertSize // int // getColors( resources_.nAutoFinishAverageInsertSize_, // CONDEF->nAutoFinishAverageInsertSize_, // pixForeground, // pixBackground ); // Widget widResourceForm2 = XtVaCreateManagedWidget( // "form2", // xmFormWidgetClass, // widRowCol, // XmNshadowThickness, 0, // otherwise black line segments // NULL ); // Widget widLabel2 = XtVaCreateManagedWidget( // "consed.autoFinishAverageInsertSize", // xmLabelWidgetClass, // widResourceForm2, // XmNleftAttachment, XmATTACH_FORM, // XmNrightAttachment, XmATTACH_FORM, // XmNtopAttachment, XmATTACH_FORM, // XmNtopOffset, 20, // XmNalignment, XmALIGNMENT_BEGINNING, // NULL ); // widAutoFinishAverageInsertSize_ = XtVaCreateManagedWidget( // "consed.autoFinishAverageInsertSizeInput", // xmTextFieldWidgetClass, // widResourceForm2, // XmNleftAttachment, XmATTACH_FORM, // XmNtopAttachment, XmATTACH_WIDGET, // XmNtopWidget, widLabel2, // XmNbottomAttachment, XmATTACH_FORM, // XmNvalue, RWCString( (long) resources_.nAutoFinishAverageInsertSize_ ).data(), // XmNforeground, pixForeground, // XmNbackground, pixBackground, // NULL ); // XtAddCallback( widAutoFinishAverageInsertSize_, // XmNlosingFocusCallback, // cbAutoFinishAverageInsertSize, // this ); // Widget widDefault2 = XtVaCreateManagedWidget( // "consed.autoFinishAverageInsertSizeInputDefault", // xmTextFieldWidgetClass, // widResourceForm2, // XmNleftAttachment, XmATTACH_POSITION, // XmNleftPosition, 50, // XmNtopAttachment, XmATTACH_WIDGET, // XmNtopWidget, widLabel2, // XmNbottomAttachment, XmATTACH_FORM, // XmNvalue, RWCString( (long) CONDEF->nAutoFinishAverageInsertSize_ ).data(), // XmNeditable, False, // XmNcursorPositionVisible, False, // XmNtraversalOn, False, // NULL ); // consed.primersPickTemplatesForPrimers: true // bool #define makeWidgetTypeBool( RESOURCE, PARAMETER_WITHOUT_PREFIX ) \ \ getColors( resources_.b ## PARAMETER_WITHOUT_PREFIX ## _, \ CONDEF->b ## PARAMETER_WITHOUT_PREFIX ## _, \ pixForeground, \ pixBackground ); \ \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## Form = XtVaCreateManagedWidget( \ "form", \ xmFormWidgetClass, \ widRowCol, \ XmNshadowThickness, 0, /* otherwise black line segments */ \ NULL ); \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## Label = XtVaCreateManagedWidget( \ #RESOURCE, \ xmLabelWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_FORM, \ XmNrightAttachment, XmATTACH_FORM, \ XmNtopAttachment, XmATTACH_FORM, \ XmNtopOffset, 20, \ XmNalignment, XmALIGNMENT_BEGINNING, \ NULL ); \ \ wid ## PARAMETER_WITHOUT_PREFIX ## RadioBox_ = XmCreateRadioBox( \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ "radio", \ NULL, \ 0 ); \ \ XtVaSetValues( wid ## PARAMETER_WITHOUT_PREFIX ## RadioBox_, \ XmNtraversalOn, True, \ XmNleftAttachment, XmATTACH_FORM, \ XmNtopAttachment, XmATTACH_WIDGET, \ XmNtopWidget, wid ## PARAMETER_WITHOUT_PREFIX ## Label, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNorientation, XmHORIZONTAL, \ XmNforeground, pixForeground, \ XmNbackground, pixBackground, \ NULL ); \ \ wid ## PARAMETER_WITHOUT_PREFIX ## True_ = XtVaCreateManagedWidget( \ "True", \ xmToggleButtonWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## RadioBox_, \ XmNset, ( resources_.b ## PARAMETER_WITHOUT_PREFIX ## _ ? True : False ), \ NULL ); \ \ XtAddCallback( wid ## PARAMETER_WITHOUT_PREFIX ## True_, \ XmNvalueChangedCallback, \ cb ## PARAMETER_WITHOUT_PREFIX , \ this ); \ \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## FalseButton = XtVaCreateManagedWidget( \ "False", \ xmToggleButtonWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## RadioBox_, \ XmNset, ( resources_.b ## PARAMETER_WITHOUT_PREFIX ## _ ? False : True ), \ NULL ); \ \ XtManageChild( wid ## PARAMETER_WITHOUT_PREFIX ## RadioBox_ ); \ \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## Default = XtVaCreateManagedWidget( \ #RESOURCE , \ xmTextFieldWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, 50, \ XmNtopAttachment, XmATTACH_WIDGET, \ XmNtopWidget, wid ## PARAMETER_WITHOUT_PREFIX ## Label, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNvalue, ( CONDEF->b ## PARAMETER_WITHOUT_PREFIX ## _ ? "True" : "False" ), \ XmNeditable, False, \ XmNcursorPositionVisible, False, \ XmNtraversalOn, False, \ NULL ); \ \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## HelpButton = XtVaCreateManagedWidget( \ "?", \ xmPushButtonWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, 46, \ XmNrightPosition, 49, \ XmNtopAttachment, XmATTACH_WIDGET, \ XmNtopWidget, wid ## PARAMETER_WITHOUT_PREFIX ## Label , \ XmNbottomAttachment, XmATTACH_FORM, \ XmNtraversalOn, False, \ NULL ); \ \ \ pHelp = new helpCallbackInfo(); \ pHelp->soResource_ = #RESOURCE ; \ pHelp->pGuiEditResources_ = this; \ \ XtAddCallback( wid ## PARAMETER_WITHOUT_PREFIX ## HelpButton, \ XmNactivateCallback, \ cbUserPushedHelp, \ pHelp ); \ // this will translate to the following: // consed.primersPickTemplatesForPrimers: true // bool // getColors( resources_.bPrimersPickTemplatesForPrimers_, // CONDEF->bPrimersPickTemplatesForPrimers_, // pixForeground, // pixBackground ); // Widget widResourceForm3 = XtVaCreateManagedWidget( // "form3", // xmFormWidgetClass, // widRowCol, // XmNshadowThickness, 0, // otherwise black line segments // NULL ); // Widget widLabel3 = XtVaCreateManagedWidget( // "consed.primersPickTemplatesForPrimers", // xmLabelWidgetClass, // widResourceForm3, // XmNleftAttachment, XmATTACH_FORM, // XmNrightAttachment, XmATTACH_FORM, // XmNtopAttachment, XmATTACH_FORM, // XmNtopOffset, 20, // XmNalignment, XmALIGNMENT_BEGINNING, // NULL ); // widPrimersPickTemplatesForPrimersRadioBox_ = XmCreateRadioBox( // widResourceForm3, // "radio", // NULL, // 0 ); // XtVaSetValues( widPrimersPickTemplatesForPrimersRadioBox_, // XmNtraversalOn, True, // XmNleftAttachment, XmATTACH_FORM, // XmNtopAttachment, XmATTACH_WIDGET, // XmNtopWidget, widLabel3, // XmNbottomAttachment, XmATTACH_FORM, // XmNorientation, XmHORIZONTAL, // XmNforeground, pixForeground, // XmNbackground, pixBackground, // NULL ); // widPrimersPickTemplatesForPrimersTrue_ = XtVaCreateManagedWidget( // "True", // xmToggleButtonWidgetClass, // widPrimersPickTemplatesForPrimersRadioBox_, // XmNset, ( resources_.bPrimersPickTemplatesForPrimers_ ? True : False ), // NULL ); // XtAddCallback( widPrimersPickTemplatesForPrimersTrue_, // XmNvalueChangedCallback, // cbPrimersPickTemplatesForPrimers, // this ); // widFalseButton = XtVaCreateManagedWidget( // "False", // xmToggleButtonWidgetClass, // widPrimersPickTemplatesForPrimersRadioBox_, // XmNset, ( consedResources::pCurrentResources_->bPrimersPickTemplatesForPrimers_ ? False : True ), // NULL ); // XtManageChild( widPrimersPickTemplatesForPrimersRadioBox_ ); // Widget widDefault3 = XtVaCreateManagedWidget( // "consed.primersPickTemplatesForPrimers", // xmTextFieldWidgetClass, // widResourceForm3, // XmNleftAttachment, XmATTACH_POSITION, // XmNleftPosition, 50, // XmNtopAttachment, XmATTACH_WIDGET, // XmNtopWidget, widLabel3, // XmNbottomAttachment, XmATTACH_FORM, // XmNvalue, ( consedResources::pDefaultResources_->bPrimersPickTemplatesForPrimers_ ? "True" : "False" ), // XmNeditable, False, // XmNcursorPositionVisible, False, // XmNtraversalOn, False, // NULL ); #define makeWidgetTypeRWCString( RESOURCE, PARAMETER_WITHOUT_PREFIX ) \ \ getColors( resources_.so ## PARAMETER_WITHOUT_PREFIX ## _, \ CONDEF->so ## PARAMETER_WITHOUT_PREFIX ## _, \ pixForeground, \ pixBackground ); \ \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## Form = XtVaCreateManagedWidget( \ "form", \ xmFormWidgetClass, \ widRowCol, \ XmNshadowThickness, 0, /* otherwise black line segments */ \ NULL ); \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## Label = XtVaCreateManagedWidget( \ #RESOURCE, \ xmLabelWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_FORM, \ XmNrightAttachment, XmATTACH_FORM, \ XmNtopAttachment, XmATTACH_FORM, \ XmNtopOffset, 20, \ XmNalignment, XmALIGNMENT_BEGINNING, \ NULL ); \ \ wid ## PARAMETER_WITHOUT_PREFIX ## _ = \ XtVaCreateManagedWidget( \ #RESOURCE "Input", \ xmTextFieldWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_FORM, \ XmNrightAttachment, XmATTACH_POSITION, \ XmNrightPosition, 45, \ XmNtopAttachment, XmATTACH_WIDGET, \ XmNtopWidget, wid ## PARAMETER_WITHOUT_PREFIX ## Label, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNvalue, resources_.so ## PARAMETER_WITHOUT_PREFIX ## _.data(), \ XmNforeground, pixForeground, \ XmNbackground, pixBackground, \ NULL ); \ \ \ XtAddCallback( wid ## PARAMETER_WITHOUT_PREFIX ## _, \ XmNlosingFocusCallback, \ cb ## PARAMETER_WITHOUT_PREFIX, \ this ); \ \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## Default = XtVaCreateManagedWidget( \ #RESOURCE "Default", \ xmTextFieldWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, 50, \ XmNrightAttachment, XmATTACH_FORM, \ XmNrightOffset, 10, \ XmNtopAttachment, XmATTACH_WIDGET, \ XmNtopWidget, wid ## PARAMETER_WITHOUT_PREFIX ## Label, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNvalue, CONDEF->so ## PARAMETER_WITHOUT_PREFIX ## _.data(), \ XmNeditable, False, \ XmNcursorPositionVisible, False, \ XmNtraversalOn, False, \ NULL ); \ \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## HelpButton = XtVaCreateManagedWidget( \ "?", \ xmPushButtonWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, 46, \ XmNrightPosition, 49, \ XmNtopAttachment, XmATTACH_WIDGET, \ XmNtopWidget, wid ## PARAMETER_WITHOUT_PREFIX ## Label , \ XmNbottomAttachment, XmATTACH_FORM, \ XmNtraversalOn, False, \ NULL ); \ \ \ pHelp = new helpCallbackInfo(); \ pHelp->soResource_ = #RESOURCE ; \ pHelp->pGuiEditResources_ = this; \ \ XtAddCallback( wid ## PARAMETER_WITHOUT_PREFIX ## HelpButton, \ XmNactivateCallback, \ cbUserPushedHelp, \ pHelp ); \ // this translates to this: // consed.primersSubcloneFullPathnameOfFileOfSequencesForScreening // RWCString // getColors( resources_.soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_, // CONDEF->soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_, // pixForeground, // pixBackground ); // Widget widResourceForm4 = XtVaCreateManagedWidget( // "form4", // xmFormWidgetClass, // widRowCol, // XmNshadowThickness, 0, // otherwise black line segments // NULL ); // Widget widLabel4 = XtVaCreateManagedWidget( // "consed.primersSubcloneFullPathnameOfFileOfSequencesForScreening", // xmLabelWidgetClass, // widResourceForm4, // XmNleftAttachment, XmATTACH_FORM, // XmNrightAttachment, XmATTACH_FORM, // XmNtopAttachment, XmATTACH_FORM, // XmNtopOffset, 20, // XmNalignment, XmALIGNMENT_BEGINNING, // NULL ); // widPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_ = // XtVaCreateManagedWidget( // "consed.primersSubcloneFullPathnameOfFileOfSequencesForScreeningInput", // xmTextFieldWidgetClass, // widResourceForm4, // XmNleftAttachment, XmATTACH_FORM, // XmNtopAttachment, XmATTACH_WIDGET, // XmNtopWidget, widLabel4, // XmNbottomAttachment, XmATTACH_FORM, // XmNvalue, resources_.soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_.data(), // XmNforeground, pixForeground, // XmNbackground, pixBackground, // NULL ); // XtAddCallback( widPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_, // XmNlosingFocusCallback, // cbPrimersSubcloneFullPathnameOfFileOfSequencesForScreening, // this ); // Widget widDefault4 = XtVaCreateManagedWidget( // "consed.primersSubcloneFullPathnameOfFileOfSequencesForScreeningDefault", // xmTextFieldWidgetClass, // widResourceForm4, // XmNleftAttachment, XmATTACH_POSITION, // XmNleftPosition, 50, // XmNtopAttachment, XmATTACH_WIDGET, // XmNtopWidget, widLabel4, // XmNbottomAttachment, XmATTACH_FORM, // XmNvalue, CONDEF->soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_.data(), // XmNeditable, False, // XmNcursorPositionVisible, False, // XmNtraversalOn, False, // NULL ); // consed.primersBadLibrariesFile: badLibraries.txt // FileName #define makeWidgetTypeFileName( RESOURCE, PARAMETER_WITHOUT_PREFIX ) \ \ getColors( resources_.fil ## PARAMETER_WITHOUT_PREFIX ## _, \ CONDEF->fil ## PARAMETER_WITHOUT_PREFIX ## _, \ pixForeground, \ pixBackground ); \ \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## Form = XtVaCreateManagedWidget( \ "form", \ xmFormWidgetClass, \ widRowCol, \ XmNshadowThickness, 0, /* otherwise black line segments */ \ NULL ); \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## Label = XtVaCreateManagedWidget( \ #RESOURCE, \ xmLabelWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_FORM, \ XmNrightAttachment, XmATTACH_FORM, \ XmNtopAttachment, XmATTACH_FORM, \ XmNtopOffset, 20, \ XmNalignment, XmALIGNMENT_BEGINNING, \ NULL ); \ \ wid ## PARAMETER_WITHOUT_PREFIX ## _ = \ XtVaCreateManagedWidget( \ #RESOURCE "Input", \ xmTextFieldWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_FORM, \ XmNrightAttachment, XmATTACH_POSITION, \ XmNrightPosition, 45, \ XmNtopAttachment, XmATTACH_WIDGET, \ XmNtopWidget, wid ## PARAMETER_WITHOUT_PREFIX ## Label, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNvalue, resources_.fil ## PARAMETER_WITHOUT_PREFIX ## _.data(), \ XmNforeground, pixForeground, \ XmNbackground, pixBackground, \ NULL ); \ \ \ XtAddCallback( wid ## PARAMETER_WITHOUT_PREFIX ## _, \ XmNlosingFocusCallback, \ cb ## PARAMETER_WITHOUT_PREFIX, \ this ); \ \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## Default = XtVaCreateManagedWidget( \ #RESOURCE "Default", \ xmTextFieldWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, 50, \ XmNrightAttachment, XmATTACH_FORM, \ XmNrightOffset, 10, \ XmNtopAttachment, XmATTACH_WIDGET, \ XmNtopWidget, wid ## PARAMETER_WITHOUT_PREFIX ## Label, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNvalue, CONDEF->fil ## PARAMETER_WITHOUT_PREFIX ## _.data(), \ XmNeditable, False, \ XmNcursorPositionVisible, False, \ XmNtraversalOn, False, \ NULL ); \ \ \ Widget wid ## PARAMETER_WITHOUT_PREFIX ## HelpButton = XtVaCreateManagedWidget( \ "?", \ xmPushButtonWidgetClass, \ wid ## PARAMETER_WITHOUT_PREFIX ## Form, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, 46, \ XmNrightPosition, 49, \ XmNtopAttachment, XmATTACH_WIDGET, \ XmNtopWidget, wid ## PARAMETER_WITHOUT_PREFIX ## Label , \ XmNbottomAttachment, XmATTACH_FORM, \ XmNtraversalOn, False, \ NULL ); \ \ \ pHelp = new helpCallbackInfo(); \ pHelp->soResource_ = #RESOURCE ; \ pHelp->pGuiEditResources_ = this; \ \ XtAddCallback( wid ## PARAMETER_WITHOUT_PREFIX ## HelpButton, \ XmNactivateCallback, \ cbUserPushedHelp, \ pHelp ); \ static void cbUserPushedHelp( Widget wid, XtPointer pClientData, XtPointer pCallData ) { helpCallbackInfo* pHelp = (helpCallbackInfo*) pClientData; TRY_CATCH_WRAPPER( pHelp->pGuiEditResources_->userPushedHelp( pHelp->soResource_ ); ); } static void cbResize( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGuiEditResources = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGuiEditResources->userResizedWindow() ); } static void cbFindFirstButton( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGuiEditResources = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGuiEditResources->userPushedFindButton( true ) ); } static void cbFindNextButton( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGuiEditResources = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGuiEditResources->userPushedFindButton( false ) ); } static void cbCancelButton( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGuiEditResources = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( delete pGuiEditResources ); } static void cbUserPushedSaveButton( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGuiEditResources = (guiEditResources*) pClientData; pGuiEditResources->userPushedSave(); } static void cbFileSelectionOK( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->userChoseFileAndPushedOK( wid, (XmFileSelectionBoxCallbackStruct*) pCallData ) ); } static void cbFileSelectionCancel( Widget wid, XtPointer pClientData, XtPointer pCallData ) { XtUnmanageChild( wid ); XtDestroyWidget( wid ); } static void cbPrintPS( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrintPS() ); } void guiEditResources :: checkPrintPS() { bool b = XmToggleButtonGetState( widPrintPSTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bPrintPS_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bPrintPS_, CONDEF->bPrintPS_, pixForeground, pixBackground ); XtVaSetValues( widPrintPSRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbDefaultTagType( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkDefaultTagType() ); } void guiEditResources :: checkDefaultTagType() { char* szValue = XmTextFieldGetString( widDefaultTagType_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soDefaultTagType_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soDefaultTagType_, CONDEF->soDefaultTagType_, pixForeground, pixBackground ); XtVaSetValues( widDefaultTagType_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbDefaultTagOnConsensusNotReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkDefaultTagOnConsensusNotReads() ); } void guiEditResources :: checkDefaultTagOnConsensusNotReads() { bool b = XmToggleButtonGetState( widDefaultTagOnConsensusNotReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bDefaultTagOnConsensusNotReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bDefaultTagOnConsensusNotReads_, CONDEF->bDefaultTagOnConsensusNotReads_, pixForeground, pixBackground ); XtVaSetValues( widDefaultTagOnConsensusNotReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishMinNumberOfErrorsFixedByAnExp( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishMinNumberOfErrorsFixedByAnExp() ); } void guiEditResources :: checkAutoFinishMinNumberOfErrorsFixedByAnExp() { char* szValue = XmTextFieldGetString( widAutoFinishMinNumberOfErrorsFixedByAnExp_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "AutoFinishMinNumberOfErrorsFixedByAnExp must be floating point numeric"; THROW_ERROR( soError ); } resources_.dAutoFinishMinNumberOfErrorsFixedByAnExp_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dAutoFinishMinNumberOfErrorsFixedByAnExp_, CONDEF->dAutoFinishMinNumberOfErrorsFixedByAnExp_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishMinNumberOfErrorsFixedByAnExp_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishRedundancy( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishRedundancy() ); } void guiEditResources :: checkAutoFinishRedundancy() { char* szValue = XmTextFieldGetString( widAutoFinishRedundancy_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "AutoFinishRedundancy must be floating point numeric"; THROW_ERROR( soError ); } resources_.dAutoFinishRedundancy_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dAutoFinishRedundancy_, CONDEF->dAutoFinishRedundancy_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishRedundancy_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishAverageInsertSize( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishAverageInsertSize() ); } void guiEditResources :: checkAutoFinishAverageInsertSize() { char* szValue = XmTextFieldGetString( widAutoFinishAverageInsertSize_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishAverageInsertSize must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishAverageInsertSize_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishAverageInsertSize_, CONDEF->nAutoFinishAverageInsertSize_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishAverageInsertSize_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMaxInsertSizeOfASubclone( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMaxInsertSizeOfASubclone() ); } void guiEditResources :: checkPrimersMaxInsertSizeOfASubclone() { char* szValue = XmTextFieldGetString( widPrimersMaxInsertSizeOfASubclone_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMaxInsertSizeOfASubclone must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMaxInsertSizeOfASubclone_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMaxInsertSizeOfASubclone_, CONDEF->nPrimersMaxInsertSizeOfASubclone_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMaxInsertSizeOfASubclone_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMaxMeltingTemp( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMaxMeltingTemp() ); } void guiEditResources :: checkPrimersMaxMeltingTemp() { char* szValue = XmTextFieldGetString( widPrimersMaxMeltingTemp_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMaxMeltingTemp must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMaxMeltingTemp_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMaxMeltingTemp_, CONDEF->nPrimersMaxMeltingTemp_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMaxMeltingTemp_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMaxMeltingTempForPCR( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMaxMeltingTempForPCR() ); } void guiEditResources :: checkPrimersMaxMeltingTempForPCR() { char* szValue = XmTextFieldGetString( widPrimersMaxMeltingTempForPCR_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMaxMeltingTempForPCR must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMaxMeltingTempForPCR_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMaxMeltingTempForPCR_, CONDEF->nPrimersMaxMeltingTempForPCR_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMaxMeltingTempForPCR_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersPickTemplatesForPrimers( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersPickTemplatesForPrimers() ); } void guiEditResources :: checkPrimersPickTemplatesForPrimers() { bool b = XmToggleButtonGetState( widPrimersPickTemplatesForPrimersTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bPrimersPickTemplatesForPrimers_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bPrimersPickTemplatesForPrimers_, CONDEF->bPrimersPickTemplatesForPrimers_, pixForeground, pixBackground ); XtVaSetValues( widPrimersPickTemplatesForPrimersRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersSubcloneFullPathnameOfFileOfSequencesForScreening( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersSubcloneFullPathnameOfFileOfSequencesForScreening() ); } void guiEditResources :: checkPrimersSubcloneFullPathnameOfFileOfSequencesForScreening() { char* szValue = XmTextFieldGetString( widPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_, CONDEF->soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_, pixForeground, pixBackground ); XtVaSetValues( widPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersCloneFullPathnameOfFileOfSequencesForScreening( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersCloneFullPathnameOfFileOfSequencesForScreening() ); } void guiEditResources :: checkPrimersCloneFullPathnameOfFileOfSequencesForScreening() { char* szValue = XmTextFieldGetString( widPrimersCloneFullPathnameOfFileOfSequencesForScreening_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soPrimersCloneFullPathnameOfFileOfSequencesForScreening_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soPrimersCloneFullPathnameOfFileOfSequencesForScreening_, CONDEF->soPrimersCloneFullPathnameOfFileOfSequencesForScreening_, pixForeground, pixBackground ); XtVaSetValues( widPrimersCloneFullPathnameOfFileOfSequencesForScreening_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMinMeltingTemp( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMinMeltingTemp() ); } void guiEditResources :: checkPrimersMinMeltingTemp() { char* szValue = XmTextFieldGetString( widPrimersMinMeltingTemp_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMinMeltingTemp must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMinMeltingTemp_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMinMeltingTemp_, CONDEF->nPrimersMinMeltingTemp_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMinMeltingTemp_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMinMeltingTempForPCR( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMinMeltingTempForPCR() ); } void guiEditResources :: checkPrimersMinMeltingTempForPCR() { char* szValue = XmTextFieldGetString( widPrimersMinMeltingTempForPCR_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMinMeltingTempForPCR must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMinMeltingTempForPCR_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMinMeltingTempForPCR_, CONDEF->nPrimersMinMeltingTempForPCR_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMinMeltingTempForPCR_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbSearchFunctionsUseUnalignedEndsOfReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkSearchFunctionsUseUnalignedEndsOfReads() ); } void guiEditResources :: checkSearchFunctionsUseUnalignedEndsOfReads() { bool b = XmToggleButtonGetState( widSearchFunctionsUseUnalignedEndsOfReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bSearchFunctionsUseUnalignedEndsOfReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bSearchFunctionsUseUnalignedEndsOfReads_, CONDEF->bSearchFunctionsUseUnalignedEndsOfReads_, pixForeground, pixBackground ); XtVaSetValues( widSearchFunctionsUseUnalignedEndsOfReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbSearchFunctionsUseLowQualityEndsOfReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkSearchFunctionsUseLowQualityEndsOfReads() ); } void guiEditResources :: checkSearchFunctionsUseLowQualityEndsOfReads() { bool b = XmToggleButtonGetState( widSearchFunctionsUseLowQualityEndsOfReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bSearchFunctionsUseLowQualityEndsOfReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bSearchFunctionsUseLowQualityEndsOfReads_, CONDEF->bSearchFunctionsUseLowQualityEndsOfReads_, pixForeground, pixBackground ); XtVaSetValues( widSearchFunctionsUseLowQualityEndsOfReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbInexactSearchForStringMaxPerCentMismatch( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkInexactSearchForStringMaxPerCentMismatch() ); } void guiEditResources :: checkInexactSearchForStringMaxPerCentMismatch() { char* szValue = XmTextFieldGetString( widInexactSearchForStringMaxPerCentMismatch_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.InexactSearchForStringMaxPerCentMismatch must be numeric"; THROW_ERROR( soError ); } resources_.nInexactSearchForStringMaxPerCentMismatch_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nInexactSearchForStringMaxPerCentMismatch_, CONDEF->nInexactSearchForStringMaxPerCentMismatch_, pixForeground, pixBackground ); XtVaSetValues( widInexactSearchForStringMaxPerCentMismatch_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbOnlyAllowOneReadWriteConsedAtATime( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkOnlyAllowOneReadWriteConsedAtATime() ); } void guiEditResources :: checkOnlyAllowOneReadWriteConsedAtATime() { bool b = XmToggleButtonGetState( widOnlyAllowOneReadWriteConsedAtATimeTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bOnlyAllowOneReadWriteConsedAtATime_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bOnlyAllowOneReadWriteConsedAtATime_, CONDEF->bOnlyAllowOneReadWriteConsedAtATime_, pixForeground, pixBackground ); XtVaSetValues( widOnlyAllowOneReadWriteConsedAtATimeRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair() ); } void guiEditResources :: checkAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair() { bool b = XmToggleButtonGetState( widAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePairTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_, CONDEF->bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePairRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrintWindowCommand( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrintWindowCommand() ); } void guiEditResources :: checkPrintWindowCommand() { char* szValue = XmTextFieldGetString( widPrintWindowCommand_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soPrintWindowCommand_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soPrintWindowCommand_, CONDEF->soPrintWindowCommand_, pixForeground, pixBackground ); XtVaSetValues( widPrintWindowCommand_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbFileOfTagTypes( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkFileOfTagTypes() ); } void guiEditResources :: checkFileOfTagTypes() { char* szValue = XmTextFieldGetString( widFileOfTagTypes_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filFileOfTagTypes_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filFileOfTagTypes_, CONDEF->filFileOfTagTypes_, pixForeground, pixBackground ); XtVaSetValues( widFileOfTagTypes_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewShowConsistentFwdRevPairs( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewShowConsistentFwdRevPairs() ); } void guiEditResources :: checkAssemblyViewShowConsistentFwdRevPairs() { bool b = XmToggleButtonGetState( widAssemblyViewShowConsistentFwdRevPairsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewShowConsistentFwdRevPairs_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewShowConsistentFwdRevPairs_, CONDEF->bAssemblyViewShowConsistentFwdRevPairs_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewShowConsistentFwdRevPairsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewShowConsistentFwdRevPairDepth( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewShowConsistentFwdRevPairDepth() ); } void guiEditResources :: checkAssemblyViewShowConsistentFwdRevPairDepth() { bool b = XmToggleButtonGetState( widAssemblyViewShowConsistentFwdRevPairDepthTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewShowConsistentFwdRevPairDepth_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewShowConsistentFwdRevPairDepth_, CONDEF->bAssemblyViewShowConsistentFwdRevPairDepth_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewShowConsistentFwdRevPairDepthRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds() ); } void guiEditResources :: checkAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds() { bool b = XmToggleButtonGetState( widAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffoldsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds_, CONDEF->bAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffoldsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs() ); } void guiEditResources :: checkAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs() { bool b = XmToggleButtonGetState( widAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs_, CONDEF->bAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewShowGapSpanningFwdRevPairs( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewShowGapSpanningFwdRevPairs() ); } void guiEditResources :: checkAssemblyViewShowGapSpanningFwdRevPairs() { bool b = XmToggleButtonGetState( widAssemblyViewShowGapSpanningFwdRevPairsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewShowGapSpanningFwdRevPairs_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewShowGapSpanningFwdRevPairs_, CONDEF->bAssemblyViewShowGapSpanningFwdRevPairs_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewShowGapSpanningFwdRevPairsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewShowWhichInconsistentFwdRevPairs( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewShowWhichInconsistentFwdRevPairs() ); } void guiEditResources :: checkAssemblyViewShowWhichInconsistentFwdRevPairs() { char* szValue = XmTextFieldGetString( widAssemblyViewShowWhichInconsistentFwdRevPairs_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soAssemblyViewShowWhichInconsistentFwdRevPairs_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soAssemblyViewShowWhichInconsistentFwdRevPairs_, CONDEF->soAssemblyViewShowWhichInconsistentFwdRevPairs_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewShowWhichInconsistentFwdRevPairs_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewShowReadDepth( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewShowReadDepth() ); } void guiEditResources :: checkAssemblyViewShowReadDepth() { bool b = XmToggleButtonGetState( widAssemblyViewShowReadDepthTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewShowReadDepth_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewShowReadDepth_, CONDEF->bAssemblyViewShowReadDepth_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewShowReadDepthRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewShowMultipleHighQualityDiscrepancies( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewShowMultipleHighQualityDiscrepancies() ); } void guiEditResources :: checkAssemblyViewShowMultipleHighQualityDiscrepancies() { bool b = XmToggleButtonGetState( widAssemblyViewShowMultipleHighQualityDiscrepanciesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewShowMultipleHighQualityDiscrepancies_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewShowMultipleHighQualityDiscrepancies_, CONDEF->bAssemblyViewShowMultipleHighQualityDiscrepancies_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewShowMultipleHighQualityDiscrepanciesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewShowRestrictionDigestCutSites( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewShowRestrictionDigestCutSites() ); } void guiEditResources :: checkAssemblyViewShowRestrictionDigestCutSites() { bool b = XmToggleButtonGetState( widAssemblyViewShowRestrictionDigestCutSitesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewShowRestrictionDigestCutSites_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewShowRestrictionDigestCutSites_, CONDEF->bAssemblyViewShowRestrictionDigestCutSites_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewShowRestrictionDigestCutSitesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewFilterSequenceMatchesBySize( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewFilterSequenceMatchesBySize() ); } void guiEditResources :: checkAssemblyViewFilterSequenceMatchesBySize() { bool b = XmToggleButtonGetState( widAssemblyViewFilterSequenceMatchesBySizeTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewFilterSequenceMatchesBySize_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewFilterSequenceMatchesBySize_, CONDEF->bAssemblyViewFilterSequenceMatchesBySize_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewFilterSequenceMatchesBySizeRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewSequenceMatchesMinSize( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewSequenceMatchesMinSize() ); } void guiEditResources :: checkAssemblyViewSequenceMatchesMinSize() { char* szValue = XmTextFieldGetString( widAssemblyViewSequenceMatchesMinSize_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AssemblyViewSequenceMatchesMinSize must be numeric"; THROW_ERROR( soError ); } resources_.nAssemblyViewSequenceMatchesMinSize_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAssemblyViewSequenceMatchesMinSize_, CONDEF->nAssemblyViewSequenceMatchesMinSize_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewSequenceMatchesMinSize_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewSequenceMatchesMaxSize( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewSequenceMatchesMaxSize() ); } void guiEditResources :: checkAssemblyViewSequenceMatchesMaxSize() { char* szValue = XmTextFieldGetString( widAssemblyViewSequenceMatchesMaxSize_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AssemblyViewSequenceMatchesMaxSize must be numeric"; THROW_ERROR( soError ); } resources_.nAssemblyViewSequenceMatchesMaxSize_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAssemblyViewSequenceMatchesMaxSize_, CONDEF->nAssemblyViewSequenceMatchesMaxSize_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewSequenceMatchesMaxSize_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewAutomaticallyStartWithConsed( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewAutomaticallyStartWithConsed() ); } void guiEditResources :: checkAssemblyViewAutomaticallyStartWithConsed() { bool b = XmToggleButtonGetState( widAssemblyViewAutomaticallyStartWithConsedTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewAutomaticallyStartWithConsed_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewAutomaticallyStartWithConsed_, CONDEF->bAssemblyViewAutomaticallyStartWithConsed_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewAutomaticallyStartWithConsedRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewDisplayTheseTagTypesOnTheseLines( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewDisplayTheseTagTypesOnTheseLines() ); } void guiEditResources :: checkAssemblyViewDisplayTheseTagTypesOnTheseLines() { char* szValue = XmTextFieldGetString( widAssemblyViewDisplayTheseTagTypesOnTheseLines_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soAssemblyViewDisplayTheseTagTypesOnTheseLines_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soAssemblyViewDisplayTheseTagTypesOnTheseLines_, CONDEF->soAssemblyViewDisplayTheseTagTypesOnTheseLines_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewDisplayTheseTagTypesOnTheseLines_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewShowTags( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewShowTags() ); } void guiEditResources :: checkAssemblyViewShowTags() { bool b = XmToggleButtonGetState( widAssemblyViewShowTagsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewShowTags_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewShowTags_, CONDEF->bAssemblyViewShowTags_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewShowTagsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoEditRecalculateHighQualitySegmentsOfReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoEditRecalculateHighQualitySegmentsOfReads() ); } void guiEditResources :: checkAutoEditRecalculateHighQualitySegmentsOfReads() { bool b = XmToggleButtonGetState( widAutoEditRecalculateHighQualitySegmentsOfReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoEditRecalculateHighQualitySegmentsOfReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoEditRecalculateHighQualitySegmentsOfReads_, CONDEF->bAutoEditRecalculateHighQualitySegmentsOfReads_, pixForeground, pixBackground ); XtVaSetValues( widAutoEditRecalculateHighQualitySegmentsOfReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoEditConvertCloneEndBasesToXs( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoEditConvertCloneEndBasesToXs() ); } void guiEditResources :: checkAutoEditConvertCloneEndBasesToXs() { bool b = XmToggleButtonGetState( widAutoEditConvertCloneEndBasesToXsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoEditConvertCloneEndBasesToXs_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoEditConvertCloneEndBasesToXs_, CONDEF->bAutoEditConvertCloneEndBasesToXs_, pixForeground, pixBackground ); XtVaSetValues( widAutoEditConvertCloneEndBasesToXsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads() ); } void guiEditResources :: checkAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads() { bool b = XmToggleButtonGetState( widAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads_, CONDEF->bAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads_, pixForeground, pixBackground ); XtVaSetValues( widAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoEditTagEditableLowConsensusQualityRegions( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoEditTagEditableLowConsensusQualityRegions() ); } void guiEditResources :: checkAutoEditTagEditableLowConsensusQualityRegions() { bool b = XmToggleButtonGetState( widAutoEditTagEditableLowConsensusQualityRegionsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoEditTagEditableLowConsensusQualityRegions_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoEditTagEditableLowConsensusQualityRegions_, CONDEF->bAutoEditTagEditableLowConsensusQualityRegions_, pixForeground, pixBackground ); XtVaSetValues( widAutoEditTagEditableLowConsensusQualityRegionsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoEditMakeFakeRead( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoEditMakeFakeRead() ); } void guiEditResources :: checkAutoEditMakeFakeRead() { bool b = XmToggleButtonGetState( widAutoEditMakeFakeReadTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoEditMakeFakeRead_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoEditMakeFakeRead_, CONDEF->bAutoEditMakeFakeRead_, pixForeground, pixBackground ); XtVaSetValues( widAutoEditMakeFakeReadRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoEditMakeFakeReadFromRead1( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoEditMakeFakeReadFromRead1() ); } void guiEditResources :: checkAutoEditMakeFakeReadFromRead1() { char* szValue = XmTextFieldGetString( widAutoEditMakeFakeReadFromRead1_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soAutoEditMakeFakeReadFromRead1_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soAutoEditMakeFakeReadFromRead1_, CONDEF->soAutoEditMakeFakeReadFromRead1_, pixForeground, pixBackground ); XtVaSetValues( widAutoEditMakeFakeReadFromRead1_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoEditMakeFakeReadFromRead2( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoEditMakeFakeReadFromRead2() ); } void guiEditResources :: checkAutoEditMakeFakeReadFromRead2() { char* szValue = XmTextFieldGetString( widAutoEditMakeFakeReadFromRead2_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soAutoEditMakeFakeReadFromRead2_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soAutoEditMakeFakeReadFromRead2_, CONDEF->soAutoEditMakeFakeReadFromRead2_, pixForeground, pixBackground ); XtVaSetValues( widAutoEditMakeFakeReadFromRead2_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoEditMakeFakeReadName( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoEditMakeFakeReadName() ); } void guiEditResources :: checkAutoEditMakeFakeReadName() { char* szValue = XmTextFieldGetString( widAutoEditMakeFakeReadName_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soAutoEditMakeFakeReadName_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soAutoEditMakeFakeReadName_, CONDEF->soAutoEditMakeFakeReadName_, pixForeground, pixBackground ); XtVaSetValues( widAutoEditMakeFakeReadName_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoEditMakeFakeReadFastaFilename( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoEditMakeFakeReadFastaFilename() ); } void guiEditResources :: checkAutoEditMakeFakeReadFastaFilename() { char* szValue = XmTextFieldGetString( widAutoEditMakeFakeReadFastaFilename_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filAutoEditMakeFakeReadFastaFilename_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filAutoEditMakeFakeReadFastaFilename_, CONDEF->filAutoEditMakeFakeReadFastaFilename_, pixForeground, pixBackground ); XtVaSetValues( widAutoEditMakeFakeReadFastaFilename_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoEditMergeAssembly( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoEditMergeAssembly() ); } void guiEditResources :: checkAutoEditMergeAssembly() { bool b = XmToggleButtonGetState( widAutoEditMergeAssemblyTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoEditMergeAssembly_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoEditMergeAssembly_, CONDEF->bAutoEditMergeAssembly_, pixForeground, pixBackground ); XtVaSetValues( widAutoEditMergeAssemblyRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoEditSecondaryAceFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoEditSecondaryAceFile() ); } void guiEditResources :: checkAutoEditSecondaryAceFile() { char* szValue = XmTextFieldGetString( widAutoEditSecondaryAceFile_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filAutoEditSecondaryAceFile_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filAutoEditSecondaryAceFile_, CONDEF->filAutoEditSecondaryAceFile_, pixForeground, pixBackground ); XtVaSetValues( widAutoEditSecondaryAceFile_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoEditFixRunsInConsensus( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoEditFixRunsInConsensus() ); } void guiEditResources :: checkAutoEditFixRunsInConsensus() { bool b = XmToggleButtonGetState( widAutoEditFixRunsInConsensusTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoEditFixRunsInConsensus_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoEditFixRunsInConsensus_, CONDEF->bAutoEditFixRunsInConsensus_, pixForeground, pixBackground ); XtVaSetValues( widAutoEditFixRunsInConsensusRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbShowAllTracesJustShowGoodTraces( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkShowAllTracesJustShowGoodTraces() ); } void guiEditResources :: checkShowAllTracesJustShowGoodTraces() { bool b = XmToggleButtonGetState( widShowAllTracesJustShowGoodTracesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bShowAllTracesJustShowGoodTraces_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bShowAllTracesJustShowGoodTraces_, CONDEF->bShowAllTracesJustShowGoodTraces_, pixForeground, pixBackground ); XtVaSetValues( widShowAllTracesJustShowGoodTracesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAddAlignedSequenceQualityOfBases( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAddAlignedSequenceQualityOfBases() ); } void guiEditResources :: checkAddAlignedSequenceQualityOfBases() { char* szValue = XmTextFieldGetString( widAddAlignedSequenceQualityOfBases_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AddAlignedSequenceQualityOfBases must be numeric"; THROW_ERROR( soError ); } resources_.nAddAlignedSequenceQualityOfBases_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAddAlignedSequenceQualityOfBases_, CONDEF->nAddAlignedSequenceQualityOfBases_, pixForeground, pixBackground ); XtVaSetValues( widAddAlignedSequenceQualityOfBases_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbMakeLightBackgroundInAlignedReadsWindowAndTracesWindow( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkMakeLightBackgroundInAlignedReadsWindowAndTracesWindow() ); } void guiEditResources :: checkMakeLightBackgroundInAlignedReadsWindowAndTracesWindow() { bool b = XmToggleButtonGetState( widMakeLightBackgroundInAlignedReadsWindowAndTracesWindowTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bMakeLightBackgroundInAlignedReadsWindowAndTracesWindow_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bMakeLightBackgroundInAlignedReadsWindowAndTracesWindow_, CONDEF->bMakeLightBackgroundInAlignedReadsWindowAndTracesWindow_, pixForeground, pixBackground ); XtVaSetValues( widMakeLightBackgroundInAlignedReadsWindowAndTracesWindowRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPutVerticalLineAtCursor( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPutVerticalLineAtCursor() ); } void guiEditResources :: checkPutVerticalLineAtCursor() { bool b = XmToggleButtonGetState( widPutVerticalLineAtCursorTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bPutVerticalLineAtCursor_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bPutVerticalLineAtCursor_, CONDEF->bPutVerticalLineAtCursor_, pixForeground, pixBackground ); XtVaSetValues( widPutVerticalLineAtCursorRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPutHorizontalLineAtCursor( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPutHorizontalLineAtCursor() ); } void guiEditResources :: checkPutHorizontalLineAtCursor() { bool b = XmToggleButtonGetState( widPutHorizontalLineAtCursorTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bPutHorizontalLineAtCursor_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bPutHorizontalLineAtCursor_, CONDEF->bPutHorizontalLineAtCursor_, pixForeground, pixBackground ); XtVaSetValues( widPutHorizontalLineAtCursorRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbHighlightedReadsFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkHighlightedReadsFile() ); } void guiEditResources :: checkHighlightedReadsFile() { char* szValue = XmTextFieldGetString( widHighlightedReadsFile_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filHighlightedReadsFile_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filHighlightedReadsFile_, CONDEF->filHighlightedReadsFile_, pixForeground, pixBackground ); XtVaSetValues( widHighlightedReadsFile_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintReadNamesInRegion( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintReadNamesInRegion() ); } void guiEditResources :: checkAutoReportPrintReadNamesInRegion() { bool b = XmToggleButtonGetState( widAutoReportPrintReadNamesInRegionTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintReadNamesInRegion_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintReadNamesInRegion_, CONDEF->bAutoReportPrintReadNamesInRegion_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintReadNamesInRegionRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintReadNamesInRegionContig( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintReadNamesInRegionContig() ); } void guiEditResources :: checkAutoReportPrintReadNamesInRegionContig() { char* szValue = XmTextFieldGetString( widAutoReportPrintReadNamesInRegionContig_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soAutoReportPrintReadNamesInRegionContig_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soAutoReportPrintReadNamesInRegionContig_, CONDEF->soAutoReportPrintReadNamesInRegionContig_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintReadNamesInRegionContig_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintReadNamesInRegionLeftPos( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintReadNamesInRegionLeftPos() ); } void guiEditResources :: checkAutoReportPrintReadNamesInRegionLeftPos() { char* szValue = XmTextFieldGetString( widAutoReportPrintReadNamesInRegionLeftPos_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoReportPrintReadNamesInRegionLeftPos must be numeric"; THROW_ERROR( soError ); } resources_.nAutoReportPrintReadNamesInRegionLeftPos_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoReportPrintReadNamesInRegionLeftPos_, CONDEF->nAutoReportPrintReadNamesInRegionLeftPos_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintReadNamesInRegionLeftPos_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintReadNamesInRegionRightPos( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintReadNamesInRegionRightPos() ); } void guiEditResources :: checkAutoReportPrintReadNamesInRegionRightPos() { char* szValue = XmTextFieldGetString( widAutoReportPrintReadNamesInRegionRightPos_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoReportPrintReadNamesInRegionRightPos must be numeric"; THROW_ERROR( soError ); } resources_.nAutoReportPrintReadNamesInRegionRightPos_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoReportPrintReadNamesInRegionRightPos_, CONDEF->nAutoReportPrintReadNamesInRegionRightPos_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintReadNamesInRegionRightPos_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintHighlyDiscrepantRegions( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintHighlyDiscrepantRegions() ); } void guiEditResources :: checkAutoReportPrintHighlyDiscrepantRegions() { bool b = XmToggleButtonGetState( widAutoReportPrintHighlyDiscrepantRegionsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintHighlyDiscrepantRegions_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintHighlyDiscrepantRegions_, CONDEF->bAutoReportPrintHighlyDiscrepantRegions_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintHighlyDiscrepantRegionsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintScaffolds( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintScaffolds() ); } void guiEditResources :: checkAutoReportPrintScaffolds() { bool b = XmToggleButtonGetState( widAutoReportPrintScaffoldsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintScaffolds_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintScaffolds_, CONDEF->bAutoReportPrintScaffolds_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintScaffoldsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNumberUnpaddedConsensusAtUserDefined( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNumberUnpaddedConsensusAtUserDefined() ); } void guiEditResources :: checkNumberUnpaddedConsensusAtUserDefined() { bool b = XmToggleButtonGetState( widNumberUnpaddedConsensusAtUserDefinedTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bNumberUnpaddedConsensusAtUserDefined_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bNumberUnpaddedConsensusAtUserDefined_, CONDEF->bNumberUnpaddedConsensusAtUserDefined_, pixForeground, pixBackground ); XtVaSetValues( widNumberUnpaddedConsensusAtUserDefinedRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintHighQualityDiscrepancies( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintHighQualityDiscrepancies() ); } void guiEditResources :: checkAutoReportPrintHighQualityDiscrepancies() { bool b = XmToggleButtonGetState( widAutoReportPrintHighQualityDiscrepanciesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintHighQualityDiscrepancies_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintHighQualityDiscrepancies_, CONDEF->bAutoReportPrintHighQualityDiscrepancies_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintHighQualityDiscrepanciesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags() ); } void guiEditResources :: checkAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags() { bool b = XmToggleButtonGetState( widAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTagsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_, CONDEF->bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTagsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportHighQualityDiscrepanciesExcludeMostPads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportHighQualityDiscrepanciesExcludeMostPads() ); } void guiEditResources :: checkAutoReportHighQualityDiscrepanciesExcludeMostPads() { bool b = XmToggleButtonGetState( widAutoReportHighQualityDiscrepanciesExcludeMostPadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportHighQualityDiscrepanciesExcludeMostPads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportHighQualityDiscrepanciesExcludeMostPads_, CONDEF->bAutoReportHighQualityDiscrepanciesExcludeMostPads_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportHighQualityDiscrepanciesExcludeMostPadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintLowConsensusQualityRegions( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintLowConsensusQualityRegions() ); } void guiEditResources :: checkAutoReportPrintLowConsensusQualityRegions() { bool b = XmToggleButtonGetState( widAutoReportPrintLowConsensusQualityRegionsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintLowConsensusQualityRegions_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintLowConsensusQualityRegions_, CONDEF->bAutoReportPrintLowConsensusQualityRegions_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintLowConsensusQualityRegionsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintSingleSubcloneRegions( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintSingleSubcloneRegions() ); } void guiEditResources :: checkAutoReportPrintSingleSubcloneRegions() { bool b = XmToggleButtonGetState( widAutoReportPrintSingleSubcloneRegionsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintSingleSubcloneRegions_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintSingleSubcloneRegions_, CONDEF->bAutoReportPrintSingleSubcloneRegions_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintSingleSubcloneRegionsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintSingleStrandedRegions( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintSingleStrandedRegions() ); } void guiEditResources :: checkAutoReportPrintSingleStrandedRegions() { bool b = XmToggleButtonGetState( widAutoReportPrintSingleStrandedRegionsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintSingleStrandedRegions_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintSingleStrandedRegions_, CONDEF->bAutoReportPrintSingleStrandedRegions_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintSingleStrandedRegionsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintLinkingForwardReversePairs( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintLinkingForwardReversePairs() ); } void guiEditResources :: checkAutoReportPrintLinkingForwardReversePairs() { bool b = XmToggleButtonGetState( widAutoReportPrintLinkingForwardReversePairsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintLinkingForwardReversePairs_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintLinkingForwardReversePairs_, CONDEF->bAutoReportPrintLinkingForwardReversePairs_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintLinkingForwardReversePairsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintFilteredInconsistentForwardReversePairs( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintFilteredInconsistentForwardReversePairs() ); } void guiEditResources :: checkAutoReportPrintFilteredInconsistentForwardReversePairs() { bool b = XmToggleButtonGetState( widAutoReportPrintFilteredInconsistentForwardReversePairsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintFilteredInconsistentForwardReversePairs_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintFilteredInconsistentForwardReversePairs_, CONDEF->bAutoReportPrintFilteredInconsistentForwardReversePairs_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintFilteredInconsistentForwardReversePairsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintAssemblySummary( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintAssemblySummary() ); } void guiEditResources :: checkAutoReportPrintAssemblySummary() { bool b = XmToggleButtonGetState( widAutoReportPrintAssemblySummaryTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintAssemblySummary_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintAssemblySummary_, CONDEF->bAutoReportPrintAssemblySummary_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintAssemblySummaryRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbShowAllTracesDoNotShowTraceIfTheseTagsPresent( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkShowAllTracesDoNotShowTraceIfTheseTagsPresent() ); } void guiEditResources :: checkShowAllTracesDoNotShowTraceIfTheseTagsPresent() { char* szValue = XmTextFieldGetString( widShowAllTracesDoNotShowTraceIfTheseTagsPresent_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soShowAllTracesDoNotShowTraceIfTheseTagsPresent_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soShowAllTracesDoNotShowTraceIfTheseTagsPresent_, CONDEF->soShowAllTracesDoNotShowTraceIfTheseTagsPresent_, pixForeground, pixBackground ); XtVaSetValues( widShowAllTracesDoNotShowTraceIfTheseTagsPresent_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNameOfFakeJoiningReadsIncludesAceFileName( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNameOfFakeJoiningReadsIncludesAceFileName() ); } void guiEditResources :: checkNameOfFakeJoiningReadsIncludesAceFileName() { bool b = XmToggleButtonGetState( widNameOfFakeJoiningReadsIncludesAceFileNameTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bNameOfFakeJoiningReadsIncludesAceFileName_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bNameOfFakeJoiningReadsIncludesAceFileName_, CONDEF->bNameOfFakeJoiningReadsIncludesAceFileName_, pixForeground, pixBackground ); XtVaSetValues( widNameOfFakeJoiningReadsIncludesAceFileNameRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbWhenUserScrollsOffWindowMillisecondsBetweenScrolling( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkWhenUserScrollsOffWindowMillisecondsBetweenScrolling() ); } void guiEditResources :: checkWhenUserScrollsOffWindowMillisecondsBetweenScrolling() { char* szValue = XmTextFieldGetString( widWhenUserScrollsOffWindowMillisecondsBetweenScrolling_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.WhenUserScrollsOffWindowMillisecondsBetweenScrolling must be numeric"; THROW_ERROR( soError ); } resources_.nWhenUserScrollsOffWindowMillisecondsBetweenScrolling_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nWhenUserScrollsOffWindowMillisecondsBetweenScrolling_, CONDEF->nWhenUserScrollsOffWindowMillisecondsBetweenScrolling_, pixForeground, pixBackground ); XtVaSetValues( widWhenUserScrollsOffWindowMillisecondsBetweenScrolling_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbWhenUserScrollsOffWindowBasesToScrollEachTime( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkWhenUserScrollsOffWindowBasesToScrollEachTime() ); } void guiEditResources :: checkWhenUserScrollsOffWindowBasesToScrollEachTime() { char* szValue = XmTextFieldGetString( widWhenUserScrollsOffWindowBasesToScrollEachTime_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.WhenUserScrollsOffWindowBasesToScrollEachTime must be numeric"; THROW_ERROR( soError ); } resources_.nWhenUserScrollsOffWindowBasesToScrollEachTime_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nWhenUserScrollsOffWindowBasesToScrollEachTime_, CONDEF->nWhenUserScrollsOffWindowBasesToScrollEachTime_, pixForeground, pixBackground ); XtVaSetValues( widWhenUserScrollsOffWindowBasesToScrollEachTime_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbCompareContigsUseBandedRatherThanFullSmithWaterman( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkCompareContigsUseBandedRatherThanFullSmithWaterman() ); } void guiEditResources :: checkCompareContigsUseBandedRatherThanFullSmithWaterman() { bool b = XmToggleButtonGetState( widCompareContigsUseBandedRatherThanFullSmithWatermanTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bCompareContigsUseBandedRatherThanFullSmithWaterman_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bCompareContigsUseBandedRatherThanFullSmithWaterman_, CONDEF->bCompareContigsUseBandedRatherThanFullSmithWaterman_, pixForeground, pixBackground ); XtVaSetValues( widCompareContigsUseBandedRatherThanFullSmithWatermanRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbCompareContigsBandSize( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkCompareContigsBandSize() ); } void guiEditResources :: checkCompareContigsBandSize() { char* szValue = XmTextFieldGetString( widCompareContigsBandSize_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.CompareContigsBandSize must be numeric"; THROW_ERROR( soError ); } resources_.nCompareContigsBandSize_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nCompareContigsBandSize_, CONDEF->nCompareContigsBandSize_, pixForeground, pixBackground ); XtVaSetValues( widCompareContigsBandSize_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany() ); } void guiEditResources :: checkAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany() { char* szValue = XmTextFieldGetString( widAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany must be numeric"; THROW_ERROR( soError ); } resources_.nAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany_, CONDEF->nAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewShowSequenceMatches( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewShowSequenceMatches() ); } void guiEditResources :: checkAssemblyViewShowSequenceMatches() { bool b = XmToggleButtonGetState( widAssemblyViewShowSequenceMatchesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewShowSequenceMatches_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewShowSequenceMatches_, CONDEF->bAssemblyViewShowSequenceMatches_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewShowSequenceMatchesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewOKToShowSequenceMatchesBetweenContigs( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewOKToShowSequenceMatchesBetweenContigs() ); } void guiEditResources :: checkAssemblyViewOKToShowSequenceMatchesBetweenContigs() { bool b = XmToggleButtonGetState( widAssemblyViewOKToShowSequenceMatchesBetweenContigsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewOKToShowSequenceMatchesBetweenContigs_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewOKToShowSequenceMatchesBetweenContigs_, CONDEF->bAssemblyViewOKToShowSequenceMatchesBetweenContigs_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewOKToShowSequenceMatchesBetweenContigsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewOKToShowSequenceMatchesWithinContigs( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewOKToShowSequenceMatchesWithinContigs() ); } void guiEditResources :: checkAssemblyViewOKToShowSequenceMatchesWithinContigs() { bool b = XmToggleButtonGetState( widAssemblyViewOKToShowSequenceMatchesWithinContigsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewOKToShowSequenceMatchesWithinContigs_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewOKToShowSequenceMatchesWithinContigs_, CONDEF->bAssemblyViewOKToShowSequenceMatchesWithinContigs_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewOKToShowSequenceMatchesWithinContigsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewOKToShowDirectSequenceMatches( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewOKToShowDirectSequenceMatches() ); } void guiEditResources :: checkAssemblyViewOKToShowDirectSequenceMatches() { bool b = XmToggleButtonGetState( widAssemblyViewOKToShowDirectSequenceMatchesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewOKToShowDirectSequenceMatches_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewOKToShowDirectSequenceMatches_, CONDEF->bAssemblyViewOKToShowDirectSequenceMatches_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewOKToShowDirectSequenceMatchesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewOKToShowInvertedSequenceMatches( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewOKToShowInvertedSequenceMatches() ); } void guiEditResources :: checkAssemblyViewOKToShowInvertedSequenceMatches() { bool b = XmToggleButtonGetState( widAssemblyViewOKToShowInvertedSequenceMatchesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewOKToShowInvertedSequenceMatches_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewOKToShowInvertedSequenceMatches_, CONDEF->bAssemblyViewOKToShowInvertedSequenceMatches_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewOKToShowInvertedSequenceMatchesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewOnlyShowSequenceMatchesToAParticularRegion( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewOnlyShowSequenceMatchesToAParticularRegion() ); } void guiEditResources :: checkAssemblyViewOnlyShowSequenceMatchesToAParticularRegion() { bool b = XmToggleButtonGetState( widAssemblyViewOnlyShowSequenceMatchesToAParticularRegionTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewOnlyShowSequenceMatchesToAParticularRegion_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewOnlyShowSequenceMatchesToAParticularRegion_, CONDEF->bAssemblyViewOnlyShowSequenceMatchesToAParticularRegion_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewOnlyShowSequenceMatchesToAParticularRegionRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewOnlyShowSequenceMatchesToThisContig( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewOnlyShowSequenceMatchesToThisContig() ); } void guiEditResources :: checkAssemblyViewOnlyShowSequenceMatchesToThisContig() { char* szValue = XmTextFieldGetString( widAssemblyViewOnlyShowSequenceMatchesToThisContig_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soAssemblyViewOnlyShowSequenceMatchesToThisContig_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soAssemblyViewOnlyShowSequenceMatchesToThisContig_, CONDEF->soAssemblyViewOnlyShowSequenceMatchesToThisContig_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewOnlyShowSequenceMatchesToThisContig_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft() ); } void guiEditResources :: checkAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft() { char* szValue = XmTextFieldGetString( widAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AssemblyViewOnlyShowSequenceMatchesToThisRegionLeft must be numeric"; THROW_ERROR( soError ); } resources_.nAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft_, CONDEF->nAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewOnlyShowSequenceMatchesToThisRegionRight( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewOnlyShowSequenceMatchesToThisRegionRight() ); } void guiEditResources :: checkAssemblyViewOnlyShowSequenceMatchesToThisRegionRight() { char* szValue = XmTextFieldGetString( widAssemblyViewOnlyShowSequenceMatchesToThisRegionRight_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AssemblyViewOnlyShowSequenceMatchesToThisRegionRight must be numeric"; THROW_ERROR( soError ); } resources_.nAssemblyViewOnlyShowSequenceMatchesToThisRegionRight_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAssemblyViewOnlyShowSequenceMatchesToThisRegionRight_, CONDEF->nAssemblyViewOnlyShowSequenceMatchesToThisRegionRight_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewOnlyShowSequenceMatchesToThisRegionRight_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs() ); } void guiEditResources :: checkAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs() { bool b = XmToggleButtonGetState( widAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs_, CONDEF->bAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar() ); } void guiEditResources :: checkAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar() { char* szValue = XmTextFieldGetString( widAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar must be numeric"; THROW_ERROR( soError ); } resources_.nAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar_, CONDEF->nAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbDefaultReadPrefix( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkDefaultReadPrefix() ); } void guiEditResources :: checkDefaultReadPrefix() { char* szValue = XmTextFieldGetString( widDefaultReadPrefix_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soDefaultReadPrefix_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soDefaultReadPrefix_, CONDEF->soDefaultReadPrefix_, pixForeground, pixBackground ); XtVaSetValues( widDefaultReadPrefix_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbReadPrefixesFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkReadPrefixesFile() ); } void guiEditResources :: checkReadPrefixesFile() { char* szValue = XmTextFieldGetString( widReadPrefixesFile_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filReadPrefixesFile_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filReadPrefixesFile_, CONDEF->filReadPrefixesFile_, pixForeground, pixBackground ); XtVaSetValues( widReadPrefixesFile_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbMaxCharsDisplayedForReadPrefix( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkMaxCharsDisplayedForReadPrefix() ); } void guiEditResources :: checkMaxCharsDisplayedForReadPrefix() { char* szValue = XmTextFieldGetString( widMaxCharsDisplayedForReadPrefix_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.MaxCharsDisplayedForReadPrefix must be numeric"; THROW_ERROR( soError ); } resources_.nMaxCharsDisplayedForReadPrefix_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nMaxCharsDisplayedForReadPrefix_, CONDEF->nMaxCharsDisplayedForReadPrefix_, pixForeground, pixBackground ); XtVaSetValues( widMaxCharsDisplayedForReadPrefix_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates() ); } void guiEditResources :: checkAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates() { char* szValue = XmTextFieldGetString( widAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_, CONDEF->nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions() ); } void guiEditResources :: checkAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions() { char* szValue = XmTextFieldGetString( widAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_, CONDEF->nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis() ); } void guiEditResources :: checkAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis() { char* szValue = XmTextFieldGetString( widAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_, CONDEF->nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishDoNotDoPCRIfEndIsExtendedByReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishDoNotDoPCRIfEndIsExtendedByReads() ); } void guiEditResources :: checkAutoFinishDoNotDoPCRIfEndIsExtendedByReads() { bool b = XmToggleButtonGetState( widAutoFinishDoNotDoPCRIfEndIsExtendedByReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_, CONDEF->bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishDoNotDoPCRIfEndIsExtendedByReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishMaxAcceptableErrorsPerMegabase( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishMaxAcceptableErrorsPerMegabase() ); } void guiEditResources :: checkAutoFinishMaxAcceptableErrorsPerMegabase() { char* szValue = XmTextFieldGetString( widAutoFinishMaxAcceptableErrorsPerMegabase_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishMaxAcceptableErrorsPerMegabase must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishMaxAcceptableErrorsPerMegabase_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishMaxAcceptableErrorsPerMegabase_, CONDEF->nAutoFinishMaxAcceptableErrorsPerMegabase_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishMaxAcceptableErrorsPerMegabase_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize() ); } void guiEditResources :: checkAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize() { char* szValue = XmTextFieldGetString( widAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_, CONDEF->nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersNumberOfBasesToBackUpToStartLooking( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersNumberOfBasesToBackUpToStartLooking() ); } void guiEditResources :: checkPrimersNumberOfBasesToBackUpToStartLooking() { char* szValue = XmTextFieldGetString( widPrimersNumberOfBasesToBackUpToStartLooking_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersNumberOfBasesToBackUpToStartLooking must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersNumberOfBasesToBackUpToStartLooking_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersNumberOfBasesToBackUpToStartLooking_, CONDEF->nPrimersNumberOfBasesToBackUpToStartLooking_, pixForeground, pixBackground ); XtVaSetValues( widPrimersNumberOfBasesToBackUpToStartLooking_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment() ); } void guiEditResources :: checkPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment() { char* szValue = XmTextFieldGetString( widPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_, CONDEF->nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersOKToChoosePrimersInSingleSubcloneRegion( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersOKToChoosePrimersInSingleSubcloneRegion() ); } void guiEditResources :: checkPrimersOKToChoosePrimersInSingleSubcloneRegion() { bool b = XmToggleButtonGetState( widPrimersOKToChoosePrimersInSingleSubcloneRegionTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bPrimersOKToChoosePrimersInSingleSubcloneRegion_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bPrimersOKToChoosePrimersInSingleSubcloneRegion_, CONDEF->bPrimersOKToChoosePrimersInSingleSubcloneRegion_, pixForeground, pixBackground ); XtVaSetValues( widPrimersOKToChoosePrimersInSingleSubcloneRegionRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersOKToChoosePrimersWhereHighQualityDiscrepancies( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersOKToChoosePrimersWhereHighQualityDiscrepancies() ); } void guiEditResources :: checkPrimersOKToChoosePrimersWhereHighQualityDiscrepancies() { bool b = XmToggleButtonGetState( widPrimersOKToChoosePrimersWhereHighQualityDiscrepanciesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_, CONDEF->bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_, pixForeground, pixBackground ); XtVaSetValues( widPrimersOKToChoosePrimersWhereHighQualityDiscrepanciesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion() ); } void guiEditResources :: checkPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion() { bool b = XmToggleButtonGetState( widPrimersOKToChoosePrimersWhereUnalignedHighQualityRegionTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_, CONDEF->bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_, pixForeground, pixBackground ); XtVaSetValues( widPrimersOKToChoosePrimersWhereUnalignedHighQualityRegionRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishCallReversesToFlankGaps( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishCallReversesToFlankGaps() ); } void guiEditResources :: checkAutoFinishCallReversesToFlankGaps() { bool b = XmToggleButtonGetState( widAutoFinishCallReversesToFlankGapsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishCallReversesToFlankGaps_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishCallReversesToFlankGaps_, CONDEF->bAutoFinishCallReversesToFlankGaps_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishCallReversesToFlankGapsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishAllowWholeCloneReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishAllowWholeCloneReads() ); } void guiEditResources :: checkAutoFinishAllowWholeCloneReads() { bool b = XmToggleButtonGetState( widAutoFinishAllowWholeCloneReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishAllowWholeCloneReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishAllowWholeCloneReads_, CONDEF->bAutoFinishAllowWholeCloneReads_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishAllowWholeCloneReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishAllowCustomPrimerSubcloneReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishAllowCustomPrimerSubcloneReads() ); } void guiEditResources :: checkAutoFinishAllowCustomPrimerSubcloneReads() { bool b = XmToggleButtonGetState( widAutoFinishAllowCustomPrimerSubcloneReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishAllowCustomPrimerSubcloneReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishAllowCustomPrimerSubcloneReads_, CONDEF->bAutoFinishAllowCustomPrimerSubcloneReads_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishAllowCustomPrimerSubcloneReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishAllowResequencingReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishAllowResequencingReads() ); } void guiEditResources :: checkAutoFinishAllowResequencingReads() { bool b = XmToggleButtonGetState( widAutoFinishAllowResequencingReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishAllowResequencingReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishAllowResequencingReads_, CONDEF->bAutoFinishAllowResequencingReads_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishAllowResequencingReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishAllowResequencingReadsOnlyForRunsAndStops( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishAllowResequencingReadsOnlyForRunsAndStops() ); } void guiEditResources :: checkAutoFinishAllowResequencingReadsOnlyForRunsAndStops() { bool b = XmToggleButtonGetState( widAutoFinishAllowResequencingReadsOnlyForRunsAndStopsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_, CONDEF->bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishAllowResequencingReadsOnlyForRunsAndStopsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishAllowDeNovoUniversalPrimerSubcloneReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishAllowDeNovoUniversalPrimerSubcloneReads() ); } void guiEditResources :: checkAutoFinishAllowDeNovoUniversalPrimerSubcloneReads() { bool b = XmToggleButtonGetState( widAutoFinishAllowDeNovoUniversalPrimerSubcloneReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_, CONDEF->bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishAllowDeNovoUniversalPrimerSubcloneReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishAllowMinilibraries( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishAllowMinilibraries() ); } void guiEditResources :: checkAutoFinishAllowMinilibraries() { bool b = XmToggleButtonGetState( widAutoFinishAllowMinilibrariesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishAllowMinilibraries_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishAllowMinilibraries_, CONDEF->bAutoFinishAllowMinilibraries_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishAllowMinilibrariesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishAllowPCR( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishAllowPCR() ); } void guiEditResources :: checkAutoFinishAllowPCR() { bool b = XmToggleButtonGetState( widAutoFinishAllowPCRTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishAllowPCR_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishAllowPCR_, CONDEF->bAutoFinishAllowPCR_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishAllowPCRRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishAllowUnorientedPCRReactions( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishAllowUnorientedPCRReactions() ); } void guiEditResources :: checkAutoFinishAllowUnorientedPCRReactions() { bool b = XmToggleButtonGetState( widAutoFinishAllowUnorientedPCRReactionsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishAllowUnorientedPCRReactions_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishAllowUnorientedPCRReactions_, CONDEF->bAutoFinishAllowUnorientedPCRReactions_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishAllowUnorientedPCRReactionsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishAllowResequencingAUniversalPrimerAutofinishRead( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishAllowResequencingAUniversalPrimerAutofinishRead() ); } void guiEditResources :: checkAutoFinishAllowResequencingAUniversalPrimerAutofinishRead() { bool b = XmToggleButtonGetState( widAutoFinishAllowResequencingAUniversalPrimerAutofinishReadTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_, CONDEF->bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishAllowResequencingAUniversalPrimerAutofinishReadRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishAlwaysCloseGapsUsingMinilibraries( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishAlwaysCloseGapsUsingMinilibraries() ); } void guiEditResources :: checkAutoFinishAlwaysCloseGapsUsingMinilibraries() { bool b = XmToggleButtonGetState( widAutoFinishAlwaysCloseGapsUsingMinilibrariesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishAlwaysCloseGapsUsingMinilibraries_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishAlwaysCloseGapsUsingMinilibraries_, CONDEF->bAutoFinishAlwaysCloseGapsUsingMinilibraries_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishAlwaysCloseGapsUsingMinilibrariesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishMaximumFinishingReadLength( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishMaximumFinishingReadLength() ); } void guiEditResources :: checkAutoFinishMaximumFinishingReadLength() { char* szValue = XmTextFieldGetString( widAutoFinishMaximumFinishingReadLength_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishMaximumFinishingReadLength must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishMaximumFinishingReadLength_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishMaximumFinishingReadLength_, CONDEF->nAutoFinishMaximumFinishingReadLength_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishMaximumFinishingReadLength_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger() ); } void guiEditResources :: checkAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger() { char* szValue = XmTextFieldGetString( widAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_, CONDEF->nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishSuggestSpecialChemistryForRunsAndStops( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishSuggestSpecialChemistryForRunsAndStops() ); } void guiEditResources :: checkAutoFinishSuggestSpecialChemistryForRunsAndStops() { bool b = XmToggleButtonGetState( widAutoFinishSuggestSpecialChemistryForRunsAndStopsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishSuggestSpecialChemistryForRunsAndStops_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishSuggestSpecialChemistryForRunsAndStops_, CONDEF->bAutoFinishSuggestSpecialChemistryForRunsAndStops_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishSuggestSpecialChemistryForRunsAndStopsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishSuggestThisManyMinilibrariesPerGap( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishSuggestThisManyMinilibrariesPerGap() ); } void guiEditResources :: checkAutoFinishSuggestThisManyMinilibrariesPerGap() { char* szValue = XmTextFieldGetString( widAutoFinishSuggestThisManyMinilibrariesPerGap_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishSuggestThisManyMinilibrariesPerGap must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishSuggestThisManyMinilibrariesPerGap_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishSuggestThisManyMinilibrariesPerGap_, CONDEF->nAutoFinishSuggestThisManyMinilibrariesPerGap_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishSuggestThisManyMinilibrariesPerGap_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersWindowSizeInLooking( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersWindowSizeInLooking() ); } void guiEditResources :: checkPrimersWindowSizeInLooking() { char* szValue = XmTextFieldGetString( widPrimersWindowSizeInLooking_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersWindowSizeInLooking must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersWindowSizeInLooking_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersWindowSizeInLooking_, CONDEF->nPrimersWindowSizeInLooking_, pixForeground, pixBackground ); XtVaSetValues( widPrimersWindowSizeInLooking_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified() ); } void guiEditResources :: checkPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified() { bool b = XmToggleButtonGetState( widPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecifiedTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_, CONDEF->bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_, pixForeground, pixBackground ); XtVaSetValues( widPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecifiedRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAlignedReadsWindowInitialCharsWide( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAlignedReadsWindowInitialCharsWide() ); } void guiEditResources :: checkAlignedReadsWindowInitialCharsWide() { char* szValue = XmTextFieldGetString( widAlignedReadsWindowInitialCharsWide_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AlignedReadsWindowInitialCharsWide must be numeric"; THROW_ERROR( soError ); } resources_.nAlignedReadsWindowInitialCharsWide_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAlignedReadsWindowInitialCharsWide_, CONDEF->nAlignedReadsWindowInitialCharsWide_, pixForeground, pixBackground ); XtVaSetValues( widAlignedReadsWindowInitialCharsWide_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAlignedReadsWindowInitialCharsHigh( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAlignedReadsWindowInitialCharsHigh() ); } void guiEditResources :: checkAlignedReadsWindowInitialCharsHigh() { char* szValue = XmTextFieldGetString( widAlignedReadsWindowInitialCharsHigh_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AlignedReadsWindowInitialCharsHigh must be numeric"; THROW_ERROR( soError ); } resources_.nAlignedReadsWindowInitialCharsHigh_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAlignedReadsWindowInitialCharsHigh_, CONDEF->nAlignedReadsWindowInitialCharsHigh_, pixForeground, pixBackground ); XtVaSetValues( widAlignedReadsWindowInitialCharsHigh_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAlignedReadsWindowMaxCharsForReadNames( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAlignedReadsWindowMaxCharsForReadNames() ); } void guiEditResources :: checkAlignedReadsWindowMaxCharsForReadNames() { char* szValue = XmTextFieldGetString( widAlignedReadsWindowMaxCharsForReadNames_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AlignedReadsWindowMaxCharsForReadNames must be numeric"; THROW_ERROR( soError ); } resources_.nAlignedReadsWindowMaxCharsForReadNames_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAlignedReadsWindowMaxCharsForReadNames_, CONDEF->nAlignedReadsWindowMaxCharsForReadNames_, pixForeground, pixBackground ); XtVaSetValues( widAlignedReadsWindowMaxCharsForReadNames_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAlignedReadsWindowAutomaticallyExpandRoomForReadNames( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAlignedReadsWindowAutomaticallyExpandRoomForReadNames() ); } void guiEditResources :: checkAlignedReadsWindowAutomaticallyExpandRoomForReadNames() { bool b = XmToggleButtonGetState( widAlignedReadsWindowAutomaticallyExpandRoomForReadNamesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAlignedReadsWindowAutomaticallyExpandRoomForReadNames_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAlignedReadsWindowAutomaticallyExpandRoomForReadNames_, CONDEF->bAlignedReadsWindowAutomaticallyExpandRoomForReadNames_, pixForeground, pixBackground ); XtVaSetValues( widAlignedReadsWindowAutomaticallyExpandRoomForReadNamesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishAllowResequencingReadsToExtendContigs( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishAllowResequencingReadsToExtendContigs() ); } void guiEditResources :: checkAutoFinishAllowResequencingReadsToExtendContigs() { bool b = XmToggleButtonGetState( widAutoFinishAllowResequencingReadsToExtendContigsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishAllowResequencingReadsToExtendContigs_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishAllowResequencingReadsToExtendContigs_, CONDEF->bAutoFinishAllowResequencingReadsToExtendContigs_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishAllowResequencingReadsToExtendContigsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishCallHowManyReversesToFlankGaps( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishCallHowManyReversesToFlankGaps() ); } void guiEditResources :: checkAutoFinishCallHowManyReversesToFlankGaps() { char* szValue = XmTextFieldGetString( widAutoFinishCallHowManyReversesToFlankGaps_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishCallHowManyReversesToFlankGaps must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishCallHowManyReversesToFlankGaps_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishCallHowManyReversesToFlankGaps_, CONDEF->nAutoFinishCallHowManyReversesToFlankGaps_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishCallHowManyReversesToFlankGaps_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishCloseGaps( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishCloseGaps() ); } void guiEditResources :: checkAutoFinishCloseGaps() { bool b = XmToggleButtonGetState( widAutoFinishCloseGapsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishCloseGaps_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishCloseGaps_, CONDEF->bAutoFinishCloseGaps_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishCloseGapsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense() ); } void guiEditResources :: checkAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense() { bool b = XmToggleButtonGetState( widAutoFinishContinueEvenThoughReadInfoDoesNotMakeSenseTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_, CONDEF->bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishContinueEvenThoughReadInfoDoesNotMakeSenseRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction() ); } void guiEditResources :: checkAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction() { char* szValue = XmTextFieldGetString( widAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "AutoFinishCostOfResequencingUniversalPrimerSubcloneReaction must be floating point numeric"; THROW_ERROR( soError ); } resources_.dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_, CONDEF->dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishCostOfCustomPrimerSubcloneReaction( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishCostOfCustomPrimerSubcloneReaction() ); } void guiEditResources :: checkAutoFinishCostOfCustomPrimerSubcloneReaction() { char* szValue = XmTextFieldGetString( widAutoFinishCostOfCustomPrimerSubcloneReaction_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "AutoFinishCostOfCustomPrimerSubcloneReaction must be floating point numeric"; THROW_ERROR( soError ); } resources_.dAutoFinishCostOfCustomPrimerSubcloneReaction_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dAutoFinishCostOfCustomPrimerSubcloneReaction_, CONDEF->dAutoFinishCostOfCustomPrimerSubcloneReaction_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishCostOfCustomPrimerSubcloneReaction_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishCostOfCustomPrimerCloneReaction( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishCostOfCustomPrimerCloneReaction() ); } void guiEditResources :: checkAutoFinishCostOfCustomPrimerCloneReaction() { char* szValue = XmTextFieldGetString( widAutoFinishCostOfCustomPrimerCloneReaction_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "AutoFinishCostOfCustomPrimerCloneReaction must be floating point numeric"; THROW_ERROR( soError ); } resources_.dAutoFinishCostOfCustomPrimerCloneReaction_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dAutoFinishCostOfCustomPrimerCloneReaction_, CONDEF->dAutoFinishCostOfCustomPrimerCloneReaction_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishCostOfCustomPrimerCloneReaction_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction() ); } void guiEditResources :: checkAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction() { char* szValue = XmTextFieldGetString( widAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "AutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction must be floating point numeric"; THROW_ERROR( soError ); } resources_.dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_, CONDEF->dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishCostOfMinilibrary( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishCostOfMinilibrary() ); } void guiEditResources :: checkAutoFinishCostOfMinilibrary() { char* szValue = XmTextFieldGetString( widAutoFinishCostOfMinilibrary_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "AutoFinishCostOfMinilibrary must be floating point numeric"; THROW_ERROR( soError ); } resources_.dAutoFinishCostOfMinilibrary_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dAutoFinishCostOfMinilibrary_, CONDEF->dAutoFinishCostOfMinilibrary_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishCostOfMinilibrary_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishCoverSingleSubcloneRegions( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishCoverSingleSubcloneRegions() ); } void guiEditResources :: checkAutoFinishCoverSingleSubcloneRegions() { bool b = XmToggleButtonGetState( widAutoFinishCoverSingleSubcloneRegionsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishCoverSingleSubcloneRegions_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishCoverSingleSubcloneRegions_, CONDEF->bAutoFinishCoverSingleSubcloneRegions_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishCoverSingleSubcloneRegionsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishCoverLowConsensusQualityRegions( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishCoverLowConsensusQualityRegions() ); } void guiEditResources :: checkAutoFinishCoverLowConsensusQualityRegions() { bool b = XmToggleButtonGetState( widAutoFinishCoverLowConsensusQualityRegionsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishCoverLowConsensusQualityRegions_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishCoverLowConsensusQualityRegions_, CONDEF->bAutoFinishCoverLowConsensusQualityRegions_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishCoverLowConsensusQualityRegionsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishDebugUniversalPrimerReadsFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishDebugUniversalPrimerReadsFile() ); } void guiEditResources :: checkAutoFinishDebugUniversalPrimerReadsFile() { char* szValue = XmTextFieldGetString( widAutoFinishDebugUniversalPrimerReadsFile_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filAutoFinishDebugUniversalPrimerReadsFile_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filAutoFinishDebugUniversalPrimerReadsFile_, CONDEF->filAutoFinishDebugUniversalPrimerReadsFile_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishDebugUniversalPrimerReadsFile_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishDebugCustomPrimerReadsFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishDebugCustomPrimerReadsFile() ); } void guiEditResources :: checkAutoFinishDebugCustomPrimerReadsFile() { char* szValue = XmTextFieldGetString( widAutoFinishDebugCustomPrimerReadsFile_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filAutoFinishDebugCustomPrimerReadsFile_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filAutoFinishDebugCustomPrimerReadsFile_, CONDEF->filAutoFinishDebugCustomPrimerReadsFile_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishDebugCustomPrimerReadsFile_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases() ); } void guiEditResources :: checkAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases() { char* szValue = XmTextFieldGetString( widAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_, CONDEF->nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases() ); } void guiEditResources :: checkAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases() { char* szValue = XmTextFieldGetString( widAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_, CONDEF->nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishDoNotFinishWhereTheseTagsAre( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishDoNotFinishWhereTheseTagsAre() ); } void guiEditResources :: checkAutoFinishDoNotFinishWhereTheseTagsAre() { char* szValue = XmTextFieldGetString( widAutoFinishDoNotFinishWhereTheseTagsAre_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soAutoFinishDoNotFinishWhereTheseTagsAre_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soAutoFinishDoNotFinishWhereTheseTagsAre_, CONDEF->soAutoFinishDoNotFinishWhereTheseTagsAre_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishDoNotFinishWhereTheseTagsAre_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishDoNotExtendContigsWhereTheseTagsAre( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishDoNotExtendContigsWhereTheseTagsAre() ); } void guiEditResources :: checkAutoFinishDoNotExtendContigsWhereTheseTagsAre() { char* szValue = XmTextFieldGetString( widAutoFinishDoNotExtendContigsWhereTheseTagsAre_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soAutoFinishDoNotExtendContigsWhereTheseTagsAre_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soAutoFinishDoNotExtendContigsWhereTheseTagsAre_, CONDEF->soAutoFinishDoNotExtendContigsWhereTheseTagsAre_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishDoNotExtendContigsWhereTheseTagsAre_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd() ); } void guiEditResources :: checkAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd() { char* szValue = XmTextFieldGetString( widAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_, CONDEF->nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbDumpContigOrderAndOrientationInfoToThisFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkDumpContigOrderAndOrientationInfoToThisFile() ); } void guiEditResources :: checkDumpContigOrderAndOrientationInfoToThisFile() { char* szValue = XmTextFieldGetString( widDumpContigOrderAndOrientationInfoToThisFile_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filDumpContigOrderAndOrientationInfoToThisFile_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filDumpContigOrderAndOrientationInfoToThisFile_, CONDEF->filDumpContigOrderAndOrientationInfoToThisFile_, pixForeground, pixBackground ); XtVaSetValues( widDumpContigOrderAndOrientationInfoToThisFile_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishDumpTemplates( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishDumpTemplates() ); } void guiEditResources :: checkAutoFinishDumpTemplates() { bool b = XmToggleButtonGetState( widAutoFinishDumpTemplatesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishDumpTemplates_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishDumpTemplates_, CONDEF->bAutoFinishDumpTemplates_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishDumpTemplatesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishExcludeContigIfOnlyThisManyReadsOrLess( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishExcludeContigIfOnlyThisManyReadsOrLess() ); } void guiEditResources :: checkAutoFinishExcludeContigIfOnlyThisManyReadsOrLess() { char* szValue = XmTextFieldGetString( widAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishExcludeContigIfOnlyThisManyReadsOrLess must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_, CONDEF->nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis() ); } void guiEditResources :: checkAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis() { char* szValue = XmTextFieldGetString( widAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "AutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis must be floating point numeric"; THROW_ERROR( soError ); } resources_.dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_, CONDEF->dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishExcludeContigIfThisManyBasesOrLess( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishExcludeContigIfThisManyBasesOrLess() ); } void guiEditResources :: checkAutoFinishExcludeContigIfThisManyBasesOrLess() { char* szValue = XmTextFieldGetString( widAutoFinishExcludeContigIfThisManyBasesOrLess_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishExcludeContigIfThisManyBasesOrLess must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishExcludeContigIfThisManyBasesOrLess_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishExcludeContigIfThisManyBasesOrLess_, CONDEF->nAutoFinishExcludeContigIfThisManyBasesOrLess_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishExcludeContigIfThisManyBasesOrLess_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions() ); } void guiEditResources :: checkAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions() { char* szValue = XmTextFieldGetString( widAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_, CONDEF->nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMinNumberOfTemplatesForPrimers( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMinNumberOfTemplatesForPrimers() ); } void guiEditResources :: checkPrimersMinNumberOfTemplatesForPrimers() { char* szValue = XmTextFieldGetString( widPrimersMinNumberOfTemplatesForPrimers_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMinNumberOfTemplatesForPrimers must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMinNumberOfTemplatesForPrimers_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMinNumberOfTemplatesForPrimers_, CONDEF->nPrimersMinNumberOfTemplatesForPrimers_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMinNumberOfTemplatesForPrimers_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus() ); } void guiEditResources :: checkAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus() { char* szValue = XmTextFieldGetString( widAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_, CONDEF->nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead() ); } void guiEditResources :: checkAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead() { char* szValue = XmTextFieldGetString( widAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_, CONDEF->nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishCDNANotGenomic( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishCDNANotGenomic() ); } void guiEditResources :: checkAutoFinishCDNANotGenomic() { bool b = XmToggleButtonGetState( widAutoFinishCDNANotGenomicTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishCDNANotGenomic_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishCDNANotGenomic_, CONDEF->bAutoFinishCDNANotGenomic_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishCDNANotGenomicRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion() ); } void guiEditResources :: checkAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion() { char* szValue = XmTextFieldGetString( widAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_, CONDEF->nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads() ); } void guiEditResources :: checkAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads() { bool b = XmToggleButtonGetState( widAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_, CONDEF->bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishPrintMinilibrariesSummaryFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishPrintMinilibrariesSummaryFile() ); } void guiEditResources :: checkAutoFinishPrintMinilibrariesSummaryFile() { bool b = XmToggleButtonGetState( widAutoFinishPrintMinilibrariesSummaryFileTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishPrintMinilibrariesSummaryFile_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishPrintMinilibrariesSummaryFile_, CONDEF->bAutoFinishPrintMinilibrariesSummaryFile_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishPrintMinilibrariesSummaryFileRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishNearGapsSuggestEachMissingReadOfReadPairs( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishNearGapsSuggestEachMissingReadOfReadPairs() ); } void guiEditResources :: checkAutoFinishNearGapsSuggestEachMissingReadOfReadPairs() { bool b = XmToggleButtonGetState( widAutoFinishNearGapsSuggestEachMissingReadOfReadPairsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_, CONDEF->bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishNearGapsSuggestEachMissingReadOfReadPairsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger() ); } void guiEditResources :: checkAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger() { char* szValue = XmTextFieldGetString( widAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_, CONDEF->nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbCheckIfTooManyWalks( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkCheckIfTooManyWalks() ); } void guiEditResources :: checkCheckIfTooManyWalks() { bool b = XmToggleButtonGetState( widCheckIfTooManyWalksTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bCheckIfTooManyWalks_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bCheckIfTooManyWalks_, CONDEF->bCheckIfTooManyWalks_, pixForeground, pixBackground ); XtVaSetValues( widCheckIfTooManyWalksRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNumberOfColumnsBeforeReadNameInAlignedReadsWindow( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNumberOfColumnsBeforeReadNameInAlignedReadsWindow() ); } void guiEditResources :: checkNumberOfColumnsBeforeReadNameInAlignedReadsWindow() { char* szValue = XmTextFieldGetString( widNumberOfColumnsBeforeReadNameInAlignedReadsWindow_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.NumberOfColumnsBeforeReadNameInAlignedReadsWindow must be numeric"; THROW_ERROR( soError ); } resources_.nNumberOfColumnsBeforeReadNameInAlignedReadsWindow_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nNumberOfColumnsBeforeReadNameInAlignedReadsWindow_, CONDEF->nNumberOfColumnsBeforeReadNameInAlignedReadsWindow_, pixForeground, pixBackground ); XtVaSetValues( widNumberOfColumnsBeforeReadNameInAlignedReadsWindow_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbCompareContigsAlignsThisManyBasesMax( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkCompareContigsAlignsThisManyBasesMax() ); } void guiEditResources :: checkCompareContigsAlignsThisManyBasesMax() { char* szValue = XmTextFieldGetString( widCompareContigsAlignsThisManyBasesMax_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.CompareContigsAlignsThisManyBasesMax must be numeric"; THROW_ERROR( soError ); } resources_.nCompareContigsAlignsThisManyBasesMax_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nCompareContigsAlignsThisManyBasesMax_, CONDEF->nCompareContigsAlignsThisManyBasesMax_, pixForeground, pixBackground ); XtVaSetValues( widCompareContigsAlignsThisManyBasesMax_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbCompressedChromatExtension( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkCompressedChromatExtension() ); } void guiEditResources :: checkCompressedChromatExtension() { char* szValue = XmTextFieldGetString( widCompressedChromatExtension_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soCompressedChromatExtension_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soCompressedChromatExtension_, CONDEF->soCompressedChromatExtension_, pixForeground, pixBackground ); XtVaSetValues( widCompressedChromatExtension_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbDimLowQualityEndsOfReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkDimLowQualityEndsOfReads() ); } void guiEditResources :: checkDimLowQualityEndsOfReads() { bool b = XmToggleButtonGetState( widDimLowQualityEndsOfReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bDimLowQualityEndsOfReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bDimLowQualityEndsOfReads_, CONDEF->bDimLowQualityEndsOfReads_, pixForeground, pixBackground ); XtVaSetValues( widDimLowQualityEndsOfReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbDimUnalignedEndsOfReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkDimUnalignedEndsOfReads() ); } void guiEditResources :: checkDimUnalignedEndsOfReads() { bool b = XmToggleButtonGetState( widDimUnalignedEndsOfReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bDimUnalignedEndsOfReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bDimUnalignedEndsOfReads_, CONDEF->bDimUnalignedEndsOfReads_, pixForeground, pixBackground ); XtVaSetValues( widDimUnalignedEndsOfReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbFakeReadsSpecifiedByFilenameExtension( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkFakeReadsSpecifiedByFilenameExtension() ); } void guiEditResources :: checkFakeReadsSpecifiedByFilenameExtension() { bool b = XmToggleButtonGetState( widFakeReadsSpecifiedByFilenameExtensionTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bFakeReadsSpecifiedByFilenameExtension_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bFakeReadsSpecifiedByFilenameExtension_, CONDEF->bFakeReadsSpecifiedByFilenameExtension_, pixForeground, pixBackground ); XtVaSetValues( widFakeReadsSpecifiedByFilenameExtensionRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbFullPathnameOfAddReads2ConsedScript( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkFullPathnameOfAddReads2ConsedScript() ); } void guiEditResources :: checkFullPathnameOfAddReads2ConsedScript() { char* szValue = XmTextFieldGetString( widFullPathnameOfAddReads2ConsedScript_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filFullPathnameOfAddReads2ConsedScript_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filFullPathnameOfAddReads2ConsedScript_, CONDEF->filFullPathnameOfAddReads2ConsedScript_, pixForeground, pixBackground ); XtVaSetValues( widFullPathnameOfAddReads2ConsedScript_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbFullPathnameOfFixContigEndScript( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkFullPathnameOfFixContigEndScript() ); } void guiEditResources :: checkFullPathnameOfFixContigEndScript() { char* szValue = XmTextFieldGetString( widFullPathnameOfFixContigEndScript_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filFullPathnameOfFixContigEndScript_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filFullPathnameOfFixContigEndScript_, CONDEF->filFullPathnameOfFixContigEndScript_, pixForeground, pixBackground ); XtVaSetValues( widFullPathnameOfFixContigEndScript_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbFixContigEndsCleanUpTemporaryFiles( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkFixContigEndsCleanUpTemporaryFiles() ); } void guiEditResources :: checkFixContigEndsCleanUpTemporaryFiles() { bool b = XmToggleButtonGetState( widFixContigEndsCleanUpTemporaryFilesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bFixContigEndsCleanUpTemporaryFiles_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bFixContigEndsCleanUpTemporaryFiles_, CONDEF->bFixContigEndsCleanUpTemporaryFiles_, pixForeground, pixBackground ); XtVaSetValues( widFixContigEndsCleanUpTemporaryFilesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbFixContigEndsMinSmithWatermanScoreToMakeJoin( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkFixContigEndsMinSmithWatermanScoreToMakeJoin() ); } void guiEditResources :: checkFixContigEndsMinSmithWatermanScoreToMakeJoin() { char* szValue = XmTextFieldGetString( widFixContigEndsMinSmithWatermanScoreToMakeJoin_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.FixContigEndsMinSmithWatermanScoreToMakeJoin must be numeric"; THROW_ERROR( soError ); } resources_.nFixContigEndsMinSmithWatermanScoreToMakeJoin_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nFixContigEndsMinSmithWatermanScoreToMakeJoin_, CONDEF->nFixContigEndsMinSmithWatermanScoreToMakeJoin_, pixForeground, pixBackground ); XtVaSetValues( widFixContigEndsMinSmithWatermanScoreToMakeJoin_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbFixContigEndsMinNumberOfReadsInContig( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkFixContigEndsMinNumberOfReadsInContig() ); } void guiEditResources :: checkFixContigEndsMinNumberOfReadsInContig() { char* szValue = XmTextFieldGetString( widFixContigEndsMinNumberOfReadsInContig_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.FixContigEndsMinNumberOfReadsInContig must be numeric"; THROW_ERROR( soError ); } resources_.nFixContigEndsMinNumberOfReadsInContig_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nFixContigEndsMinNumberOfReadsInContig_, CONDEF->nFixContigEndsMinNumberOfReadsInContig_, pixForeground, pixBackground ); XtVaSetValues( widFixContigEndsMinNumberOfReadsInContig_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbFullPathnameOfCrossMatch( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkFullPathnameOfCrossMatch() ); } void guiEditResources :: checkFullPathnameOfCrossMatch() { char* szValue = XmTextFieldGetString( widFullPathnameOfCrossMatch_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filFullPathnameOfCrossMatch_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filFullPathnameOfCrossMatch_, CONDEF->filFullPathnameOfCrossMatch_, pixForeground, pixBackground ); XtVaSetValues( widFullPathnameOfCrossMatch_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbFullPathnameOfPhred( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkFullPathnameOfPhred() ); } void guiEditResources :: checkFullPathnameOfPhred() { char* szValue = XmTextFieldGetString( widFullPathnameOfPhred_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filFullPathnameOfPhred_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filFullPathnameOfPhred_, CONDEF->filFullPathnameOfPhred_, pixForeground, pixBackground ); XtVaSetValues( widFullPathnameOfPhred_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbFullPathnameOfMiniassemblyScript( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkFullPathnameOfMiniassemblyScript() ); } void guiEditResources :: checkFullPathnameOfMiniassemblyScript() { char* szValue = XmTextFieldGetString( widFullPathnameOfMiniassemblyScript_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filFullPathnameOfMiniassemblyScript_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filFullPathnameOfMiniassemblyScript_, CONDEF->filFullPathnameOfMiniassemblyScript_, pixForeground, pixBackground ); XtVaSetValues( widFullPathnameOfMiniassemblyScript_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbGunzipFullPath( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkGunzipFullPath() ); } void guiEditResources :: checkGunzipFullPath() { char* szValue = XmTextFieldGetString( widGunzipFullPath_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soGunzipFullPath_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soGunzipFullPath_, CONDEF->soGunzipFullPath_, pixForeground, pixBackground ); XtVaSetValues( widGunzipFullPath_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbFullPathnameOfFilter454ReadsScript( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkFullPathnameOfFilter454ReadsScript() ); } void guiEditResources :: checkFullPathnameOfFilter454ReadsScript() { char* szValue = XmTextFieldGetString( widFullPathnameOfFilter454ReadsScript_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filFullPathnameOfFilter454ReadsScript_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filFullPathnameOfFilter454ReadsScript_, CONDEF->filFullPathnameOfFilter454ReadsScript_, pixForeground, pixBackground ); XtVaSetValues( widFullPathnameOfFilter454ReadsScript_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbFilter454ReadsAgainstThis( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkFilter454ReadsAgainstThis() ); } void guiEditResources :: checkFilter454ReadsAgainstThis() { char* szValue = XmTextFieldGetString( widFilter454ReadsAgainstThis_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filFilter454ReadsAgainstThis_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filFilter454ReadsAgainstThis_, CONDEF->filFilter454ReadsAgainstThis_, pixForeground, pixBackground ); XtVaSetValues( widFilter454ReadsAgainstThis_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cb454LinkerSequences( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->check454LinkerSequences() ); } void guiEditResources :: check454LinkerSequences() { char* szValue = XmTextFieldGetString( wid454LinkerSequences_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.fil454LinkerSequences_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.fil454LinkerSequences_, CONDEF->fil454LinkerSequences_, pixForeground, pixBackground ); XtVaSetValues( wid454LinkerSequences_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbHideSomeTagTypesAtStartup( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkHideSomeTagTypesAtStartup() ); } void guiEditResources :: checkHideSomeTagTypesAtStartup() { bool b = XmToggleButtonGetState( widHideSomeTagTypesAtStartupTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bHideSomeTagTypesAtStartup_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bHideSomeTagTypesAtStartup_, CONDEF->bHideSomeTagTypesAtStartup_, pixForeground, pixBackground ); XtVaSetValues( widHideSomeTagTypesAtStartupRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbMaximumNumberOfTracesShown( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkMaximumNumberOfTracesShown() ); } void guiEditResources :: checkMaximumNumberOfTracesShown() { char* szValue = XmTextFieldGetString( widMaximumNumberOfTracesShown_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.MaximumNumberOfTracesShown must be numeric"; THROW_ERROR( soError ); } resources_.nMaximumNumberOfTracesShown_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nMaximumNumberOfTracesShown_, CONDEF->nMaximumNumberOfTracesShown_, pixForeground, pixBackground ); XtVaSetValues( widMaximumNumberOfTracesShown_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNavigateAutomaticTracePopup( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNavigateAutomaticTracePopup() ); } void guiEditResources :: checkNavigateAutomaticTracePopup() { bool b = XmToggleButtonGetState( widNavigateAutomaticTracePopupTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bNavigateAutomaticTracePopup_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bNavigateAutomaticTracePopup_, CONDEF->bNavigateAutomaticTracePopup_, pixForeground, pixBackground ); XtVaSetValues( widNavigateAutomaticTracePopupRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNavigateAutomaticAllTracesPopup( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNavigateAutomaticAllTracesPopup() ); } void guiEditResources :: checkNavigateAutomaticAllTracesPopup() { bool b = XmToggleButtonGetState( widNavigateAutomaticAllTracesPopupTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bNavigateAutomaticAllTracesPopup_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bNavigateAutomaticAllTracesPopup_, CONDEF->bNavigateAutomaticAllTracesPopup_, pixForeground, pixBackground ); XtVaSetValues( widNavigateAutomaticAllTracesPopupRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMinimumLengthOfAPrimer( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMinimumLengthOfAPrimer() ); } void guiEditResources :: checkPrimersMinimumLengthOfAPrimer() { char* szValue = XmTextFieldGetString( widPrimersMinimumLengthOfAPrimer_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMinimumLengthOfAPrimer must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMinimumLengthOfAPrimer_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMinimumLengthOfAPrimer_, CONDEF->nPrimersMinimumLengthOfAPrimer_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMinimumLengthOfAPrimer_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMaximumLengthOfAPrimer( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMaximumLengthOfAPrimer() ); } void guiEditResources :: checkPrimersMaximumLengthOfAPrimer() { char* szValue = XmTextFieldGetString( widPrimersMaximumLengthOfAPrimer_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMaximumLengthOfAPrimer must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMaximumLengthOfAPrimer_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMaximumLengthOfAPrimer_, CONDEF->nPrimersMaximumLengthOfAPrimer_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMaximumLengthOfAPrimer_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMinimumLengthOfAPrimerForPCR( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMinimumLengthOfAPrimerForPCR() ); } void guiEditResources :: checkPrimersMinimumLengthOfAPrimerForPCR() { char* szValue = XmTextFieldGetString( widPrimersMinimumLengthOfAPrimerForPCR_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMinimumLengthOfAPrimerForPCR must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMinimumLengthOfAPrimerForPCR_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMinimumLengthOfAPrimerForPCR_, CONDEF->nPrimersMinimumLengthOfAPrimerForPCR_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMinimumLengthOfAPrimerForPCR_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMaximumLengthOfAPrimerForPCR( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMaximumLengthOfAPrimerForPCR() ); } void guiEditResources :: checkPrimersMaximumLengthOfAPrimerForPCR() { char* szValue = XmTextFieldGetString( widPrimersMaximumLengthOfAPrimerForPCR_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMaximumLengthOfAPrimerForPCR must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMaximumLengthOfAPrimerForPCR_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMaximumLengthOfAPrimerForPCR_, CONDEF->nPrimersMaximumLengthOfAPrimerForPCR_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMaximumLengthOfAPrimerForPCR_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMaxMeltingTempDifferenceForPCR( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMaxMeltingTempDifferenceForPCR() ); } void guiEditResources :: checkPrimersMaxMeltingTempDifferenceForPCR() { char* szValue = XmTextFieldGetString( widPrimersMaxMeltingTempDifferenceForPCR_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "PrimersMaxMeltingTempDifferenceForPCR must be floating point numeric"; THROW_ERROR( soError ); } resources_.dPrimersMaxMeltingTempDifferenceForPCR_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dPrimersMaxMeltingTempDifferenceForPCR_, CONDEF->dPrimersMaxMeltingTempDifferenceForPCR_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMaxMeltingTempDifferenceForPCR_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMaxPCRPrimerPairsToDisplay( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMaxPCRPrimerPairsToDisplay() ); } void guiEditResources :: checkPrimersMaxPCRPrimerPairsToDisplay() { char* szValue = XmTextFieldGetString( widPrimersMaxPCRPrimerPairsToDisplay_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMaxPCRPrimerPairsToDisplay must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMaxPCRPrimerPairsToDisplay_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMaxPCRPrimerPairsToDisplay_, CONDEF->nPrimersMaxPCRPrimerPairsToDisplay_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMaxPCRPrimerPairsToDisplay_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersCheckJustSomePCRPrimerPairsRatherThanAll( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersCheckJustSomePCRPrimerPairsRatherThanAll() ); } void guiEditResources :: checkPrimersCheckJustSomePCRPrimerPairsRatherThanAll() { bool b = XmToggleButtonGetState( widPrimersCheckJustSomePCRPrimerPairsRatherThanAllTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_, CONDEF->bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_, pixForeground, pixBackground ); XtVaSetValues( widPrimersCheckJustSomePCRPrimerPairsRatherThanAllRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersNumberOfTemplatesToDisplayInFront( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersNumberOfTemplatesToDisplayInFront() ); } void guiEditResources :: checkPrimersNumberOfTemplatesToDisplayInFront() { char* szValue = XmTextFieldGetString( widPrimersNumberOfTemplatesToDisplayInFront_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersNumberOfTemplatesToDisplayInFront must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersNumberOfTemplatesToDisplayInFront_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersNumberOfTemplatesToDisplayInFront_, CONDEF->nPrimersNumberOfTemplatesToDisplayInFront_, pixForeground, pixBackground ); XtVaSetValues( widPrimersNumberOfTemplatesToDisplayInFront_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMaxLengthOfMononucleotideRepeat( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMaxLengthOfMononucleotideRepeat() ); } void guiEditResources :: checkPrimersMaxLengthOfMononucleotideRepeat() { char* szValue = XmTextFieldGetString( widPrimersMaxLengthOfMononucleotideRepeat_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMaxLengthOfMononucleotideRepeat must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMaxLengthOfMononucleotideRepeat_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMaxLengthOfMononucleotideRepeat_, CONDEF->nPrimersMaxLengthOfMononucleotideRepeat_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMaxLengthOfMononucleotideRepeat_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersBadLibrariesFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersBadLibrariesFile() ); } void guiEditResources :: checkPrimersBadLibrariesFile() { char* szValue = XmTextFieldGetString( widPrimersBadLibrariesFile_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filPrimersBadLibrariesFile_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filPrimersBadLibrariesFile_, CONDEF->filPrimersBadLibrariesFile_, pixForeground, pixBackground ); XtVaSetValues( widPrimersBadLibrariesFile_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersLibrariesInfoFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersLibrariesInfoFile() ); } void guiEditResources :: checkPrimersLibrariesInfoFile() { char* szValue = XmTextFieldGetString( widPrimersLibrariesInfoFile_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filPrimersLibrariesInfoFile_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filPrimersLibrariesInfoFile_, CONDEF->filPrimersLibrariesInfoFile_, pixForeground, pixBackground ); XtVaSetValues( widPrimersLibrariesInfoFile_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersBadTemplatesFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersBadTemplatesFile() ); } void guiEditResources :: checkPrimersBadTemplatesFile() { char* szValue = XmTextFieldGetString( widPrimersBadTemplatesFile_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filPrimersBadTemplatesFile_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filPrimersBadTemplatesFile_, CONDEF->filPrimersBadTemplatesFile_, pixForeground, pixBackground ); XtVaSetValues( widPrimersBadTemplatesFile_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersChooseTemplatesByPositionInsteadOfQuality( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersChooseTemplatesByPositionInsteadOfQuality() ); } void guiEditResources :: checkPrimersChooseTemplatesByPositionInsteadOfQuality() { bool b = XmToggleButtonGetState( widPrimersChooseTemplatesByPositionInsteadOfQualityTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bPrimersChooseTemplatesByPositionInsteadOfQuality_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bPrimersChooseTemplatesByPositionInsteadOfQuality_, CONDEF->bPrimersChooseTemplatesByPositionInsteadOfQuality_, pixForeground, pixBackground ); XtVaSetValues( widPrimersChooseTemplatesByPositionInsteadOfQualityRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersWhenChoosingATemplateMinPotentialReadLength( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersWhenChoosingATemplateMinPotentialReadLength() ); } void guiEditResources :: checkPrimersWhenChoosingATemplateMinPotentialReadLength() { char* szValue = XmTextFieldGetString( widPrimersWhenChoosingATemplateMinPotentialReadLength_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersWhenChoosingATemplateMinPotentialReadLength must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersWhenChoosingATemplateMinPotentialReadLength_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersWhenChoosingATemplateMinPotentialReadLength_, CONDEF->nPrimersWhenChoosingATemplateMinPotentialReadLength_, pixForeground, pixBackground ); XtVaSetValues( widPrimersWhenChoosingATemplateMinPotentialReadLength_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersWindowSizeInLookingForPCR( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersWindowSizeInLookingForPCR() ); } void guiEditResources :: checkPrimersWindowSizeInLookingForPCR() { char* szValue = XmTextFieldGetString( widPrimersWindowSizeInLookingForPCR_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersWindowSizeInLookingForPCR must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersWindowSizeInLookingForPCR_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersWindowSizeInLookingForPCR_, CONDEF->nPrimersWindowSizeInLookingForPCR_, pixForeground, pixBackground ); XtVaSetValues( widPrimersWindowSizeInLookingForPCR_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbQualityThresholdForFindingHighQualityDiscrepancies( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkQualityThresholdForFindingHighQualityDiscrepancies() ); } void guiEditResources :: checkQualityThresholdForFindingHighQualityDiscrepancies() { char* szValue = XmTextFieldGetString( widQualityThresholdForFindingHighQualityDiscrepancies_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.QualityThresholdForFindingHighQualityDiscrepancies must be numeric"; THROW_ERROR( soError ); } resources_.nQualityThresholdForFindingHighQualityDiscrepancies_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nQualityThresholdForFindingHighQualityDiscrepancies_, CONDEF->nQualityThresholdForFindingHighQualityDiscrepancies_, pixForeground, pixBackground ); XtVaSetValues( widQualityThresholdForFindingHighQualityDiscrepancies_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbQualityThresholdForNavigateByDepthOfCoverage( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkQualityThresholdForNavigateByDepthOfCoverage() ); } void guiEditResources :: checkQualityThresholdForNavigateByDepthOfCoverage() { char* szValue = XmTextFieldGetString( widQualityThresholdForNavigateByDepthOfCoverage_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.QualityThresholdForNavigateByDepthOfCoverage must be numeric"; THROW_ERROR( soError ); } resources_.nQualityThresholdForNavigateByDepthOfCoverage_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nQualityThresholdForNavigateByDepthOfCoverage_, CONDEF->nQualityThresholdForNavigateByDepthOfCoverage_, pixForeground, pixBackground ); XtVaSetValues( widQualityThresholdForNavigateByDepthOfCoverage_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNavigateByHighDepthOfCoverageNotLow( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNavigateByHighDepthOfCoverageNotLow() ); } void guiEditResources :: checkNavigateByHighDepthOfCoverageNotLow() { bool b = XmToggleButtonGetState( widNavigateByHighDepthOfCoverageNotLowTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bNavigateByHighDepthOfCoverageNotLow_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bNavigateByHighDepthOfCoverageNotLow_, CONDEF->bNavigateByHighDepthOfCoverageNotLow_, pixForeground, pixBackground ); XtVaSetValues( widNavigateByHighDepthOfCoverageNotLowRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbMinDepthForNavigateByDepthOfCoverage( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkMinDepthForNavigateByDepthOfCoverage() ); } void guiEditResources :: checkMinDepthForNavigateByDepthOfCoverage() { char* szValue = XmTextFieldGetString( widMinDepthForNavigateByDepthOfCoverage_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.MinDepthForNavigateByDepthOfCoverage must be numeric"; THROW_ERROR( soError ); } resources_.nMinDepthForNavigateByDepthOfCoverage_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nMinDepthForNavigateByDepthOfCoverage_, CONDEF->nMinDepthForNavigateByDepthOfCoverage_, pixForeground, pixBackground ); XtVaSetValues( widMinDepthForNavigateByDepthOfCoverage_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbDefaultVectorPathnameForRestrictionFragments( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkDefaultVectorPathnameForRestrictionFragments() ); } void guiEditResources :: checkDefaultVectorPathnameForRestrictionFragments() { char* szValue = XmTextFieldGetString( widDefaultVectorPathnameForRestrictionFragments_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filDefaultVectorPathnameForRestrictionFragments_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filDefaultVectorPathnameForRestrictionFragments_, CONDEF->filDefaultVectorPathnameForRestrictionFragments_, pixForeground, pixBackground ); XtVaSetValues( widDefaultVectorPathnameForRestrictionFragments_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbFileOfAdditionalRestrictionEnzymes( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkFileOfAdditionalRestrictionEnzymes() ); } void guiEditResources :: checkFileOfAdditionalRestrictionEnzymes() { char* szValue = XmTextFieldGetString( widFileOfAdditionalRestrictionEnzymes_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filFileOfAdditionalRestrictionEnzymes_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filFileOfAdditionalRestrictionEnzymes_, CONDEF->filFileOfAdditionalRestrictionEnzymes_, pixForeground, pixBackground ); XtVaSetValues( widFileOfAdditionalRestrictionEnzymes_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbCommonRestrictionEnzymes( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkCommonRestrictionEnzymes() ); } void guiEditResources :: checkCommonRestrictionEnzymes() { char* szValue = XmTextFieldGetString( widCommonRestrictionEnzymes_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soCommonRestrictionEnzymes_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soCommonRestrictionEnzymes_, CONDEF->soCommonRestrictionEnzymes_, pixForeground, pixBackground ); XtVaSetValues( widCommonRestrictionEnzymes_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbDefaultSelectedRestrictionEnzymes( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkDefaultSelectedRestrictionEnzymes() ); } void guiEditResources :: checkDefaultSelectedRestrictionEnzymes() { char* szValue = XmTextFieldGetString( widDefaultSelectedRestrictionEnzymes_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soDefaultSelectedRestrictionEnzymes_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soDefaultSelectedRestrictionEnzymes_, CONDEF->soDefaultSelectedRestrictionEnzymes_, pixForeground, pixBackground ); XtVaSetValues( widDefaultSelectedRestrictionEnzymes_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbRestrictionEnzymesActualFragmentsFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkRestrictionEnzymesActualFragmentsFile() ); } void guiEditResources :: checkRestrictionEnzymesActualFragmentsFile() { char* szValue = XmTextFieldGetString( widRestrictionEnzymesActualFragmentsFile_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filRestrictionEnzymesActualFragmentsFile_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filRestrictionEnzymesActualFragmentsFile_, CONDEF->filRestrictionEnzymesActualFragmentsFile_, pixForeground, pixBackground ); XtVaSetValues( widRestrictionEnzymesActualFragmentsFile_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbRestrictionDigestInitialWindowSizeInTextRows( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkRestrictionDigestInitialWindowSizeInTextRows() ); } void guiEditResources :: checkRestrictionDigestInitialWindowSizeInTextRows() { char* szValue = XmTextFieldGetString( widRestrictionDigestInitialWindowSizeInTextRows_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.RestrictionDigestInitialWindowSizeInTextRows must be numeric"; THROW_ERROR( soError ); } resources_.nRestrictionDigestInitialWindowSizeInTextRows_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nRestrictionDigestInitialWindowSizeInTextRows_, CONDEF->nRestrictionDigestInitialWindowSizeInTextRows_, pixForeground, pixBackground ); XtVaSetValues( widRestrictionDigestInitialWindowSizeInTextRows_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize() ); } void guiEditResources :: checkRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize() { char* szValue = XmTextFieldGetString( widRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.RestrictionDigestDoNoShowAreaOfFragmentsOverThisSize must be numeric"; THROW_ERROR( soError ); } resources_.nRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize_, CONDEF->nRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize_, pixForeground, pixBackground ); XtVaSetValues( widRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbShowReadsAlphabetically( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkShowReadsAlphabetically() ); } void guiEditResources :: checkShowReadsAlphabetically() { bool b = XmToggleButtonGetState( widShowReadsAlphabeticallyTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bShowReadsAlphabetically_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bShowReadsAlphabetically_, CONDEF->bShowReadsAlphabetically_, pixForeground, pixBackground ); XtVaSetValues( widShowReadsAlphabeticallyRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbShowReadsInAlignedReadsWindowOrderedByFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkShowReadsInAlignedReadsWindowOrderedByFile() ); } void guiEditResources :: checkShowReadsInAlignedReadsWindowOrderedByFile() { bool b = XmToggleButtonGetState( widShowReadsInAlignedReadsWindowOrderedByFileTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bShowReadsInAlignedReadsWindowOrderedByFile_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bShowReadsInAlignedReadsWindowOrderedByFile_, CONDEF->bShowReadsInAlignedReadsWindowOrderedByFile_, pixForeground, pixBackground ); XtVaSetValues( widShowReadsInAlignedReadsWindowOrderedByFileRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbShowReadsInAlignedReadsWindowOrderedByThisFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkShowReadsInAlignedReadsWindowOrderedByThisFile() ); } void guiEditResources :: checkShowReadsInAlignedReadsWindowOrderedByThisFile() { char* szValue = XmTextFieldGetString( widShowReadsInAlignedReadsWindowOrderedByThisFile_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filShowReadsInAlignedReadsWindowOrderedByThisFile_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filShowReadsInAlignedReadsWindowOrderedByThisFile_, CONDEF->filShowReadsInAlignedReadsWindowOrderedByThisFile_, pixForeground, pixBackground ); XtVaSetValues( widShowReadsInAlignedReadsWindowOrderedByThisFile_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbShowReadsAtCursorSortedHow( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkShowReadsAtCursorSortedHow() ); } void guiEditResources :: checkShowReadsAtCursorSortedHow() { char* szValue = XmTextFieldGetString( widShowReadsAtCursorSortedHow_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soShowReadsAtCursorSortedHow_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soShowReadsAtCursorSortedHow_, CONDEF->soShowReadsAtCursorSortedHow_, pixForeground, pixBackground ); XtVaSetValues( widShowReadsAtCursorSortedHow_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbShowABIBasesInTraceWindow( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkShowABIBasesInTraceWindow() ); } void guiEditResources :: checkShowABIBasesInTraceWindow() { bool b = XmToggleButtonGetState( widShowABIBasesInTraceWindowTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bShowABIBasesInTraceWindow_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bShowABIBasesInTraceWindow_, CONDEF->bShowABIBasesInTraceWindow_, pixForeground, pixBackground ); XtVaSetValues( widShowABIBasesInTraceWindowRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbTracesWindowInitialPixelHeight( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkTracesWindowInitialPixelHeight() ); } void guiEditResources :: checkTracesWindowInitialPixelHeight() { char* szValue = XmTextFieldGetString( widTracesWindowInitialPixelHeight_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.TracesWindowInitialPixelHeight must be numeric"; THROW_ERROR( soError ); } resources_.nTracesWindowInitialPixelHeight_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nTracesWindowInitialPixelHeight_, CONDEF->nTracesWindowInitialPixelHeight_, pixForeground, pixBackground ); XtVaSetValues( widTracesWindowInitialPixelHeight_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewWindowInitialPixelHeight( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewWindowInitialPixelHeight() ); } void guiEditResources :: checkAssemblyViewWindowInitialPixelHeight() { char* szValue = XmTextFieldGetString( widAssemblyViewWindowInitialPixelHeight_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AssemblyViewWindowInitialPixelHeight must be numeric"; THROW_ERROR( soError ); } resources_.nAssemblyViewWindowInitialPixelHeight_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAssemblyViewWindowInitialPixelHeight_, CONDEF->nAssemblyViewWindowInitialPixelHeight_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewWindowInitialPixelHeight_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewFileOfTemplatesToNotShow( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewFileOfTemplatesToNotShow() ); } void guiEditResources :: checkAssemblyViewFileOfTemplatesToNotShow() { char* szValue = XmTextFieldGetString( widAssemblyViewFileOfTemplatesToNotShow_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filAssemblyViewFileOfTemplatesToNotShow_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filAssemblyViewFileOfTemplatesToNotShow_, CONDEF->filAssemblyViewFileOfTemplatesToNotShow_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewFileOfTemplatesToNotShow_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewCrossMatchMinmatch( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewCrossMatchMinmatch() ); } void guiEditResources :: checkAssemblyViewCrossMatchMinmatch() { char* szValue = XmTextFieldGetString( widAssemblyViewCrossMatchMinmatch_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AssemblyViewCrossMatchMinmatch must be numeric"; THROW_ERROR( soError ); } resources_.nAssemblyViewCrossMatchMinmatch_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAssemblyViewCrossMatchMinmatch_, CONDEF->nAssemblyViewCrossMatchMinmatch_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewCrossMatchMinmatch_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewCrossMatchMinscore( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewCrossMatchMinscore() ); } void guiEditResources :: checkAssemblyViewCrossMatchMinscore() { char* szValue = XmTextFieldGetString( widAssemblyViewCrossMatchMinscore_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AssemblyViewCrossMatchMinscore must be numeric"; THROW_ERROR( soError ); } resources_.nAssemblyViewCrossMatchMinscore_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAssemblyViewCrossMatchMinscore_, CONDEF->nAssemblyViewCrossMatchMinscore_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewCrossMatchMinscore_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewFindSequenceMatchesForConsedScript( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewFindSequenceMatchesForConsedScript() ); } void guiEditResources :: checkAssemblyViewFindSequenceMatchesForConsedScript() { char* szValue = XmTextFieldGetString( widAssemblyViewFindSequenceMatchesForConsedScript_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filAssemblyViewFindSequenceMatchesForConsedScript_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filAssemblyViewFindSequenceMatchesForConsedScript_, CONDEF->filAssemblyViewFindSequenceMatchesForConsedScript_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewFindSequenceMatchesForConsedScript_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewCrossmatchMinmatch( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewCrossmatchMinmatch() ); } void guiEditResources :: checkAssemblyViewCrossmatchMinmatch() { char* szValue = XmTextFieldGetString( widAssemblyViewCrossmatchMinmatch_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AssemblyViewCrossmatchMinmatch must be numeric"; THROW_ERROR( soError ); } resources_.nAssemblyViewCrossmatchMinmatch_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAssemblyViewCrossmatchMinmatch_, CONDEF->nAssemblyViewCrossmatchMinmatch_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewCrossmatchMinmatch_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewCrossmatchMinscore( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewCrossmatchMinscore() ); } void guiEditResources :: checkAssemblyViewCrossmatchMinscore() { char* szValue = XmTextFieldGetString( widAssemblyViewCrossmatchMinscore_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AssemblyViewCrossmatchMinscore must be numeric"; THROW_ERROR( soError ); } resources_.nAssemblyViewCrossmatchMinscore_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAssemblyViewCrossmatchMinscore_, CONDEF->nAssemblyViewCrossmatchMinscore_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewCrossmatchMinscore_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewSequenceMatchesMinimumSimilarity( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewSequenceMatchesMinimumSimilarity() ); } void guiEditResources :: checkAssemblyViewSequenceMatchesMinimumSimilarity() { char* szValue = XmTextFieldGetString( widAssemblyViewSequenceMatchesMinimumSimilarity_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AssemblyViewSequenceMatchesMinimumSimilarity must be numeric"; THROW_ERROR( soError ); } resources_.nAssemblyViewSequenceMatchesMinimumSimilarity_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAssemblyViewSequenceMatchesMinimumSimilarity_, CONDEF->nAssemblyViewSequenceMatchesMinimumSimilarity_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewSequenceMatchesMinimumSimilarity_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbTracesWindowInitialPixelWidth( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkTracesWindowInitialPixelWidth() ); } void guiEditResources :: checkTracesWindowInitialPixelWidth() { char* szValue = XmTextFieldGetString( widTracesWindowInitialPixelWidth_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.TracesWindowInitialPixelWidth must be numeric"; THROW_ERROR( soError ); } resources_.nTracesWindowInitialPixelWidth_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nTracesWindowInitialPixelWidth_, CONDEF->nTracesWindowInitialPixelWidth_, pixForeground, pixBackground ); XtVaSetValues( widTracesWindowInitialPixelWidth_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewWindowInitialPixelWidth( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewWindowInitialPixelWidth() ); } void guiEditResources :: checkAssemblyViewWindowInitialPixelWidth() { char* szValue = XmTextFieldGetString( widAssemblyViewWindowInitialPixelWidth_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AssemblyViewWindowInitialPixelWidth must be numeric"; THROW_ERROR( soError ); } resources_.nAssemblyViewWindowInitialPixelWidth_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAssemblyViewWindowInitialPixelWidth_, CONDEF->nAssemblyViewWindowInitialPixelWidth_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewWindowInitialPixelWidth_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutomaticallyScaleTraces( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutomaticallyScaleTraces() ); } void guiEditResources :: checkAutomaticallyScaleTraces() { bool b = XmToggleButtonGetState( widAutomaticallyScaleTracesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutomaticallyScaleTraces_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutomaticallyScaleTraces_, CONDEF->bAutomaticallyScaleTraces_, pixForeground, pixBackground ); XtVaSetValues( widAutomaticallyScaleTracesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight() ); } void guiEditResources :: checkAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight() { char* szValue = XmTextFieldGetString( widAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "AutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight must be floating point numeric"; THROW_ERROR( soError ); } resources_.dAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight_, CONDEF->dAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight_, pixForeground, pixBackground ); XtVaSetValues( widAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutomaticallyScaleTracesSamplePeakPercentile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutomaticallyScaleTracesSamplePeakPercentile() ); } void guiEditResources :: checkAutomaticallyScaleTracesSamplePeakPercentile() { char* szValue = XmTextFieldGetString( widAutomaticallyScaleTracesSamplePeakPercentile_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutomaticallyScaleTracesSamplePeakPercentile must be numeric"; THROW_ERROR( soError ); } resources_.nAutomaticallyScaleTracesSamplePeakPercentile_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutomaticallyScaleTracesSamplePeakPercentile_, CONDEF->nAutomaticallyScaleTracesSamplePeakPercentile_, pixForeground, pixBackground ); XtVaSetValues( widAutomaticallyScaleTracesSamplePeakPercentile_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbVerticalTraceMagnification( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkVerticalTraceMagnification() ); } void guiEditResources :: checkVerticalTraceMagnification() { char* szValue = XmTextFieldGetString( widVerticalTraceMagnification_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.VerticalTraceMagnification must be numeric"; THROW_ERROR( soError ); } resources_.nVerticalTraceMagnification_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nVerticalTraceMagnification_, CONDEF->nVerticalTraceMagnification_, pixForeground, pixBackground ); XtVaSetValues( widVerticalTraceMagnification_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbUserDefinedKeys( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkUserDefinedKeys() ); } void guiEditResources :: checkUserDefinedKeys() { char* szValue = XmTextFieldGetString( widUserDefinedKeys_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soUserDefinedKeys_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soUserDefinedKeys_, CONDEF->soUserDefinedKeys_, pixForeground, pixBackground ); XtVaSetValues( widUserDefinedKeys_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbProgramsForUserDefinedKeys( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkProgramsForUserDefinedKeys() ); } void guiEditResources :: checkProgramsForUserDefinedKeys() { char* szValue = XmTextFieldGetString( widProgramsForUserDefinedKeys_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soProgramsForUserDefinedKeys_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soProgramsForUserDefinedKeys_, CONDEF->soProgramsForUserDefinedKeys_, pixForeground, pixBackground ); XtVaSetValues( widProgramsForUserDefinedKeys_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbArgumentsToPassToUserDefinedPrograms( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkArgumentsToPassToUserDefinedPrograms() ); } void guiEditResources :: checkArgumentsToPassToUserDefinedPrograms() { char* szValue = XmTextFieldGetString( widArgumentsToPassToUserDefinedPrograms_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soArgumentsToPassToUserDefinedPrograms_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soArgumentsToPassToUserDefinedPrograms_, CONDEF->soArgumentsToPassToUserDefinedPrograms_, pixForeground, pixBackground ); XtVaSetValues( widArgumentsToPassToUserDefinedPrograms_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbTagsToApplyWithUserDefinedKeys( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkTagsToApplyWithUserDefinedKeys() ); } void guiEditResources :: checkTagsToApplyWithUserDefinedKeys() { char* szValue = XmTextFieldGetString( widTagsToApplyWithUserDefinedKeys_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soTagsToApplyWithUserDefinedKeys_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soTagsToApplyWithUserDefinedKeys_, CONDEF->soTagsToApplyWithUserDefinedKeys_, pixForeground, pixBackground ); XtVaSetValues( widTagsToApplyWithUserDefinedKeys_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbSnpGenomeUseInsertionPolymorphisms( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkSnpGenomeUseInsertionPolymorphisms() ); } void guiEditResources :: checkSnpGenomeUseInsertionPolymorphisms() { bool b = XmToggleButtonGetState( widSnpGenomeUseInsertionPolymorphismsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bSnpGenomeUseInsertionPolymorphisms_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bSnpGenomeUseInsertionPolymorphisms_, CONDEF->bSnpGenomeUseInsertionPolymorphisms_, pixForeground, pixBackground ); XtVaSetValues( widSnpGenomeUseInsertionPolymorphismsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbListOfTagTypesToHide( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkListOfTagTypesToHide() ); } void guiEditResources :: checkListOfTagTypesToHide() { char* szValue = XmTextFieldGetString( widListOfTagTypesToHide_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soListOfTagTypesToHide_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soListOfTagTypesToHide_, CONDEF->soListOfTagTypesToHide_, pixForeground, pixBackground ); XtVaSetValues( widListOfTagTypesToHide_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbListOfOptionalWordsToSaveInListOfReadNames( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkListOfOptionalWordsToSaveInListOfReadNames() ); } void guiEditResources :: checkListOfOptionalWordsToSaveInListOfReadNames() { char* szValue = XmTextFieldGetString( widListOfOptionalWordsToSaveInListOfReadNames_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soListOfOptionalWordsToSaveInListOfReadNames_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soListOfOptionalWordsToSaveInListOfReadNames_, CONDEF->soListOfOptionalWordsToSaveInListOfReadNames_, pixForeground, pixBackground ); XtVaSetValues( widListOfOptionalWordsToSaveInListOfReadNames_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbExtendConsensusWithHighQuality( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkExtendConsensusWithHighQuality() ); } void guiEditResources :: checkExtendConsensusWithHighQuality() { bool b = XmToggleButtonGetState( widExtendConsensusWithHighQualityTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bExtendConsensusWithHighQuality_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bExtendConsensusWithHighQuality_, CONDEF->bExtendConsensusWithHighQuality_, pixForeground, pixBackground ); XtVaSetValues( widExtendConsensusWithHighQualityRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbFastStartup( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkFastStartup() ); } void guiEditResources :: checkFastStartup() { bool b = XmToggleButtonGetState( widFastStartupTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bFastStartup_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bFastStartup_, CONDEF->bFastStartup_, pixForeground, pixBackground ); XtVaSetValues( widFastStartupRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbFastStartupFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkFastStartupFile() ); } void guiEditResources :: checkFastStartupFile() { char* szValue = XmTextFieldGetString( widFastStartupFile_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filFastStartupFile_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filFastStartupFile_, CONDEF->filFastStartupFile_, pixForeground, pixBackground ); XtVaSetValues( widFastStartupFile_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAlwaysRunProgramToGetChromats( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAlwaysRunProgramToGetChromats() ); } void guiEditResources :: checkAlwaysRunProgramToGetChromats() { char* szValue = XmTextFieldGetString( widAlwaysRunProgramToGetChromats_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soAlwaysRunProgramToGetChromats_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soAlwaysRunProgramToGetChromats_, CONDEF->soAlwaysRunProgramToGetChromats_, pixForeground, pixBackground ); XtVaSetValues( widAlwaysRunProgramToGetChromats_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbProgramToRunToGetChromats( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkProgramToRunToGetChromats() ); } void guiEditResources :: checkProgramToRunToGetChromats() { char* szValue = XmTextFieldGetString( widProgramToRunToGetChromats_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filProgramToRunToGetChromats_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filProgramToRunToGetChromats_, CONDEF->filProgramToRunToGetChromats_, pixForeground, pixBackground ); XtVaSetValues( widProgramToRunToGetChromats_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbProgramToRunToGetChromatsOf454Reads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkProgramToRunToGetChromatsOf454Reads() ); } void guiEditResources :: checkProgramToRunToGetChromatsOf454Reads() { char* szValue = XmTextFieldGetString( widProgramToRunToGetChromatsOf454Reads_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filProgramToRunToGetChromatsOf454Reads_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filProgramToRunToGetChromatsOf454Reads_, CONDEF->filProgramToRunToGetChromatsOf454Reads_, pixForeground, pixBackground ); XtVaSetValues( widProgramToRunToGetChromatsOf454Reads_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbCreateFakeChromatsForSolexaReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkCreateFakeChromatsForSolexaReads() ); } void guiEditResources :: checkCreateFakeChromatsForSolexaReads() { bool b = XmToggleButtonGetState( widCreateFakeChromatsForSolexaReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bCreateFakeChromatsForSolexaReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bCreateFakeChromatsForSolexaReads_, CONDEF->bCreateFakeChromatsForSolexaReads_, pixForeground, pixBackground ); XtVaSetValues( widCreateFakeChromatsForSolexaReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishUseLongModelReadRatherThanShort( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishUseLongModelReadRatherThanShort() ); } void guiEditResources :: checkAutoFinishUseLongModelReadRatherThanShort() { bool b = XmToggleButtonGetState( widAutoFinishUseLongModelReadRatherThanShortTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishUseLongModelReadRatherThanShort_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishUseLongModelReadRatherThanShort_, CONDEF->bAutoFinishUseLongModelReadRatherThanShort_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishUseLongModelReadRatherThanShortRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAskAgainIfWantToQuitConsedIfThisManyReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAskAgainIfWantToQuitConsedIfThisManyReads() ); } void guiEditResources :: checkAskAgainIfWantToQuitConsedIfThisManyReads() { char* szValue = XmTextFieldGetString( widAskAgainIfWantToQuitConsedIfThisManyReads_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AskAgainIfWantToQuitConsedIfThisManyReads must be numeric"; THROW_ERROR( soError ); } resources_.nAskAgainIfWantToQuitConsedIfThisManyReads_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAskAgainIfWantToQuitConsedIfThisManyReads_, CONDEF->nAskAgainIfWantToQuitConsedIfThisManyReads_, pixForeground, pixBackground ); XtVaSetValues( widAskAgainIfWantToQuitConsedIfThisManyReads_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrintWindowInstructions( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrintWindowInstructions() ); } void guiEditResources :: checkPrintWindowInstructions() { char* szValue = XmTextFieldGetString( widPrintWindowInstructions_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soPrintWindowInstructions_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soPrintWindowInstructions_, CONDEF->soPrintWindowInstructions_, pixForeground, pixBackground ); XtVaSetValues( widPrintWindowInstructions_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAllowMultipleSearchForStringWindows( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAllowMultipleSearchForStringWindows() ); } void guiEditResources :: checkAllowMultipleSearchForStringWindows() { bool b = XmToggleButtonGetState( widAllowMultipleSearchForStringWindowsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAllowMultipleSearchForStringWindows_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAllowMultipleSearchForStringWindows_, CONDEF->bAllowMultipleSearchForStringWindows_, pixForeground, pixBackground ); XtVaSetValues( widAllowMultipleSearchForStringWindowsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoPCRAmplifyFalseProductsOKIfLargerThanThis( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoPCRAmplifyFalseProductsOKIfLargerThanThis() ); } void guiEditResources :: checkAutoPCRAmplifyFalseProductsOKIfLargerThanThis() { char* szValue = XmTextFieldGetString( widAutoPCRAmplifyFalseProductsOKIfLargerThanThis_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoPCRAmplifyFalseProductsOKIfLargerThanThis must be numeric"; THROW_ERROR( soError ); } resources_.nAutoPCRAmplifyFalseProductsOKIfLargerThanThis_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoPCRAmplifyFalseProductsOKIfLargerThanThis_, CONDEF->nAutoPCRAmplifyFalseProductsOKIfLargerThanThis_, pixForeground, pixBackground ); XtVaSetValues( widAutoPCRAmplifyFalseProductsOKIfLargerThanThis_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoPCRAmplifyMakePrimerOutOfFirstRegion( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoPCRAmplifyMakePrimerOutOfFirstRegion() ); } void guiEditResources :: checkAutoPCRAmplifyMakePrimerOutOfFirstRegion() { bool b = XmToggleButtonGetState( widAutoPCRAmplifyMakePrimerOutOfFirstRegionTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoPCRAmplifyMakePrimerOutOfFirstRegion_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoPCRAmplifyMakePrimerOutOfFirstRegion_, CONDEF->bAutoPCRAmplifyMakePrimerOutOfFirstRegion_, pixForeground, pixBackground ); XtVaSetValues( widAutoPCRAmplifyMakePrimerOutOfFirstRegionRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct() ); } void guiEditResources :: checkAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct() { char* szValue = XmTextFieldGetString( widAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct must be numeric"; THROW_ERROR( soError ); } resources_.nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_, CONDEF->nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_, pixForeground, pixBackground ); XtVaSetValues( widAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAddNewReadsRecalculateConsensusQuality( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAddNewReadsRecalculateConsensusQuality() ); } void guiEditResources :: checkAddNewReadsRecalculateConsensusQuality() { bool b = XmToggleButtonGetState( widAddNewReadsRecalculateConsensusQualityTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAddNewReadsRecalculateConsensusQuality_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAddNewReadsRecalculateConsensusQuality_, CONDEF->bAddNewReadsRecalculateConsensusQuality_, pixForeground, pixBackground ); XtVaSetValues( widAddNewReadsRecalculateConsensusQualityRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAddNewReadsPutReadIntoItsOwnContig( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAddNewReadsPutReadIntoItsOwnContig() ); } void guiEditResources :: checkAddNewReadsPutReadIntoItsOwnContig() { char* szValue = XmTextFieldGetString( widAddNewReadsPutReadIntoItsOwnContig_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soAddNewReadsPutReadIntoItsOwnContig_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soAddNewReadsPutReadIntoItsOwnContig_, CONDEF->soAddNewReadsPutReadIntoItsOwnContig_, pixForeground, pixBackground ); XtVaSetValues( widAddNewReadsPutReadIntoItsOwnContig_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAddNewReadsCheckThatCrossMatchRunCorrectly( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAddNewReadsCheckThatCrossMatchRunCorrectly() ); } void guiEditResources :: checkAddNewReadsCheckThatCrossMatchRunCorrectly() { bool b = XmToggleButtonGetState( widAddNewReadsCheckThatCrossMatchRunCorrectlyTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAddNewReadsCheckThatCrossMatchRunCorrectly_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAddNewReadsCheckThatCrossMatchRunCorrectly_, CONDEF->bAddNewReadsCheckThatCrossMatchRunCorrectly_, pixForeground, pixBackground ); XtVaSetValues( widAddNewReadsCheckThatCrossMatchRunCorrectlyRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewNumberOfRowsOfTags( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewNumberOfRowsOfTags() ); } void guiEditResources :: checkAssemblyViewNumberOfRowsOfTags() { char* szValue = XmTextFieldGetString( widAssemblyViewNumberOfRowsOfTags_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AssemblyViewNumberOfRowsOfTags must be numeric"; THROW_ERROR( soError ); } resources_.nAssemblyViewNumberOfRowsOfTags_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAssemblyViewNumberOfRowsOfTags_, CONDEF->nAssemblyViewNumberOfRowsOfTags_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewNumberOfRowsOfTags_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbWarnUserWhenTryingToEditAllReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkWarnUserWhenTryingToEditAllReads() ); } void guiEditResources :: checkWarnUserWhenTryingToEditAllReads() { bool b = XmToggleButtonGetState( widWarnUserWhenTryingToEditAllReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bWarnUserWhenTryingToEditAllReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bWarnUserWhenTryingToEditAllReads_, CONDEF->bWarnUserWhenTryingToEditAllReads_, pixForeground, pixBackground ); XtVaSetValues( widWarnUserWhenTryingToEditAllReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbMaybeXKEYSYMDBPath( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkMaybeXKEYSYMDBPath() ); } void guiEditResources :: checkMaybeXKEYSYMDBPath() { char* szValue = XmTextFieldGetString( widMaybeXKEYSYMDBPath_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filMaybeXKEYSYMDBPath_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filMaybeXKEYSYMDBPath_, CONDEF->filMaybeXKEYSYMDBPath_, pixForeground, pixBackground ); XtVaSetValues( widMaybeXKEYSYMDBPath_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbMaybeXKEYSYMDBPath2( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkMaybeXKEYSYMDBPath2() ); } void guiEditResources :: checkMaybeXKEYSYMDBPath2() { char* szValue = XmTextFieldGetString( widMaybeXKEYSYMDBPath2_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filMaybeXKEYSYMDBPath2_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filMaybeXKEYSYMDBPath2_, CONDEF->filMaybeXKEYSYMDBPath2_, pixForeground, pixBackground ); XtVaSetValues( widMaybeXKEYSYMDBPath2_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAmountToMoveWithBigLeftAndRightArrows( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAmountToMoveWithBigLeftAndRightArrows() ); } void guiEditResources :: checkAmountToMoveWithBigLeftAndRightArrows() { char* szValue = XmTextFieldGetString( widAmountToMoveWithBigLeftAndRightArrows_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AmountToMoveWithBigLeftAndRightArrows must be numeric"; THROW_ERROR( soError ); } resources_.nAmountToMoveWithBigLeftAndRightArrows_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAmountToMoveWithBigLeftAndRightArrows_, CONDEF->nAmountToMoveWithBigLeftAndRightArrows_, pixForeground, pixBackground ); XtVaSetValues( widAmountToMoveWithBigLeftAndRightArrows_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNavigateByHighlyDiscrepantPositionsMinDiscrepantReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNavigateByHighlyDiscrepantPositionsMinDiscrepantReads() ); } void guiEditResources :: checkNavigateByHighlyDiscrepantPositionsMinDiscrepantReads() { char* szValue = XmTextFieldGetString( widNavigateByHighlyDiscrepantPositionsMinDiscrepantReads_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.NavigateByHighlyDiscrepantPositionsMinDiscrepantReads must be numeric"; THROW_ERROR( soError ); } resources_.nNavigateByHighlyDiscrepantPositionsMinDiscrepantReads_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nNavigateByHighlyDiscrepantPositionsMinDiscrepantReads_, CONDEF->nNavigateByHighlyDiscrepantPositionsMinDiscrepantReads_, pixForeground, pixBackground ); XtVaSetValues( widNavigateByHighlyDiscrepantPositionsMinDiscrepantReads_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage() ); } void guiEditResources :: checkNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage() { char* szValue = XmTextFieldGetString( widNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.NavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage must be numeric"; THROW_ERROR( soError ); } resources_.nNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage_, CONDEF->nNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage_, pixForeground, pixBackground ); XtVaSetValues( widNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality() ); } void guiEditResources :: checkNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality() { char* szValue = XmTextFieldGetString( widNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.NavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality must be numeric"; THROW_ERROR( soError ); } resources_.nNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality_, CONDEF->nNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality_, pixForeground, pixBackground ); XtVaSetValues( widNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNavigateByHighlyDiscrepantPositionsJustListIndels( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNavigateByHighlyDiscrepantPositionsJustListIndels() ); } void guiEditResources :: checkNavigateByHighlyDiscrepantPositionsJustListIndels() { bool b = XmToggleButtonGetState( widNavigateByHighlyDiscrepantPositionsJustListIndelsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bNavigateByHighlyDiscrepantPositionsJustListIndels_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bNavigateByHighlyDiscrepantPositionsJustListIndels_, CONDEF->bNavigateByHighlyDiscrepantPositionsJustListIndels_, pixForeground, pixBackground ); XtVaSetValues( widNavigateByHighlyDiscrepantPositionsJustListIndelsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation() ); } void guiEditResources :: checkNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation() { bool b = XmToggleButtonGetState( widNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocationTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation_, CONDEF->bNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation_, pixForeground, pixBackground ); XtVaSetValues( widNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocationRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus() ); } void guiEditResources :: checkNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus() { bool b = XmToggleButtonGetState( widNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensusTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus_, CONDEF->bNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus_, pixForeground, pixBackground ); XtVaSetValues( widNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensusRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus() ); } void guiEditResources :: checkNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus() { char* szValue = XmTextFieldGetString( widNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus_, CONDEF->soNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus_, pixForeground, pixBackground ); XtVaSetValues( widNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPhdBallDirectory( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPhdBallDirectory() ); } void guiEditResources :: checkPhdBallDirectory() { char* szValue = XmTextFieldGetString( widPhdBallDirectory_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filPhdBallDirectory_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filPhdBallDirectory_, CONDEF->filPhdBallDirectory_, pixForeground, pixBackground ); XtVaSetValues( widPhdBallDirectory_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNewAceFileFOF( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNewAceFileFOF() ); } void guiEditResources :: checkNewAceFileFOF() { char* szValue = XmTextFieldGetString( widNewAceFileFOF_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filNewAceFileFOF_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filNewAceFileFOF_, CONDEF->filNewAceFileFOF_, pixForeground, pixBackground ); XtVaSetValues( widNewAceFileFOF_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNavigateByHighOrLowDepthCoalesceRegionsIfThisClose( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNavigateByHighOrLowDepthCoalesceRegionsIfThisClose() ); } void guiEditResources :: checkNavigateByHighOrLowDepthCoalesceRegionsIfThisClose() { char* szValue = XmTextFieldGetString( widNavigateByHighOrLowDepthCoalesceRegionsIfThisClose_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.NavigateByHighOrLowDepthCoalesceRegionsIfThisClose must be numeric"; THROW_ERROR( soError ); } resources_.nNavigateByHighOrLowDepthCoalesceRegionsIfThisClose_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nNavigateByHighOrLowDepthCoalesceRegionsIfThisClose_, CONDEF->nNavigateByHighOrLowDepthCoalesceRegionsIfThisClose_, pixForeground, pixBackground ); XtVaSetValues( widNavigateByHighOrLowDepthCoalesceRegionsIfThisClose_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbRemoveReadsDeleteNotJustPutInOwnContig( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkRemoveReadsDeleteNotJustPutInOwnContig() ); } void guiEditResources :: checkRemoveReadsDeleteNotJustPutInOwnContig() { bool b = XmToggleButtonGetState( widRemoveReadsDeleteNotJustPutInOwnContigTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bRemoveReadsDeleteNotJustPutInOwnContig_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bRemoveReadsDeleteNotJustPutInOwnContig_, CONDEF->bRemoveReadsDeleteNotJustPutInOwnContig_, pixForeground, pixBackground ); XtVaSetValues( widRemoveReadsDeleteNotJustPutInOwnContigRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPaired454LeftReadExtension( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPaired454LeftReadExtension() ); } void guiEditResources :: checkPaired454LeftReadExtension() { char* szValue = XmTextFieldGetString( widPaired454LeftReadExtension_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soPaired454LeftReadExtension_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soPaired454LeftReadExtension_, CONDEF->soPaired454LeftReadExtension_, pixForeground, pixBackground ); XtVaSetValues( widPaired454LeftReadExtension_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPaired454RightReadExtension( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPaired454RightReadExtension() ); } void guiEditResources :: checkPaired454RightReadExtension() { char* szValue = XmTextFieldGetString( widPaired454RightReadExtension_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soPaired454RightReadExtension_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soPaired454RightReadExtension_, CONDEF->soPaired454RightReadExtension_, pixForeground, pixBackground ); XtVaSetValues( widPaired454RightReadExtension_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbSnpGenome1MSnps( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkSnpGenome1MSnps() ); } void guiEditResources :: checkSnpGenome1MSnps() { char* szValue = XmTextFieldGetString( widSnpGenome1MSnps_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filSnpGenome1MSnps_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filSnpGenome1MSnps_, CONDEF->filSnpGenome1MSnps_, pixForeground, pixBackground ); XtVaSetValues( widSnpGenome1MSnps_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbDiffChromosomesExcludeDeletions( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkDiffChromosomesExcludeDeletions() ); } void guiEditResources :: checkDiffChromosomesExcludeDeletions() { bool b = XmToggleButtonGetState( widDiffChromosomesExcludeDeletionsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bDiffChromosomesExcludeDeletions_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bDiffChromosomesExcludeDeletions_, CONDEF->bDiffChromosomesExcludeDeletions_, pixForeground, pixBackground ); XtVaSetValues( widDiffChromosomesExcludeDeletionsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbSnpGenomeFilterByWeight( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkSnpGenomeFilterByWeight() ); } void guiEditResources :: checkSnpGenomeFilterByWeight() { bool b = XmToggleButtonGetState( widSnpGenomeFilterByWeightTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bSnpGenomeFilterByWeight_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bSnpGenomeFilterByWeight_, CONDEF->bSnpGenomeFilterByWeight_, pixForeground, pixBackground ); XtVaSetValues( widSnpGenomeFilterByWeightRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbWantReadsUpToThisFarFromSnps( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkWantReadsUpToThisFarFromSnps() ); } void guiEditResources :: checkWantReadsUpToThisFarFromSnps() { char* szValue = XmTextFieldGetString( widWantReadsUpToThisFarFromSnps_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.WantReadsUpToThisFarFromSnps must be numeric"; THROW_ERROR( soError ); } resources_.nWantReadsUpToThisFarFromSnps_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nWantReadsUpToThisFarFromSnps_, CONDEF->nWantReadsUpToThisFarFromSnps_, pixForeground, pixBackground ); XtVaSetValues( widWantReadsUpToThisFarFromSnps_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPhaster2PhdBallSaveWhichMate( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPhaster2PhdBallSaveWhichMate() ); } void guiEditResources :: checkPhaster2PhdBallSaveWhichMate() { char* szValue = XmTextFieldGetString( widPhaster2PhdBallSaveWhichMate_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soPhaster2PhdBallSaveWhichMate_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soPhaster2PhdBallSaveWhichMate_, CONDEF->soPhaster2PhdBallSaveWhichMate_, pixForeground, pixBackground ); XtVaSetValues( widPhaster2PhdBallSaveWhichMate_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPhaster2PhdBallSaveInPhasterFormat( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPhaster2PhdBallSaveInPhasterFormat() ); } void guiEditResources :: checkPhaster2PhdBallSaveInPhasterFormat() { bool b = XmToggleButtonGetState( widPhaster2PhdBallSaveInPhasterFormatTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bPhaster2PhdBallSaveInPhasterFormat_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bPhaster2PhdBallSaveInPhasterFormat_, CONDEF->bPhaster2PhdBallSaveInPhasterFormat_, pixForeground, pixBackground ); XtVaSetValues( widPhaster2PhdBallSaveInPhasterFormatRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPhaster2PhdBallCalculateNewLocationsFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPhaster2PhdBallCalculateNewLocationsFile() ); } void guiEditResources :: checkPhaster2PhdBallCalculateNewLocationsFile() { bool b = XmToggleButtonGetState( widPhaster2PhdBallCalculateNewLocationsFileTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bPhaster2PhdBallCalculateNewLocationsFile_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bPhaster2PhdBallCalculateNewLocationsFile_, CONDEF->bPhaster2PhdBallCalculateNewLocationsFile_, pixForeground, pixBackground ); XtVaSetValues( widPhaster2PhdBallCalculateNewLocationsFileRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPhdBall2FastaIgnoreLowQualityReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPhdBall2FastaIgnoreLowQualityReads() ); } void guiEditResources :: checkPhdBall2FastaIgnoreLowQualityReads() { bool b = XmToggleButtonGetState( widPhdBall2FastaIgnoreLowQualityReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bPhdBall2FastaIgnoreLowQualityReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bPhdBall2FastaIgnoreLowQualityReads_, CONDEF->bPhdBall2FastaIgnoreLowQualityReads_, pixForeground, pixBackground ); XtVaSetValues( widPhdBall2FastaIgnoreLowQualityReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPhdBall2FastaLowestAverageQuality( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPhdBall2FastaLowestAverageQuality() ); } void guiEditResources :: checkPhdBall2FastaLowestAverageQuality() { char* szValue = XmTextFieldGetString( widPhdBall2FastaLowestAverageQuality_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PhdBall2FastaLowestAverageQuality must be numeric"; THROW_ERROR( soError ); } resources_.nPhdBall2FastaLowestAverageQuality_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPhdBall2FastaLowestAverageQuality_, CONDEF->nPhdBall2FastaLowestAverageQuality_, pixForeground, pixBackground ); XtVaSetValues( widPhdBall2FastaLowestAverageQuality_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNextPhredPipelineControlFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNextPhredPipelineControlFile() ); } void guiEditResources :: checkNextPhredPipelineControlFile() { char* szValue = XmTextFieldGetString( widNextPhredPipelineControlFile_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filNextPhredPipelineControlFile_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filNextPhredPipelineControlFile_, CONDEF->filNextPhredPipelineControlFile_, pixForeground, pixBackground ); XtVaSetValues( widNextPhredPipelineControlFile_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNextPhredPipelineTiffPerlScript( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNextPhredPipelineTiffPerlScript() ); } void guiEditResources :: checkNextPhredPipelineTiffPerlScript() { char* szValue = XmTextFieldGetString( widNextPhredPipelineTiffPerlScript_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filNextPhredPipelineTiffPerlScript_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filNextPhredPipelineTiffPerlScript_, CONDEF->filNextPhredPipelineTiffPerlScript_, pixForeground, pixBackground ); XtVaSetValues( widNextPhredPipelineTiffPerlScript_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNextPhredPipelinePhasterPerlScript( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNextPhredPipelinePhasterPerlScript() ); } void guiEditResources :: checkNextPhredPipelinePhasterPerlScript() { char* szValue = XmTextFieldGetString( widNextPhredPipelinePhasterPerlScript_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filNextPhredPipelinePhasterPerlScript_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filNextPhredPipelinePhasterPerlScript_, CONDEF->filNextPhredPipelinePhasterPerlScript_, pixForeground, pixBackground ); XtVaSetValues( widNextPhredPipelinePhasterPerlScript_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNextPhredPipelineVersion( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNextPhredPipelineVersion() ); } void guiEditResources :: checkNextPhredPipelineVersion() { char* szValue = XmTextFieldGetString( widNextPhredPipelineVersion_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soNextPhredPipelineVersion_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soNextPhredPipelineVersion_, CONDEF->soNextPhredPipelineVersion_, pixForeground, pixBackground ); XtVaSetValues( widNextPhredPipelineVersion_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbNextPhredPipelineMainDirectory( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkNextPhredPipelineMainDirectory() ); } void guiEditResources :: checkNextPhredPipelineMainDirectory() { char* szValue = XmTextFieldGetString( widNextPhredPipelineMainDirectory_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soNextPhredPipelineMainDirectory_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soNextPhredPipelineMainDirectory_, CONDEF->soNextPhredPipelineMainDirectory_, pixForeground, pixBackground ); XtVaSetValues( widNextPhredPipelineMainDirectory_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbMaxNumberOfReadsPerPhdBall( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkMaxNumberOfReadsPerPhdBall() ); } void guiEditResources :: checkMaxNumberOfReadsPerPhdBall() { char* szValue = XmTextFieldGetString( widMaxNumberOfReadsPerPhdBall_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.MaxNumberOfReadsPerPhdBall must be numeric"; THROW_ERROR( soError ); } resources_.nMaxNumberOfReadsPerPhdBall_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nMaxNumberOfReadsPerPhdBall_, CONDEF->nMaxNumberOfReadsPerPhdBall_, pixForeground, pixBackground ); XtVaSetValues( widMaxNumberOfReadsPerPhdBall_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbUserWantsToSaveToThisAceFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkUserWantsToSaveToThisAceFile() ); } void guiEditResources :: checkUserWantsToSaveToThisAceFile() { char* szValue = XmTextFieldGetString( widUserWantsToSaveToThisAceFile_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filUserWantsToSaveToThisAceFile_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filUserWantsToSaveToThisAceFile_, CONDEF->filUserWantsToSaveToThisAceFile_, pixForeground, pixBackground ); XtVaSetValues( widUserWantsToSaveToThisAceFile_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishEmulate9_66Behavior( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishEmulate9_66Behavior() ); } void guiEditResources :: checkAutoFinishEmulate9_66Behavior() { bool b = XmToggleButtonGetState( widAutoFinishEmulate9_66BehaviorTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishEmulate9_66Behavior_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishEmulate9_66Behavior_, CONDEF->bAutoFinishEmulate9_66Behavior_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishEmulate9_66BehaviorRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersPCRPrimersGroupedIntoWindowOfThisManyBases( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersPCRPrimersGroupedIntoWindowOfThisManyBases() ); } void guiEditResources :: checkPrimersPCRPrimersGroupedIntoWindowOfThisManyBases() { char* szValue = XmTextFieldGetString( widPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersPCRPrimersGroupedIntoWindowOfThisManyBases must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_, CONDEF->nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_, pixForeground, pixBackground ); XtVaSetValues( widPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups() ); } void guiEditResources :: checkPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups() { char* szValue = XmTextFieldGetString( widPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersLookForThisManyPCRPrimerPairsPerPairOfGroups must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_, CONDEF->nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_, pixForeground, pixBackground ); XtVaSetValues( widPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs() ); } void guiEditResources :: checkAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs() { char* szValue = XmTextFieldGetString( widAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "AutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs must be floating point numeric"; THROW_ERROR( soError ); } resources_.dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_, CONDEF->dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent() ); } void guiEditResources :: checkAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent() { bool b = XmToggleButtonGetState( widAutoFinishCheckThatReadsFromTheSameTemplateAreConsistentTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_, CONDEF->bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishCheckThatReadsFromTheSameTemplateAreConsistentRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether() ); } void guiEditResources :: checkAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether() { bool b = XmToggleButtonGetState( widAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogetherTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_, CONDEF->bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogetherRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether() ); } void guiEditResources :: checkAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether() { bool b = XmToggleButtonGetState( widAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogetherTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_, CONDEF->bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogetherRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean() ); } void guiEditResources :: checkAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean() { char* szValue = XmTextFieldGetString( widAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "AutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean must be floating point numeric"; THROW_ERROR( soError ); } resources_.dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_, CONDEF->dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize() ); } void guiEditResources :: checkAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize() { char* szValue = XmTextFieldGetString( widAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_, CONDEF->nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize() ); } void guiEditResources :: checkAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize() { char* szValue = XmTextFieldGetString( widAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "AutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize must be floating point numeric"; THROW_ERROR( soError ); } resources_.dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_, CONDEF->dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead() ); } void guiEditResources :: checkAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead() { char* szValue = XmTextFieldGetString( widAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_, CONDEF->nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp() ); } void guiEditResources :: checkAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp() { char* szValue = XmTextFieldGetString( widAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_, CONDEF->nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishNumberOfBasesBetweenContigsAssumed( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishNumberOfBasesBetweenContigsAssumed() ); } void guiEditResources :: checkAutoFinishNumberOfBasesBetweenContigsAssumed() { char* szValue = XmTextFieldGetString( widAutoFinishNumberOfBasesBetweenContigsAssumed_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishNumberOfBasesBetweenContigsAssumed must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishNumberOfBasesBetweenContigsAssumed_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishNumberOfBasesBetweenContigsAssumed_, CONDEF->nAutoFinishNumberOfBasesBetweenContigsAssumed_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishNumberOfBasesBetweenContigsAssumed_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishPotentialHighQualityPartOfReadStart( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishPotentialHighQualityPartOfReadStart() ); } void guiEditResources :: checkAutoFinishPotentialHighQualityPartOfReadStart() { char* szValue = XmTextFieldGetString( widAutoFinishPotentialHighQualityPartOfReadStart_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishPotentialHighQualityPartOfReadStart must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishPotentialHighQualityPartOfReadStart_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishPotentialHighQualityPartOfReadStart_, CONDEF->nAutoFinishPotentialHighQualityPartOfReadStart_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishPotentialHighQualityPartOfReadStart_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishPotentialHighQualityPartOfReadEnd( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishPotentialHighQualityPartOfReadEnd() ); } void guiEditResources :: checkAutoFinishPotentialHighQualityPartOfReadEnd() { char* szValue = XmTextFieldGetString( widAutoFinishPotentialHighQualityPartOfReadEnd_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishPotentialHighQualityPartOfReadEnd must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishPotentialHighQualityPartOfReadEnd_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishPotentialHighQualityPartOfReadEnd_, CONDEF->nAutoFinishPotentialHighQualityPartOfReadEnd_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishPotentialHighQualityPartOfReadEnd_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishPrintCustomNavigationFileForChosenReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishPrintCustomNavigationFileForChosenReads() ); } void guiEditResources :: checkAutoFinishPrintCustomNavigationFileForChosenReads() { bool b = XmToggleButtonGetState( widAutoFinishPrintCustomNavigationFileForChosenReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishPrintCustomNavigationFileForChosenReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishPrintCustomNavigationFileForChosenReads_, CONDEF->bAutoFinishPrintCustomNavigationFileForChosenReads_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishPrintCustomNavigationFileForChosenReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch() ); } void guiEditResources :: checkAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch() { char* szValue = XmTextFieldGetString( widAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_, CONDEF->nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishTagOligosWhenDoExperiments( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishTagOligosWhenDoExperiments() ); } void guiEditResources :: checkAutoFinishTagOligosWhenDoExperiments() { bool b = XmToggleButtonGetState( widAutoFinishTagOligosWhenDoExperimentsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoFinishTagOligosWhenDoExperiments_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoFinishTagOligosWhenDoExperiments_, CONDEF->bAutoFinishTagOligosWhenDoExperiments_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishTagOligosWhenDoExperimentsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbCountPads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkCountPads() ); } void guiEditResources :: checkCountPads() { bool b = XmToggleButtonGetState( widCountPadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bCountPads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bCountPads_, CONDEF->bCountPads_, pixForeground, pixBackground ); XtVaSetValues( widCountPadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbDebugging( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkDebugging() ); } void guiEditResources :: checkDebugging() { char* szValue = XmTextFieldGetString( widDebugging_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.Debugging must be numeric"; THROW_ERROR( soError ); } resources_.nDebugging_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nDebugging_, CONDEF->nDebugging_, pixForeground, pixBackground ); XtVaSetValues( widDebugging_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbDebugging2( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkDebugging2() ); } void guiEditResources :: checkDebugging2() { char* szValue = XmTextFieldGetString( widDebugging2_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.Debugging2 must be numeric"; THROW_ERROR( soError ); } resources_.nDebugging2_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nDebugging2_, CONDEF->nDebugging2_, pixForeground, pixBackground ); XtVaSetValues( widDebugging2_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbDebugging3( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkDebugging3() ); } void guiEditResources :: checkDebugging3() { char* szValue = XmTextFieldGetString( widDebugging3_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.Debugging3 must be numeric"; THROW_ERROR( soError ); } resources_.nDebugging3_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nDebugging3_, CONDEF->nDebugging3_, pixForeground, pixBackground ); XtVaSetValues( widDebugging3_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbDebuggingString( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkDebuggingString() ); } void guiEditResources :: checkDebuggingString() { char* szValue = XmTextFieldGetString( widDebuggingString_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soDebuggingString_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soDebuggingString_, CONDEF->soDebuggingString_, pixForeground, pixBackground ); XtVaSetValues( widDebuggingString_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion() ); } void guiEditResources :: checkIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion() { char* szValue = XmTextFieldGetString( widIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.IgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion must be numeric"; THROW_ERROR( soError ); } resources_.nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_, CONDEF->nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_, pixForeground, pixBackground ); XtVaSetValues( widIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbIgnoreUnalignedHighQualitySegmentsShorterThanThis( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkIgnoreUnalignedHighQualitySegmentsShorterThanThis() ); } void guiEditResources :: checkIgnoreUnalignedHighQualitySegmentsShorterThanThis() { char* szValue = XmTextFieldGetString( widIgnoreUnalignedHighQualitySegmentsShorterThanThis_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.IgnoreUnalignedHighQualitySegmentsShorterThanThis must be numeric"; THROW_ERROR( soError ); } resources_.nIgnoreUnalignedHighQualitySegmentsShorterThanThis_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nIgnoreUnalignedHighQualitySegmentsShorterThanThis_, CONDEF->nIgnoreUnalignedHighQualitySegmentsShorterThanThis_, pixForeground, pixBackground ); XtVaSetValues( widIgnoreUnalignedHighQualitySegmentsShorterThanThis_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersLookThisFarForForwardVectorInsertJunction( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersLookThisFarForForwardVectorInsertJunction() ); } void guiEditResources :: checkPrimersLookThisFarForForwardVectorInsertJunction() { char* szValue = XmTextFieldGetString( widPrimersLookThisFarForForwardVectorInsertJunction_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersLookThisFarForForwardVectorInsertJunction must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersLookThisFarForForwardVectorInsertJunction_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersLookThisFarForForwardVectorInsertJunction_, CONDEF->nPrimersLookThisFarForForwardVectorInsertJunction_, pixForeground, pixBackground ); XtVaSetValues( widPrimersLookThisFarForForwardVectorInsertJunction_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersDNAConcentrationNanomolar( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersDNAConcentrationNanomolar() ); } void guiEditResources :: checkPrimersDNAConcentrationNanomolar() { char* szValue = XmTextFieldGetString( widPrimersDNAConcentrationNanomolar_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "PrimersDNAConcentrationNanomolar must be floating point numeric"; THROW_ERROR( soError ); } resources_.dPrimersDNAConcentrationNanomolar_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dPrimersDNAConcentrationNanomolar_, CONDEF->dPrimersDNAConcentrationNanomolar_, pixForeground, pixBackground ); XtVaSetValues( widPrimersDNAConcentrationNanomolar_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMaxMatchElsewhereScore( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMaxMatchElsewhereScore() ); } void guiEditResources :: checkPrimersMaxMatchElsewhereScore() { char* szValue = XmTextFieldGetString( widPrimersMaxMatchElsewhereScore_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMaxMatchElsewhereScore must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMaxMatchElsewhereScore_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMaxMatchElsewhereScore_, CONDEF->nPrimersMaxMatchElsewhereScore_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMaxMatchElsewhereScore_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMaxMatchElsewhereScoreForPCR( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMaxMatchElsewhereScoreForPCR() ); } void guiEditResources :: checkPrimersMaxMatchElsewhereScoreForPCR() { char* szValue = XmTextFieldGetString( widPrimersMaxMatchElsewhereScoreForPCR_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMaxMatchElsewhereScoreForPCR must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMaxMatchElsewhereScoreForPCR_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMaxMatchElsewhereScoreForPCR_, CONDEF->nPrimersMaxMatchElsewhereScoreForPCR_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMaxMatchElsewhereScoreForPCR_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMaxSelfMatchScore( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMaxSelfMatchScore() ); } void guiEditResources :: checkPrimersMaxSelfMatchScore() { char* szValue = XmTextFieldGetString( widPrimersMaxSelfMatchScore_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMaxSelfMatchScore must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMaxSelfMatchScore_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMaxSelfMatchScore_, CONDEF->nPrimersMaxSelfMatchScore_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMaxSelfMatchScore_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMaxPrimerDimerScoreForPCR( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMaxPrimerDimerScoreForPCR() ); } void guiEditResources :: checkPrimersMaxPrimerDimerScoreForPCR() { char* szValue = XmTextFieldGetString( widPrimersMaxPrimerDimerScoreForPCR_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMaxPrimerDimerScoreForPCR must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMaxPrimerDimerScoreForPCR_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMaxPrimerDimerScoreForPCR_, CONDEF->nPrimersMaxPrimerDimerScoreForPCR_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMaxPrimerDimerScoreForPCR_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersMinQuality( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersMinQuality() ); } void guiEditResources :: checkPrimersMinQuality() { char* szValue = XmTextFieldGetString( widPrimersMinQuality_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersMinQuality must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersMinQuality_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersMinQuality_, CONDEF->nPrimersMinQuality_, pixForeground, pixBackground ); XtVaSetValues( widPrimersMinQuality_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersPrintInfoOnRejectedTemplates( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersPrintInfoOnRejectedTemplates() ); } void guiEditResources :: checkPrimersPrintInfoOnRejectedTemplates() { bool b = XmToggleButtonGetState( widPrimersPrintInfoOnRejectedTemplatesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bPrimersPrintInfoOnRejectedTemplates_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bPrimersPrintInfoOnRejectedTemplates_, CONDEF->bPrimersPrintInfoOnRejectedTemplates_, pixForeground, pixBackground ); XtVaSetValues( widPrimersPrintInfoOnRejectedTemplatesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersSaltConcentrationMillimolar( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersSaltConcentrationMillimolar() ); } void guiEditResources :: checkPrimersSaltConcentrationMillimolar() { char* szValue = XmTextFieldGetString( widPrimersSaltConcentrationMillimolar_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "PrimersSaltConcentrationMillimolar must be floating point numeric"; THROW_ERROR( soError ); } resources_.dPrimersSaltConcentrationMillimolar_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dPrimersSaltConcentrationMillimolar_, CONDEF->dPrimersSaltConcentrationMillimolar_, pixForeground, pixBackground ); XtVaSetValues( widPrimersSaltConcentrationMillimolar_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersScreenForVector( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersScreenForVector() ); } void guiEditResources :: checkPrimersScreenForVector() { bool b = XmToggleButtonGetState( widPrimersScreenForVectorTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bPrimersScreenForVector_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bPrimersScreenForVector_, CONDEF->bPrimersScreenForVector_, pixForeground, pixBackground ); XtVaSetValues( widPrimersScreenForVectorRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads() ); } void guiEditResources :: checkPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads() { char* szValue = XmTextFieldGetString( widPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_, CONDEF->nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_, pixForeground, pixBackground ); XtVaSetValues( widPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbPrimersTooManyVectorBasesInWalkingRead( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkPrimersTooManyVectorBasesInWalkingRead() ); } void guiEditResources :: checkPrimersTooManyVectorBasesInWalkingRead() { char* szValue = XmTextFieldGetString( widPrimersTooManyVectorBasesInWalkingRead_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.PrimersTooManyVectorBasesInWalkingRead must be numeric"; THROW_ERROR( soError ); } resources_.nPrimersTooManyVectorBasesInWalkingRead_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nPrimersTooManyVectorBasesInWalkingRead_, CONDEF->nPrimersTooManyVectorBasesInWalkingRead_, pixForeground, pixBackground ); XtVaSetValues( widPrimersTooManyVectorBasesInWalkingRead_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbQualityThresholdForLowConsensusQuality( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkQualityThresholdForLowConsensusQuality() ); } void guiEditResources :: checkQualityThresholdForLowConsensusQuality() { char* szValue = XmTextFieldGetString( widQualityThresholdForLowConsensusQuality_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.QualityThresholdForLowConsensusQuality must be numeric"; THROW_ERROR( soError ); } resources_.nQualityThresholdForLowConsensusQuality_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nQualityThresholdForLowConsensusQuality_, CONDEF->nQualityThresholdForLowConsensusQuality_, pixForeground, pixBackground ); XtVaSetValues( widQualityThresholdForLowConsensusQuality_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbTagColorPerCentOfBase( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkTagColorPerCentOfBase() ); } void guiEditResources :: checkTagColorPerCentOfBase() { char* szValue = XmTextFieldGetString( widTagColorPerCentOfBase_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.TagColorPerCentOfBase must be numeric"; THROW_ERROR( soError ); } resources_.nTagColorPerCentOfBase_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nTagColorPerCentOfBase_, CONDEF->nTagColorPerCentOfBase_, pixForeground, pixBackground ); XtVaSetValues( widTagColorPerCentOfBase_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbUncompressedChromatDirectory( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkUncompressedChromatDirectory() ); } void guiEditResources :: checkUncompressedChromatDirectory() { char* szValue = XmTextFieldGetString( widUncompressedChromatDirectory_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soUncompressedChromatDirectory_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soUncompressedChromatDirectory_, CONDEF->soUncompressedChromatDirectory_, pixForeground, pixBackground ); XtVaSetValues( widUncompressedChromatDirectory_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cb454sff2scfDirectory( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->check454sff2scfDirectory() ); } void guiEditResources :: check454sff2scfDirectory() { char* szValue = XmTextFieldGetString( wid454sff2scfDirectory_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.fil454sff2scfDirectory_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.fil454sff2scfDirectory_, CONDEF->fil454sff2scfDirectory_, pixForeground, pixBackground ); XtVaSetValues( wid454sff2scfDirectory_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion() ); } void guiEditResources :: checkWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion() { char* szValue = XmTextFieldGetString( widWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.WhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion must be numeric"; THROW_ERROR( soError ); } resources_.nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion_, CONDEF->nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion_, pixForeground, pixBackground ); XtVaSetValues( widWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbWriteThisAceFormat( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkWriteThisAceFormat() ); } void guiEditResources :: checkWriteThisAceFormat() { char* szValue = XmTextFieldGetString( widWriteThisAceFormat_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.WriteThisAceFormat must be numeric"; THROW_ERROR( soError ); } resources_.nWriteThisAceFormat_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nWriteThisAceFormat_, CONDEF->nWriteThisAceFormat_, pixForeground, pixBackground ); XtVaSetValues( widWriteThisAceFormat_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbDumpCoreIfBoundsError( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkDumpCoreIfBoundsError() ); } void guiEditResources :: checkDumpCoreIfBoundsError() { bool b = XmToggleButtonGetState( widDumpCoreIfBoundsErrorTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bDumpCoreIfBoundsError_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bDumpCoreIfBoundsError_, CONDEF->bDumpCoreIfBoundsError_, pixForeground, pixBackground ); XtVaSetValues( widDumpCoreIfBoundsErrorRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishMinSmithWatermanScoreOfARun( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishMinSmithWatermanScoreOfARun() ); } void guiEditResources :: checkAutoFinishMinSmithWatermanScoreOfARun() { char* szValue = XmTextFieldGetString( widAutoFinishMinSmithWatermanScoreOfARun_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoFinishMinSmithWatermanScoreOfARun must be numeric"; THROW_ERROR( soError ); } resources_.nAutoFinishMinSmithWatermanScoreOfARun_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoFinishMinSmithWatermanScoreOfARun_, CONDEF->nAutoFinishMinSmithWatermanScoreOfARun_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishMinSmithWatermanScoreOfARun_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes() ); } void guiEditResources :: checkAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes() { char* szValue = XmTextFieldGetString( widAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "AutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes must be floating point numeric"; THROW_ERROR( soError ); } resources_.dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_, CONDEF->dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_, pixForeground, pixBackground ); XtVaSetValues( widAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbRestrictionDigestMaximumBasesToCompareToVector( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkRestrictionDigestMaximumBasesToCompareToVector() ); } void guiEditResources :: checkRestrictionDigestMaximumBasesToCompareToVector() { char* szValue = XmTextFieldGetString( widRestrictionDigestMaximumBasesToCompareToVector_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.RestrictionDigestMaximumBasesToCompareToVector must be numeric"; THROW_ERROR( soError ); } resources_.nRestrictionDigestMaximumBasesToCompareToVector_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nRestrictionDigestMaximumBasesToCompareToVector_, CONDEF->nRestrictionDigestMaximumBasesToCompareToVector_, pixForeground, pixBackground ); XtVaSetValues( widRestrictionDigestMaximumBasesToCompareToVector_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbRestrictionDigestZoomFactor( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkRestrictionDigestZoomFactor() ); } void guiEditResources :: checkRestrictionDigestZoomFactor() { char* szValue = XmTextFieldGetString( widRestrictionDigestZoomFactor_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "RestrictionDigestZoomFactor must be floating point numeric"; THROW_ERROR( soError ); } resources_.dRestrictionDigestZoomFactor_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dRestrictionDigestZoomFactor_, CONDEF->dRestrictionDigestZoomFactor_, pixForeground, pixBackground ); XtVaSetValues( widRestrictionDigestZoomFactor_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbRestrictionDigestZoomFactorForNavigate( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkRestrictionDigestZoomFactorForNavigate() ); } void guiEditResources :: checkRestrictionDigestZoomFactorForNavigate() { char* szValue = XmTextFieldGetString( widRestrictionDigestZoomFactorForNavigate_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "RestrictionDigestZoomFactorForNavigate must be floating point numeric"; THROW_ERROR( soError ); } resources_.dRestrictionDigestZoomFactorForNavigate_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dRestrictionDigestZoomFactorForNavigate_, CONDEF->dRestrictionDigestZoomFactorForNavigate_, pixForeground, pixBackground ); XtVaSetValues( widRestrictionDigestZoomFactorForNavigate_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbRestrictionDigestToleranceInPositionUnits( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkRestrictionDigestToleranceInPositionUnits() ); } void guiEditResources :: checkRestrictionDigestToleranceInPositionUnits() { char* szValue = XmTextFieldGetString( widRestrictionDigestToleranceInPositionUnits_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.RestrictionDigestToleranceInPositionUnits must be numeric"; THROW_ERROR( soError ); } resources_.nRestrictionDigestToleranceInPositionUnits_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nRestrictionDigestToleranceInPositionUnits_, CONDEF->nRestrictionDigestToleranceInPositionUnits_, pixForeground, pixBackground ); XtVaSetValues( widRestrictionDigestToleranceInPositionUnits_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoPCRAmplifyTooManySeriousFalseMatches( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoPCRAmplifyTooManySeriousFalseMatches() ); } void guiEditResources :: checkAutoPCRAmplifyTooManySeriousFalseMatches() { char* szValue = XmTextFieldGetString( widAutoPCRAmplifyTooManySeriousFalseMatches_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoPCRAmplifyTooManySeriousFalseMatches must be numeric"; THROW_ERROR( soError ); } resources_.nAutoPCRAmplifyTooManySeriousFalseMatches_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoPCRAmplifyTooManySeriousFalseMatches_, CONDEF->nAutoPCRAmplifyTooManySeriousFalseMatches_, pixForeground, pixBackground ); XtVaSetValues( widAutoPCRAmplifyTooManySeriousFalseMatches_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewZoomFactor( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewZoomFactor() ); } void guiEditResources :: checkAssemblyViewZoomFactor() { char* szValue = XmTextFieldGetString( widAssemblyViewZoomFactor_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "AssemblyViewZoomFactor must be floating point numeric"; THROW_ERROR( soError ); } resources_.dAssemblyViewZoomFactor_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dAssemblyViewZoomFactor_, CONDEF->dAssemblyViewZoomFactor_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewZoomFactor_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewFilterInconsistentFwdRevPairsIfThisClose( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewFilterInconsistentFwdRevPairsIfThisClose() ); } void guiEditResources :: checkAssemblyViewFilterInconsistentFwdRevPairsIfThisClose() { char* szValue = XmTextFieldGetString( widAssemblyViewFilterInconsistentFwdRevPairsIfThisClose_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AssemblyViewFilterInconsistentFwdRevPairsIfThisClose must be numeric"; THROW_ERROR( soError ); } resources_.nAssemblyViewFilterInconsistentFwdRevPairsIfThisClose_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAssemblyViewFilterInconsistentFwdRevPairsIfThisClose_, CONDEF->nAssemblyViewFilterInconsistentFwdRevPairsIfThisClose_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewFilterInconsistentFwdRevPairsIfThisClose_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewGridCellWidthInPixels( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewGridCellWidthInPixels() ); } void guiEditResources :: checkAssemblyViewGridCellWidthInPixels() { char* szValue = XmTextFieldGetString( widAssemblyViewGridCellWidthInPixels_ ); RWCString soValue = szValue; XtFree( szValue ); double d; if ( !bIsNumericDouble( soValue, d ) ) { RWCString soError = "AssemblyViewGridCellWidthInPixels must be floating point numeric"; THROW_ERROR( soError ); } resources_.dAssemblyViewGridCellWidthInPixels_ = d; Pixel pixForeground; Pixel pixBackground; getColors( resources_.dAssemblyViewGridCellWidthInPixels_, CONDEF->dAssemblyViewGridCellWidthInPixels_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewGridCellWidthInPixels_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewCursorSensitivityInPixels( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewCursorSensitivityInPixels() ); } void guiEditResources :: checkAssemblyViewCursorSensitivityInPixels() { char* szValue = XmTextFieldGetString( widAssemblyViewCursorSensitivityInPixels_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AssemblyViewCursorSensitivityInPixels must be numeric"; THROW_ERROR( soError ); } resources_.nAssemblyViewCursorSensitivityInPixels_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAssemblyViewCursorSensitivityInPixels_, CONDEF->nAssemblyViewCursorSensitivityInPixels_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewCursorSensitivityInPixels_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAssemblyViewReadDepthQuality( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAssemblyViewReadDepthQuality() ); } void guiEditResources :: checkAssemblyViewReadDepthQuality() { char* szValue = XmTextFieldGetString( widAssemblyViewReadDepthQuality_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AssemblyViewReadDepthQuality must be numeric"; THROW_ERROR( soError ); } resources_.nAssemblyViewReadDepthQuality_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAssemblyViewReadDepthQuality_, CONDEF->nAssemblyViewReadDepthQuality_, pixForeground, pixBackground ); XtVaSetValues( widAssemblyViewReadDepthQuality_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbShowAllTracesMaxNumberOfTracesToShowAtOnce( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkShowAllTracesMaxNumberOfTracesToShowAtOnce() ); } void guiEditResources :: checkShowAllTracesMaxNumberOfTracesToShowAtOnce() { char* szValue = XmTextFieldGetString( widShowAllTracesMaxNumberOfTracesToShowAtOnce_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.ShowAllTracesMaxNumberOfTracesToShowAtOnce must be numeric"; THROW_ERROR( soError ); } resources_.nShowAllTracesMaxNumberOfTracesToShowAtOnce_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nShowAllTracesMaxNumberOfTracesToShowAtOnce_, CONDEF->nShowAllTracesMaxNumberOfTracesToShowAtOnce_, pixForeground, pixBackground ); XtVaSetValues( widShowAllTracesMaxNumberOfTracesToShowAtOnce_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess() ); } void guiEditResources :: checkAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess() { char* szValue = XmTextFieldGetString( widAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess must be numeric"; THROW_ERROR( soError ); } resources_.nAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess_, CONDEF->nAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess_, pixForeground, pixBackground ); XtVaSetValues( widAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbJustForPrimateProject( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkJustForPrimateProject() ); } void guiEditResources :: checkJustForPrimateProject() { bool b = XmToggleButtonGetState( widJustForPrimateProjectTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bJustForPrimateProject_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bJustForPrimateProject_, CONDEF->bJustForPrimateProject_, pixForeground, pixBackground ); XtVaSetValues( widJustForPrimateProjectRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbSolexaFilesAreAssumedToBeHere( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkSolexaFilesAreAssumedToBeHere() ); } void guiEditResources :: checkSolexaFilesAreAssumedToBeHere() { char* szValue = XmTextFieldGetString( widSolexaFilesAreAssumedToBeHere_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filSolexaFilesAreAssumedToBeHere_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filSolexaFilesAreAssumedToBeHere_, CONDEF->filSolexaFilesAreAssumedToBeHere_, pixForeground, pixBackground ); XtVaSetValues( widSolexaFilesAreAssumedToBeHere_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbSolexaAlignmentFilesPerInsertingPadsCycle( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkSolexaAlignmentFilesPerInsertingPadsCycle() ); } void guiEditResources :: checkSolexaAlignmentFilesPerInsertingPadsCycle() { char* szValue = XmTextFieldGetString( widSolexaAlignmentFilesPerInsertingPadsCycle_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.SolexaAlignmentFilesPerInsertingPadsCycle must be numeric"; THROW_ERROR( soError ); } resources_.nSolexaAlignmentFilesPerInsertingPadsCycle_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nSolexaAlignmentFilesPerInsertingPadsCycle_, CONDEF->nSolexaAlignmentFilesPerInsertingPadsCycle_, pixForeground, pixBackground ); XtVaSetValues( widSolexaAlignmentFilesPerInsertingPadsCycle_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbSolexaAlignmentsPerAlignmentFile( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkSolexaAlignmentsPerAlignmentFile() ); } void guiEditResources :: checkSolexaAlignmentsPerAlignmentFile() { char* szValue = XmTextFieldGetString( widSolexaAlignmentsPerAlignmentFile_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.SolexaAlignmentsPerAlignmentFile must be numeric"; THROW_ERROR( soError ); } resources_.nSolexaAlignmentsPerAlignmentFile_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nSolexaAlignmentsPerAlignmentFile_, CONDEF->nSolexaAlignmentsPerAlignmentFile_, pixForeground, pixBackground ); XtVaSetValues( widSolexaAlignmentsPerAlignmentFile_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbSolexaFastqFilesArePhredQualityNotSolexaQuality( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkSolexaFastqFilesArePhredQualityNotSolexaQuality() ); } void guiEditResources :: checkSolexaFastqFilesArePhredQualityNotSolexaQuality() { bool b = XmToggleButtonGetState( widSolexaFastqFilesArePhredQualityNotSolexaQualityTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bSolexaFastqFilesArePhredQualityNotSolexaQuality_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bSolexaFastqFilesArePhredQualityNotSolexaQuality_, CONDEF->bSolexaFastqFilesArePhredQualityNotSolexaQuality_, pixForeground, pixBackground ); XtVaSetValues( widSolexaFastqFilesArePhredQualityNotSolexaQualityRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbSolexa64FastqOrSanger33Fastq( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkSolexa64FastqOrSanger33Fastq() ); } void guiEditResources :: checkSolexa64FastqOrSanger33Fastq() { char* szValue = XmTextFieldGetString( widSolexa64FastqOrSanger33Fastq_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soSolexa64FastqOrSanger33Fastq_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soSolexa64FastqOrSanger33Fastq_, CONDEF->soSolexa64FastqOrSanger33Fastq_, pixForeground, pixBackground ); XtVaSetValues( widSolexa64FastqOrSanger33Fastq_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbMaximumReadsInReadList( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkMaximumReadsInReadList() ); } void guiEditResources :: checkMaximumReadsInReadList() { char* szValue = XmTextFieldGetString( widMaximumReadsInReadList_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.MaximumReadsInReadList must be numeric"; THROW_ERROR( soError ); } resources_.nMaximumReadsInReadList_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nMaximumReadsInReadList_, CONDEF->nMaximumReadsInReadList_, pixForeground, pixBackground ); XtVaSetValues( widMaximumReadsInReadList_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbMaxLengthOfReadsInapLocatedFragment2( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkMaxLengthOfReadsInapLocatedFragment2() ); } void guiEditResources :: checkMaxLengthOfReadsInapLocatedFragment2() { char* szValue = XmTextFieldGetString( widMaxLengthOfReadsInapLocatedFragment2_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.MaxLengthOfReadsInapLocatedFragment2 must be numeric"; THROW_ERROR( soError ); } resources_.nMaxLengthOfReadsInapLocatedFragment2_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nMaxLengthOfReadsInapLocatedFragment2_, CONDEF->nMaxLengthOfReadsInapLocatedFragment2_, pixForeground, pixBackground ); XtVaSetValues( widMaxLengthOfReadsInapLocatedFragment2_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbMaximumStartupErrorsToReport( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkMaximumStartupErrorsToReport() ); } void guiEditResources :: checkMaximumStartupErrorsToReport() { char* szValue = XmTextFieldGetString( widMaximumStartupErrorsToReport_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.MaximumStartupErrorsToReport must be numeric"; THROW_ERROR( soError ); } resources_.nMaximumStartupErrorsToReport_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nMaximumStartupErrorsToReport_, CONDEF->nMaximumStartupErrorsToReport_, pixForeground, pixBackground ); XtVaSetValues( widMaximumStartupErrorsToReport_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cb454LinkerAlignmentMatchScore( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->check454LinkerAlignmentMatchScore() ); } void guiEditResources :: check454LinkerAlignmentMatchScore() { char* szValue = XmTextFieldGetString( wid454LinkerAlignmentMatchScore_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.454LinkerAlignmentMatchScore must be numeric"; THROW_ERROR( soError ); } resources_.n454LinkerAlignmentMatchScore_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.n454LinkerAlignmentMatchScore_, CONDEF->n454LinkerAlignmentMatchScore_, pixForeground, pixBackground ); XtVaSetValues( wid454LinkerAlignmentMatchScore_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cb454LinkerAlignmentMismatchScore( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->check454LinkerAlignmentMismatchScore() ); } void guiEditResources :: check454LinkerAlignmentMismatchScore() { char* szValue = XmTextFieldGetString( wid454LinkerAlignmentMismatchScore_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.454LinkerAlignmentMismatchScore must be numeric"; THROW_ERROR( soError ); } resources_.n454LinkerAlignmentMismatchScore_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.n454LinkerAlignmentMismatchScore_, CONDEF->n454LinkerAlignmentMismatchScore_, pixForeground, pixBackground ); XtVaSetValues( wid454LinkerAlignmentMismatchScore_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cb454LinkerAlignmentIndelScore( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->check454LinkerAlignmentIndelScore() ); } void guiEditResources :: check454LinkerAlignmentIndelScore() { char* szValue = XmTextFieldGetString( wid454LinkerAlignmentIndelScore_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.454LinkerAlignmentIndelScore must be numeric"; THROW_ERROR( soError ); } resources_.n454LinkerAlignmentIndelScore_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.n454LinkerAlignmentIndelScore_, CONDEF->n454LinkerAlignmentIndelScore_, pixForeground, pixBackground ); XtVaSetValues( wid454LinkerAlignmentIndelScore_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbFilter454ReadsDeleteCrossMatchOutput( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkFilter454ReadsDeleteCrossMatchOutput() ); } void guiEditResources :: checkFilter454ReadsDeleteCrossMatchOutput() { bool b = XmToggleButtonGetState( widFilter454ReadsDeleteCrossMatchOutputTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bFilter454ReadsDeleteCrossMatchOutput_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bFilter454ReadsDeleteCrossMatchOutput_, CONDEF->bFilter454ReadsDeleteCrossMatchOutput_, pixForeground, pixBackground ); XtVaSetValues( widFilter454ReadsDeleteCrossMatchOutputRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportAllNeededSpeciesCode( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportAllNeededSpeciesCode() ); } void guiEditResources :: checkAutoReportAllNeededSpeciesCode() { char* szValue = XmTextFieldGetString( widAutoReportAllNeededSpeciesCode_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoReportAllNeededSpeciesCode must be numeric"; THROW_ERROR( soError ); } resources_.nAutoReportAllNeededSpeciesCode_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoReportAllNeededSpeciesCode_, CONDEF->nAutoReportAllNeededSpeciesCode_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportAllNeededSpeciesCode_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportUseCommasInBigNumbers( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportUseCommasInBigNumbers() ); } void guiEditResources :: checkAutoReportUseCommasInBigNumbers() { bool b = XmToggleButtonGetState( widAutoReportUseCommasInBigNumbersTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportUseCommasInBigNumbers_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportUseCommasInBigNumbers_, CONDEF->bAutoReportUseCommasInBigNumbers_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportUseCommasInBigNumbersRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintToCompareToReich( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintToCompareToReich() ); } void guiEditResources :: checkAutoReportPrintToCompareToReich() { bool b = XmToggleButtonGetState( widAutoReportPrintToCompareToReichTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintToCompareToReich_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintToCompareToReich_, CONDEF->bAutoReportPrintToCompareToReich_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintToCompareToReichRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites() ); } void guiEditResources :: checkAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites() { bool b = XmToggleButtonGetState( widAutoReportOnlyAllowSitesThatAreBetweenAcceptableSitesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_, CONDEF->bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportOnlyAllowSitesThatAreBetweenAcceptableSitesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod() ); } void guiEditResources :: checkAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod() { bool b = XmToggleButtonGetState( widAutoReportDeaminationMutationsDeterminedByMoreAccurateMethodTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_, CONDEF->bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportDeaminationMutationsDeterminedByMoreAccurateMethodRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportChooseTreesUsingBadData( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportChooseTreesUsingBadData() ); } void guiEditResources :: checkAutoReportChooseTreesUsingBadData() { bool b = XmToggleButtonGetState( widAutoReportChooseTreesUsingBadDataTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportChooseTreesUsingBadData_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportChooseTreesUsingBadData_, CONDEF->bAutoReportChooseTreesUsingBadData_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportChooseTreesUsingBadDataRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportChooseTreesByCountingDeaminationMutations( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportChooseTreesByCountingDeaminationMutations() ); } void guiEditResources :: checkAutoReportChooseTreesByCountingDeaminationMutations() { bool b = XmToggleButtonGetState( widAutoReportChooseTreesByCountingDeaminationMutationsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportChooseTreesByCountingDeaminationMutations_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportChooseTreesByCountingDeaminationMutations_, CONDEF->bAutoReportChooseTreesByCountingDeaminationMutations_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportChooseTreesByCountingDeaminationMutationsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportChooseTreesUsingKimura( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportChooseTreesUsingKimura() ); } void guiEditResources :: checkAutoReportChooseTreesUsingKimura() { bool b = XmToggleButtonGetState( widAutoReportChooseTreesUsingKimuraTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportChooseTreesUsingKimura_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportChooseTreesUsingKimura_, CONDEF->bAutoReportChooseTreesUsingKimura_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportChooseTreesUsingKimuraRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintCrudeChimpHumanMutations( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintCrudeChimpHumanMutations() ); } void guiEditResources :: checkAutoReportPrintCrudeChimpHumanMutations() { bool b = XmToggleButtonGetState( widAutoReportPrintCrudeChimpHumanMutationsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintCrudeChimpHumanMutations_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintCrudeChimpHumanMutations_, CONDEF->bAutoReportPrintCrudeChimpHumanMutations_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintCrudeChimpHumanMutationsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintPositionsForGraham( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintPositionsForGraham() ); } void guiEditResources :: checkAutoReportPrintPositionsForGraham() { bool b = XmToggleButtonGetState( widAutoReportPrintPositionsForGrahamTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintPositionsForGraham_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintPositionsForGraham_, CONDEF->bAutoReportPrintPositionsForGraham_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintPositionsForGrahamRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintAncestralCpGs( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintAncestralCpGs() ); } void guiEditResources :: checkAutoReportPrintAncestralCpGs() { bool b = XmToggleButtonGetState( widAutoReportPrintAncestralCpGsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintAncestralCpGs_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintAncestralCpGs_, CONDEF->bAutoReportPrintAncestralCpGs_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintAncestralCpGsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintCpGMutations( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintCpGMutations() ); } void guiEditResources :: checkAutoReportPrintCpGMutations() { bool b = XmToggleButtonGetState( widAutoReportPrintCpGMutationsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintCpGMutations_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintCpGMutations_, CONDEF->bAutoReportPrintCpGMutations_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintCpGMutationsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintMutationsWithContext( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintMutationsWithContext() ); } void guiEditResources :: checkAutoReportPrintMutationsWithContext() { bool b = XmToggleButtonGetState( widAutoReportPrintMutationsWithContextTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintMutationsWithContext_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintMutationsWithContext_, CONDEF->bAutoReportPrintMutationsWithContext_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintMutationsWithContextRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportCountAllMutationsML( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportCountAllMutationsML() ); } void guiEditResources :: checkAutoReportCountAllMutationsML() { bool b = XmToggleButtonGetState( widAutoReportCountAllMutationsMLTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportCountAllMutationsML_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportCountAllMutationsML_, CONDEF->bAutoReportCountAllMutationsML_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportCountAllMutationsMLRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportCountAllMutations( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportCountAllMutations() ); } void guiEditResources :: checkAutoReportCountAllMutations() { bool b = XmToggleButtonGetState( widAutoReportCountAllMutationsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportCountAllMutations_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportCountAllMutations_, CONDEF->bAutoReportCountAllMutations_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportCountAllMutationsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportIgnoreMultipleTrees( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportIgnoreMultipleTrees() ); } void guiEditResources :: checkAutoReportIgnoreMultipleTrees() { bool b = XmToggleButtonGetState( widAutoReportIgnoreMultipleTreesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportIgnoreMultipleTrees_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportIgnoreMultipleTrees_, CONDEF->bAutoReportIgnoreMultipleTrees_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportIgnoreMultipleTreesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportCountAcceptableColumnsWithNoneOnLeft( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportCountAcceptableColumnsWithNoneOnLeft() ); } void guiEditResources :: checkAutoReportCountAcceptableColumnsWithNoneOnLeft() { bool b = XmToggleButtonGetState( widAutoReportCountAcceptableColumnsWithNoneOnLeftTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportCountAcceptableColumnsWithNoneOnLeft_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportCountAcceptableColumnsWithNoneOnLeft_, CONDEF->bAutoReportCountAcceptableColumnsWithNoneOnLeft_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportCountAcceptableColumnsWithNoneOnLeftRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintFlankedColumns4( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintFlankedColumns4() ); } void guiEditResources :: checkAutoReportPrintFlankedColumns4() { bool b = XmToggleButtonGetState( widAutoReportPrintFlankedColumns4True_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintFlankedColumns4_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintFlankedColumns4_, CONDEF->bAutoReportPrintFlankedColumns4_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintFlankedColumns4RadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportUseAnnotationFormat( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportUseAnnotationFormat() ); } void guiEditResources :: checkAutoReportUseAnnotationFormat() { bool b = XmToggleButtonGetState( widAutoReportUseAnnotationFormatTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportUseAnnotationFormat_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportUseAnnotationFormat_, CONDEF->bAutoReportUseAnnotationFormat_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportUseAnnotationFormatRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintFlankedColumns3( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintFlankedColumns3() ); } void guiEditResources :: checkAutoReportPrintFlankedColumns3() { bool b = XmToggleButtonGetState( widAutoReportPrintFlankedColumns3True_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintFlankedColumns3_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintFlankedColumns3_, CONDEF->bAutoReportPrintFlankedColumns3_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintFlankedColumns3RadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintFlankedColumns2( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintFlankedColumns2() ); } void guiEditResources :: checkAutoReportPrintFlankedColumns2() { bool b = XmToggleButtonGetState( widAutoReportPrintFlankedColumns2True_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintFlankedColumns2_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintFlankedColumns2_, CONDEF->bAutoReportPrintFlankedColumns2_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintFlankedColumns2RadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintFlankedColumns( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintFlankedColumns() ); } void guiEditResources :: checkAutoReportPrintFlankedColumns() { bool b = XmToggleButtonGetState( widAutoReportPrintFlankedColumnsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintFlankedColumns_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintFlankedColumns_, CONDEF->bAutoReportPrintFlankedColumns_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintFlankedColumnsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportHighQualitySegmentData( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportHighQualitySegmentData() ); } void guiEditResources :: checkAutoReportHighQualitySegmentData() { bool b = XmToggleButtonGetState( widAutoReportHighQualitySegmentDataTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportHighQualitySegmentData_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportHighQualitySegmentData_, CONDEF->bAutoReportHighQualitySegmentData_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportHighQualitySegmentDataRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportGoodReadsBug( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportGoodReadsBug() ); } void guiEditResources :: checkAutoReportGoodReadsBug() { bool b = XmToggleButtonGetState( widAutoReportGoodReadsBugTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportGoodReadsBug_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportGoodReadsBug_, CONDEF->bAutoReportGoodReadsBug_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportGoodReadsBugRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportDiscrepancyRateInFlankedRegions( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportDiscrepancyRateInFlankedRegions() ); } void guiEditResources :: checkAutoReportDiscrepancyRateInFlankedRegions() { bool b = XmToggleButtonGetState( widAutoReportDiscrepancyRateInFlankedRegionsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportDiscrepancyRateInFlankedRegions_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportDiscrepancyRateInFlankedRegions_, CONDEF->bAutoReportDiscrepancyRateInFlankedRegions_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportDiscrepancyRateInFlankedRegionsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportDiscrepancyRateInFlankedRegions2( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportDiscrepancyRateInFlankedRegions2() ); } void guiEditResources :: checkAutoReportDiscrepancyRateInFlankedRegions2() { bool b = XmToggleButtonGetState( widAutoReportDiscrepancyRateInFlankedRegions2True_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportDiscrepancyRateInFlankedRegions2_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportDiscrepancyRateInFlankedRegions2_, CONDEF->bAutoReportDiscrepancyRateInFlankedRegions2_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportDiscrepancyRateInFlankedRegions2RadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportDiscrepancyRateInFlankedRegions4( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportDiscrepancyRateInFlankedRegions4() ); } void guiEditResources :: checkAutoReportDiscrepancyRateInFlankedRegions4() { bool b = XmToggleButtonGetState( widAutoReportDiscrepancyRateInFlankedRegions4True_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportDiscrepancyRateInFlankedRegions4_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportDiscrepancyRateInFlankedRegions4_, CONDEF->bAutoReportDiscrepancyRateInFlankedRegions4_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportDiscrepancyRateInFlankedRegions4RadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportDiscrepancyRateInFlankedRegions5( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportDiscrepancyRateInFlankedRegions5() ); } void guiEditResources :: checkAutoReportDiscrepancyRateInFlankedRegions5() { bool b = XmToggleButtonGetState( widAutoReportDiscrepancyRateInFlankedRegions5True_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportDiscrepancyRateInFlankedRegions5_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportDiscrepancyRateInFlankedRegions5_, CONDEF->bAutoReportDiscrepancyRateInFlankedRegions5_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportDiscrepancyRateInFlankedRegions5RadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportSingleSignalOrQuality( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportSingleSignalOrQuality() ); } void guiEditResources :: checkAutoReportSingleSignalOrQuality() { bool b = XmToggleButtonGetState( widAutoReportSingleSignalOrQualityTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportSingleSignalOrQuality_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportSingleSignalOrQuality_, CONDEF->bAutoReportSingleSignalOrQuality_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportSingleSignalOrQualityRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportLowQualityBasesInHQS( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportLowQualityBasesInHQS() ); } void guiEditResources :: checkAutoReportLowQualityBasesInHQS() { bool b = XmToggleButtonGetState( widAutoReportLowQualityBasesInHQSTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportLowQualityBasesInHQS_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportLowQualityBasesInHQS_, CONDEF->bAutoReportLowQualityBasesInHQS_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportLowQualityBasesInHQSRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportCompareHQSWithLQS( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportCompareHQSWithLQS() ); } void guiEditResources :: checkAutoReportCompareHQSWithLQS() { bool b = XmToggleButtonGetState( widAutoReportCompareHQSWithLQSTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportCompareHQSWithLQS_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportCompareHQSWithLQS_, CONDEF->bAutoReportCompareHQSWithLQS_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportCompareHQSWithLQSRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportCountColumnsForGroupsOfSpecies( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportCountColumnsForGroupsOfSpecies() ); } void guiEditResources :: checkAutoReportCountColumnsForGroupsOfSpecies() { bool b = XmToggleButtonGetState( widAutoReportCountColumnsForGroupsOfSpeciesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportCountColumnsForGroupsOfSpecies_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportCountColumnsForGroupsOfSpecies_, CONDEF->bAutoReportCountColumnsForGroupsOfSpecies_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportCountColumnsForGroupsOfSpeciesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportSingleSignalInfo( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportSingleSignalInfo() ); } void guiEditResources :: checkAutoReportSingleSignalInfo() { bool b = XmToggleButtonGetState( widAutoReportSingleSignalInfoTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportSingleSignalInfo_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportSingleSignalInfo_, CONDEF->bAutoReportSingleSignalInfo_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportSingleSignalInfoRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportSingleSignalInfo2( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportSingleSignalInfo2() ); } void guiEditResources :: checkAutoReportSingleSignalInfo2() { bool b = XmToggleButtonGetState( widAutoReportSingleSignalInfo2True_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportSingleSignalInfo2_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportSingleSignalInfo2_, CONDEF->bAutoReportSingleSignalInfo2_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportSingleSignalInfo2RadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportCompareTopAndBottomStrands( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportCompareTopAndBottomStrands() ); } void guiEditResources :: checkAutoReportCompareTopAndBottomStrands() { bool b = XmToggleButtonGetState( widAutoReportCompareTopAndBottomStrandsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportCompareTopAndBottomStrands_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportCompareTopAndBottomStrands_, CONDEF->bAutoReportCompareTopAndBottomStrands_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportCompareTopAndBottomStrandsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportCompareTopAndBottomStrandsNoHuman( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportCompareTopAndBottomStrandsNoHuman() ); } void guiEditResources :: checkAutoReportCompareTopAndBottomStrandsNoHuman() { bool b = XmToggleButtonGetState( widAutoReportCompareTopAndBottomStrandsNoHumanTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportCompareTopAndBottomStrandsNoHuman_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportCompareTopAndBottomStrandsNoHuman_, CONDEF->bAutoReportCompareTopAndBottomStrandsNoHuman_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportCompareTopAndBottomStrandsNoHumanRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportCompareTopAndBottomStrands2( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportCompareTopAndBottomStrands2() ); } void guiEditResources :: checkAutoReportCompareTopAndBottomStrands2() { bool b = XmToggleButtonGetState( widAutoReportCompareTopAndBottomStrands2True_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportCompareTopAndBottomStrands2_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportCompareTopAndBottomStrands2_, CONDEF->bAutoReportCompareTopAndBottomStrands2_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportCompareTopAndBottomStrands2RadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportCompareTopAndBottomStrands3( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportCompareTopAndBottomStrands3() ); } void guiEditResources :: checkAutoReportCompareTopAndBottomStrands3() { bool b = XmToggleButtonGetState( widAutoReportCompareTopAndBottomStrands3True_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportCompareTopAndBottomStrands3_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportCompareTopAndBottomStrands3_, CONDEF->bAutoReportCompareTopAndBottomStrands3_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportCompareTopAndBottomStrands3RadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportCompareTopAndBottomStrands4( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportCompareTopAndBottomStrands4() ); } void guiEditResources :: checkAutoReportCompareTopAndBottomStrands4() { bool b = XmToggleButtonGetState( widAutoReportCompareTopAndBottomStrands4True_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportCompareTopAndBottomStrands4_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportCompareTopAndBottomStrands4_, CONDEF->bAutoReportCompareTopAndBottomStrands4_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportCompareTopAndBottomStrands4RadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportTopStrandPinnedPosition( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportTopStrandPinnedPosition() ); } void guiEditResources :: checkAutoReportTopStrandPinnedPosition() { char* szValue = XmTextFieldGetString( widAutoReportTopStrandPinnedPosition_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoReportTopStrandPinnedPosition must be numeric"; THROW_ERROR( soError ); } resources_.nAutoReportTopStrandPinnedPosition_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoReportTopStrandPinnedPosition_, CONDEF->nAutoReportTopStrandPinnedPosition_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportTopStrandPinnedPosition_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportBottomStrandPinnedPosition( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportBottomStrandPinnedPosition() ); } void guiEditResources :: checkAutoReportBottomStrandPinnedPosition() { char* szValue = XmTextFieldGetString( widAutoReportBottomStrandPinnedPosition_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoReportBottomStrandPinnedPosition must be numeric"; THROW_ERROR( soError ); } resources_.nAutoReportBottomStrandPinnedPosition_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoReportBottomStrandPinnedPosition_, CONDEF->nAutoReportBottomStrandPinnedPosition_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportBottomStrandPinnedPosition_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportCompareTopAndBottomStrandsWithHuman( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportCompareTopAndBottomStrandsWithHuman() ); } void guiEditResources :: checkAutoReportCompareTopAndBottomStrandsWithHuman() { bool b = XmToggleButtonGetState( widAutoReportCompareTopAndBottomStrandsWithHumanTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportCompareTopAndBottomStrandsWithHuman_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportCompareTopAndBottomStrandsWithHuman_, CONDEF->bAutoReportCompareTopAndBottomStrandsWithHuman_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportCompareTopAndBottomStrandsWithHumanRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintLengthsOfAlignedSegmentsOfReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintLengthsOfAlignedSegmentsOfReads() ); } void guiEditResources :: checkAutoReportPrintLengthsOfAlignedSegmentsOfReads() { bool b = XmToggleButtonGetState( widAutoReportPrintLengthsOfAlignedSegmentsOfReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintLengthsOfAlignedSegmentsOfReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintLengthsOfAlignedSegmentsOfReads_, CONDEF->bAutoReportPrintLengthsOfAlignedSegmentsOfReads_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintLengthsOfAlignedSegmentsOfReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads() ); } void guiEditResources :: checkAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads() { bool b = XmToggleButtonGetState( widAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_, CONDEF->bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintIfReadsAreCorrectlyAligned( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintIfReadsAreCorrectlyAligned() ); } void guiEditResources :: checkAutoReportPrintIfReadsAreCorrectlyAligned() { bool b = XmToggleButtonGetState( widAutoReportPrintIfReadsAreCorrectlyAlignedTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintIfReadsAreCorrectlyAligned_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintIfReadsAreCorrectlyAligned_, CONDEF->bAutoReportPrintIfReadsAreCorrectlyAligned_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintIfReadsAreCorrectlyAlignedRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportCalculateErrorProbabilitiesByComparingPTroPPan( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportCalculateErrorProbabilitiesByComparingPTroPPan() ); } void guiEditResources :: checkAutoReportCalculateErrorProbabilitiesByComparingPTroPPan() { bool b = XmToggleButtonGetState( widAutoReportCalculateErrorProbabilitiesByComparingPTroPPanTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_, CONDEF->bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportCalculateErrorProbabilitiesByComparingPTroPPanRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies() ); } void guiEditResources :: checkAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies() { bool b = XmToggleButtonGetState( widAutoReportPrintAgreeDisagreeBetweenPairsOfSpeciesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_, CONDEF->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintAgreeDisagreeBetweenPairsOfSpeciesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2() ); } void guiEditResources :: checkAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2() { bool b = XmToggleButtonGetState( widAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2True_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_, CONDEF->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2RadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportFilterSingleSignal( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportFilterSingleSignal() ); } void guiEditResources :: checkAutoReportFilterSingleSignal() { bool b = XmToggleButtonGetState( widAutoReportFilterSingleSignalTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportFilterSingleSignal_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportFilterSingleSignal_, CONDEF->bAutoReportFilterSingleSignal_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportFilterSingleSignalRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportGoodHitReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportGoodHitReads() ); } void guiEditResources :: checkAutoReportGoodHitReads() { char* szValue = XmTextFieldGetString( widAutoReportGoodHitReads_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filAutoReportGoodHitReads_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filAutoReportGoodHitReads_, CONDEF->filAutoReportGoodHitReads_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportGoodHitReads_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportQualityWindowLow( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportQualityWindowLow() ); } void guiEditResources :: checkAutoReportQualityWindowLow() { char* szValue = XmTextFieldGetString( widAutoReportQualityWindowLow_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoReportQualityWindowLow must be numeric"; THROW_ERROR( soError ); } resources_.nAutoReportQualityWindowLow_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoReportQualityWindowLow_, CONDEF->nAutoReportQualityWindowLow_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportQualityWindowLow_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportQualityWindowHigh( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportQualityWindowHigh() ); } void guiEditResources :: checkAutoReportQualityWindowHigh() { char* szValue = XmTextFieldGetString( widAutoReportQualityWindowHigh_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoReportQualityWindowHigh must be numeric"; THROW_ERROR( soError ); } resources_.nAutoReportQualityWindowHigh_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoReportQualityWindowHigh_, CONDEF->nAutoReportQualityWindowHigh_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportQualityWindowHigh_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintNumberOfIsolatedPadsForEachSpecies( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintNumberOfIsolatedPadsForEachSpecies() ); } void guiEditResources :: checkAutoReportPrintNumberOfIsolatedPadsForEachSpecies() { bool b = XmToggleButtonGetState( widAutoReportPrintNumberOfIsolatedPadsForEachSpeciesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_, CONDEF->bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintNumberOfIsolatedPadsForEachSpeciesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintNumberOfIsolatedPads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintNumberOfIsolatedPads() ); } void guiEditResources :: checkAutoReportPrintNumberOfIsolatedPads() { bool b = XmToggleButtonGetState( widAutoReportPrintNumberOfIsolatedPadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintNumberOfIsolatedPads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintNumberOfIsolatedPads_, CONDEF->bAutoReportPrintNumberOfIsolatedPads_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintNumberOfIsolatedPadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportIsolatedPadsOfReadsWithThisPattern( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportIsolatedPadsOfReadsWithThisPattern() ); } void guiEditResources :: checkAutoReportIsolatedPadsOfReadsWithThisPattern() { char* szValue = XmTextFieldGetString( widAutoReportIsolatedPadsOfReadsWithThisPattern_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soAutoReportIsolatedPadsOfReadsWithThisPattern_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soAutoReportIsolatedPadsOfReadsWithThisPattern_, CONDEF->soAutoReportIsolatedPadsOfReadsWithThisPattern_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportIsolatedPadsOfReadsWithThisPattern_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy() ); } void guiEditResources :: checkAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy() { char* szValue = XmTextFieldGetString( widAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy must be numeric"; THROW_ERROR( soError ); } resources_.nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_, CONDEF->nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportMaxSizeOfDiscrepantRegion( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportMaxSizeOfDiscrepantRegion() ); } void guiEditResources :: checkAutoReportMaxSizeOfDiscrepantRegion() { char* szValue = XmTextFieldGetString( widAutoReportMaxSizeOfDiscrepantRegion_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoReportMaxSizeOfDiscrepantRegion must be numeric"; THROW_ERROR( soError ); } resources_.nAutoReportMaxSizeOfDiscrepantRegion_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoReportMaxSizeOfDiscrepantRegion_, CONDEF->nAutoReportMaxSizeOfDiscrepantRegion_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportMaxSizeOfDiscrepantRegion_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportSizeOfDiscrepantRegion( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportSizeOfDiscrepantRegion() ); } void guiEditResources :: checkAutoReportSizeOfDiscrepantRegion() { char* szValue = XmTextFieldGetString( widAutoReportSizeOfDiscrepantRegion_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoReportSizeOfDiscrepantRegion must be numeric"; THROW_ERROR( soError ); } resources_.nAutoReportSizeOfDiscrepantRegion_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoReportSizeOfDiscrepantRegion_, CONDEF->nAutoReportSizeOfDiscrepantRegion_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportSizeOfDiscrepantRegion_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintMinimumQualityHistogram( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintMinimumQualityHistogram() ); } void guiEditResources :: checkAutoReportPrintMinimumQualityHistogram() { bool b = XmToggleButtonGetState( widAutoReportPrintMinimumQualityHistogramTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintMinimumQualityHistogram_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintMinimumQualityHistogram_, CONDEF->bAutoReportPrintMinimumQualityHistogram_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintMinimumQualityHistogramRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintDiscrepantRegions( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintDiscrepantRegions() ); } void guiEditResources :: checkAutoReportPrintDiscrepantRegions() { bool b = XmToggleButtonGetState( widAutoReportPrintDiscrepantRegionsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintDiscrepantRegions_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintDiscrepantRegions_, CONDEF->bAutoReportPrintDiscrepantRegions_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintDiscrepantRegionsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintBasesInDiscrepantRegions( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintBasesInDiscrepantRegions() ); } void guiEditResources :: checkAutoReportPrintBasesInDiscrepantRegions() { bool b = XmToggleButtonGetState( widAutoReportPrintBasesInDiscrepantRegionsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintBasesInDiscrepantRegions_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintBasesInDiscrepantRegions_, CONDEF->bAutoReportPrintBasesInDiscrepantRegions_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintBasesInDiscrepantRegionsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis() ); } void guiEditResources :: checkAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis() { char* szValue = XmTextFieldGetString( widAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_, CONDEF->soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportBackboneReadHasThisStringInIt( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportBackboneReadHasThisStringInIt() ); } void guiEditResources :: checkAutoReportBackboneReadHasThisStringInIt() { char* szValue = XmTextFieldGetString( widAutoReportBackboneReadHasThisStringInIt_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soAutoReportBackboneReadHasThisStringInIt_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soAutoReportBackboneReadHasThisStringInIt_, CONDEF->soAutoReportBackboneReadHasThisStringInIt_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportBackboneReadHasThisStringInIt_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold() ); } void guiEditResources :: checkAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold() { bool b = XmToggleButtonGetState( widAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThresholdTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_, CONDEF->bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThresholdRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintSpeciesAlignment( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintSpeciesAlignment() ); } void guiEditResources :: checkAutoReportPrintSpeciesAlignment() { bool b = XmToggleButtonGetState( widAutoReportPrintSpeciesAlignmentTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintSpeciesAlignment_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintSpeciesAlignment_, CONDEF->bAutoReportPrintSpeciesAlignment_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintSpeciesAlignmentRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintReadAlignment( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintReadAlignment() ); } void guiEditResources :: checkAutoReportPrintReadAlignment() { bool b = XmToggleButtonGetState( widAutoReportPrintReadAlignmentTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintReadAlignment_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintReadAlignment_, CONDEF->bAutoReportPrintReadAlignment_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintReadAlignmentRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintTheseReads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintTheseReads() ); } void guiEditResources :: checkAutoReportPrintTheseReads() { char* szValue = XmTextFieldGetString( widAutoReportPrintTheseReads_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.filAutoReportPrintTheseReads_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.filAutoReportPrintTheseReads_, CONDEF->filAutoReportPrintTheseReads_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintTheseReads_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintReadPositions( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintReadPositions() ); } void guiEditResources :: checkAutoReportPrintReadPositions() { bool b = XmToggleButtonGetState( widAutoReportPrintReadPositionsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintReadPositions_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintReadPositions_, CONDEF->bAutoReportPrintReadPositions_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintReadPositionsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrintChosenReadName( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrintChosenReadName() ); } void guiEditResources :: checkAutoReportPrintChosenReadName() { bool b = XmToggleButtonGetState( widAutoReportPrintChosenReadNameTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportPrintChosenReadName_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportPrintChosenReadName_, CONDEF->bAutoReportPrintChosenReadName_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrintChosenReadNameRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted() ); } void guiEditResources :: checkAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted() { char* szValue = XmTextFieldGetString( widAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoReportNumbersOfCharactersOfChosenReadNameToBePrinted must be numeric"; THROW_ERROR( soError ); } resources_.nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_, CONDEF->nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportPrefix( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportPrefix() ); } void guiEditResources :: checkAutoReportPrefix() { char* szValue = XmTextFieldGetString( widAutoReportPrefix_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soAutoReportPrefix_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soAutoReportPrefix_, CONDEF->soAutoReportPrefix_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportPrefix_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportUseOldCriteriaForDeletingColumnsOfPads( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportUseOldCriteriaForDeletingColumnsOfPads() ); } void guiEditResources :: checkAutoReportUseOldCriteriaForDeletingColumnsOfPads() { bool b = XmToggleButtonGetState( widAutoReportUseOldCriteriaForDeletingColumnsOfPadsTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportUseOldCriteriaForDeletingColumnsOfPads_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportUseOldCriteriaForDeletingColumnsOfPads_, CONDEF->bAutoReportUseOldCriteriaForDeletingColumnsOfPads_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportUseOldCriteriaForDeletingColumnsOfPadsRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues() ); } void guiEditResources :: checkAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues() { bool b = XmToggleButtonGetState( widAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValuesTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_, CONDEF->bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValuesRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportFlankingBasesMustBeSingleSignal( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportFlankingBasesMustBeSingleSignal() ); } void guiEditResources :: checkAutoReportFlankingBasesMustBeSingleSignal() { bool b = XmToggleButtonGetState( widAutoReportFlankingBasesMustBeSingleSignalTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportFlankingBasesMustBeSingleSignal_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportFlankingBasesMustBeSingleSignal_, CONDEF->bAutoReportFlankingBasesMustBeSingleSignal_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportFlankingBasesMustBeSingleSignalRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportMinimumQualityOfFlankingBases( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportMinimumQualityOfFlankingBases() ); } void guiEditResources :: checkAutoReportMinimumQualityOfFlankingBases() { char* szValue = XmTextFieldGetString( widAutoReportMinimumQualityOfFlankingBases_ ); RWCString soValue = szValue; XtFree( szValue ); int n; if ( !bIsNumericMaybeWithWhitespace( soValue, n ) ) { RWCString soError = "consed.AutoReportMinimumQualityOfFlankingBases must be numeric"; THROW_ERROR( soError ); } resources_.nAutoReportMinimumQualityOfFlankingBases_ = n; Pixel pixForeground; Pixel pixBackground; getColors( resources_.nAutoReportMinimumQualityOfFlankingBases_, CONDEF->nAutoReportMinimumQualityOfFlankingBases_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportMinimumQualityOfFlankingBases_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportFlankingBasesMustBeInHighQualitySegment( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportFlankingBasesMustBeInHighQualitySegment() ); } void guiEditResources :: checkAutoReportFlankingBasesMustBeInHighQualitySegment() { bool b = XmToggleButtonGetState( widAutoReportFlankingBasesMustBeInHighQualitySegmentTrue_ ); // this is no way this can be invalid, so no checks are needed resources_.bAutoReportFlankingBasesMustBeInHighQualitySegment_ = b; Pixel pixForeground; Pixel pixBackground; getColors( resources_.bAutoReportFlankingBasesMustBeInHighQualitySegment_, CONDEF->bAutoReportFlankingBasesMustBeInHighQualitySegment_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportFlankingBasesMustBeInHighQualitySegmentRadioBox_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } static void cbAutoReportSpecies( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiEditResources* pGER = (guiEditResources*) pClientData; TRY_CATCH_WRAPPER( pGER->checkAutoReportSpecies() ); } void guiEditResources :: checkAutoReportSpecies() { char* szValue = XmTextFieldGetString( widAutoReportSpecies_ ); RWCString soValue = szValue; XtFree( szValue ); resources_.soAutoReportSpecies_ = soValue; Pixel pixForeground; Pixel pixBackground; getColors( resources_.soAutoReportSpecies_, CONDEF->soAutoReportSpecies_, pixForeground, pixBackground ); XtVaSetValues( widAutoReportSpecies_, XmNforeground, pixForeground, XmNbackground, pixBackground, NULL ); } // guiEditResources.cpp.part3 void guiEditResources :: createWindow() { PleaseWait* pPleaseWait = new PleaseWait(); resources_ = *consedResources::pCurrentResources_; Widget widFalseButton; // these are needed by the makeWidget... macros Pixel pixForeground; Pixel pixBackground; // get colors for when the resource is different pixValueChangedForegroundColor_ = ulGetXColorForColorName( "cornsilk" ); pixValueChangedBackgroundColor_ = ulGetXColorForColorName( "red" ); int nArgs; Arg aArg[50]; if ( bStandAlone_ ) { widPopupShell_ = GAPP->widGetTopLevel(); } else { widPopupShell_ = XtVaCreatePopupShell( "Edit Consed/Autofinish Parameters", topLevelShellWidgetClass, GAPP->widGetTopLevel(), XmNtitle, "Edit Parameters", XmNnoResize, False, XmNtransient, False, XmNdeleteResponse, XmDO_NOTHING, NULL ); handleWindowManagerDelete2( widPopupShell_, cbCancelButton, this ); } // create a form widget Widget widTopForm = XtVaCreateManagedWidget( "top form", xmFormWidgetClass, widPopupShell_, XmNshadowThickness, 0, XmNborderWidth, 0, NULL ); XtVaGetValues( widTopForm, XmNforeground, &pixValueUnchangedForegroundColor_, XmNbackground, &pixValueUnchangedBackgroundColor_, NULL ); // labels on the top of the form Widget widColumn1Label = XtVaCreateManagedWidget( "current values:", xmLabelWidgetClass, widTopForm, XmNtopAttachment, XmATTACH_FORM, XmNleftAttachment, XmATTACH_FORM, XmNalignment, XmALIGNMENT_BEGINNING, NULL ); Widget widAttachWidgetToBottomOfThis = widColumn1Label; Widget widColumn2Label = XtVaCreateManagedWidget( "default values:", xmLabelWidgetClass, widTopForm, XmNtopAttachment, XmATTACH_FORM, XmNleftAttachment, XmATTACH_POSITION, XmNleftPosition, 50, XmNalignment, XmALIGNMENT_BEGINNING, NULL ); // put buttons on the bottom of the form widSaveButton_ = XtVaCreateManagedWidget( "Save", xmPushButtonWidgetClass, widTopForm, XmNbottomAttachment, XmATTACH_FORM, XmNbottomOffset, 10, XmNleftAttachment, XmATTACH_POSITION, XmNleftPosition, 4, XmNrightAttachment, XmATTACH_POSITION, XmNrightPosition, 16, NULL ); Widget widAttachWidgetsToTopOfThis = widSaveButton_; XtAddCallback( widSaveButton_, XmNactivateCallback, cbUserPushedSaveButton, this ); widCancelButton_ = XtVaCreateManagedWidget( "Dismiss", xmPushButtonWidgetClass, widTopForm, XmNbottomAttachment, XmATTACH_FORM, XmNbottomOffset, 10, XmNleftAttachment, XmATTACH_POSITION, XmNleftPosition, 84, XmNrightAttachment, XmATTACH_POSITION, XmNrightPosition, 96, NULL ); XtAddCallback( widCancelButton_, XmNactivateCallback, cbCancelButton, this ); // create a set of 3 radio buttons: one for just user // one for project // one for all users and all projects Widget widWhichConsedrcRadioBox = XmCreateRadioBox( widTopForm, "radio", NULL, 0 ); XtVaSetValues( widWhichConsedrcRadioBox, XmNtraversalOn, True, XmNbottomAttachment, XmATTACH_WIDGET, XmNbottomOffset, 20, XmNbottomWidget, widAttachWidgetsToTopOfThis, XmNleftAttachment, XmATTACH_FORM, XmNrightAttachment, XmATTACH_FORM, XmNorientation, XmHORIZONTAL, NULL ); XtManageChild( widWhichConsedrcRadioBox ); widAttachWidgetsToTopOfThis = widWhichConsedrcRadioBox; widUserRadioButton_ = XtVaCreateManagedWidget( "just user", xmToggleButtonWidgetClass, widWhichConsedrcRadioBox, XmNset, True, NULL ); widProjectRadioButton_ = XtVaCreateManagedWidget( "just project", xmToggleButtonWidgetClass, widWhichConsedrcRadioBox, XmNset, False, NULL ); widAllUsersAllProjectsRadioButton_ = XtVaCreateManagedWidget( "all users/all projects", xmToggleButtonWidgetClass, widWhichConsedrcRadioBox, XmNset, False, NULL ); Widget widEnterParameterLabel = XtVaCreateManagedWidget( "Find Parameter:", xmLabelWidgetClass, widTopForm, XmNleftAttachment, XmATTACH_FORM, XmNleftOffset, 10, NULL ); widEnterParameter_ = XtVaCreateManagedWidget( "Find Parameter", xmTextFieldWidgetClass, widTopForm, XmNbottomAttachment, XmATTACH_WIDGET, XmNbottomWidget, widAttachWidgetsToTopOfThis, XmNbottomOffset, 10, NULL ); XtAddCallback( widEnterParameter_, XmNactivateCallback, cbFindFirstButton, this ); // funny business to avoid circular dependency of // widEnterParameter_ and widEnterParameterLabel Dimension dimWidthOfLabel; XtVaGetValues( widEnterParameterLabel, XmNwidth, &dimWidthOfLabel, NULL ); XtVaSetValues( widEnterParameter_, XmNleftAttachment, XmATTACH_FORM, XmNleftOffset, ( dimWidthOfLabel + 10 + 10 ), NULL ); XtVaSetValues( widEnterParameterLabel, XmNbottomAttachment, XmATTACH_OPPOSITE_WIDGET, XmNbottomWidget, widEnterParameter_, XmNtopAttachment, XmATTACH_OPPOSITE_WIDGET, XmNtopWidget, widEnterParameter_, NULL ); widAttachWidgetsToTopOfThis = widEnterParameterLabel; Widget widFindFirst = XtVaCreateManagedWidget( "Find First", xmPushButtonWidgetClass, widTopForm, XmNtopAttachment, XmATTACH_OPPOSITE_WIDGET, XmNtopWidget, widEnterParameter_, XmNbottomAttachment, XmATTACH_OPPOSITE_WIDGET, XmNbottomWidget, widEnterParameter_, XmNleftAttachment, XmATTACH_WIDGET, XmNleftWidget, widEnterParameter_, XmNleftOffset, 10, NULL ); XtAddCallback( widFindFirst, XmNactivateCallback, cbFindFirstButton, this ); Widget widFindNext = XtVaCreateManagedWidget( "Find Next", xmPushButtonWidgetClass, widTopForm, XmNtopAttachment, XmATTACH_OPPOSITE_WIDGET, XmNtopWidget, widEnterParameter_, XmNbottomAttachment, XmATTACH_OPPOSITE_WIDGET, XmNbottomWidget, widEnterParameter_, XmNleftAttachment, XmATTACH_WIDGET, XmNleftWidget, widFindFirst, XmNleftOffset, 10, NULL ); XtAddCallback( widFindNext, XmNactivateCallback, cbFindNextButton, this ); widScrolledWindow_ = XtVaCreateManagedWidget( "scrolled", xmScrolledWindowWidgetClass, widTopForm, XmNtopAttachment, XmATTACH_WIDGET, XmNtopWidget, widAttachWidgetToBottomOfThis, XmNleftAttachment, XmATTACH_FORM, XmNrightAttachment, XmATTACH_FORM, XmNbottomAttachment, XmATTACH_WIDGET, XmNbottomWidget, widAttachWidgetsToTopOfThis, XmNbottomOffset, 20, XmNscrollingPolicy, XmAUTOMATIC, XmNscrollBarDisplayPolicy, XmSTATIC, XmNheight, (Dimension) GuiApp::nGetFontHeight() * 50, NULL ); Widget widRowCol = XtVaCreateManagedWidget( "rowcol", xmRowColumnWidgetClass, widScrolledWindow_, XmNorientation, XmVERTICAL, XmNnumColumns, 1, XmNpacking, XmPACK_COLUMN, NULL ); // this funny business is to make boxes expand when the user expands // the scrolling window XmScrolledWindowSetAreas( widScrolledWindow_, NULL, NULL, widRowCol ); XtVaGetValues( widScrolledWindow_, XmNclipWindow, &widClipWindow_, NULL ); XtAddCallback( widClipWindow_, XmNresizeCallback, cbResize, this ); helpCallbackInfo* pHelp = NULL; // this is where all the of the computer-generated widgets go // guiEditResources.cpp.part4 makeWidgetTypeBool( consed.printPS, PrintPS ); makeWidgetTypeRWCString( consed.defaultTagType, DefaultTagType ); makeWidgetTypeBool( consed.defaultTagOnConsensusNotReads, DefaultTagOnConsensusNotReads ); makeWidgetTypeDouble( consed.autoFinishMinNumberOfErrorsFixedByAnExp, AutoFinishMinNumberOfErrorsFixedByAnExp ); makeWidgetTypeDouble( consed.autoFinishRedundancy, AutoFinishRedundancy ); makeWidgetTypeInt( consed.autoFinishAverageInsertSize, AutoFinishAverageInsertSize ); makeWidgetTypeInt( consed.primersMaxInsertSizeOfASubclone, PrimersMaxInsertSizeOfASubclone ); makeWidgetTypeInt( consed.primersMaxMeltingTemp, PrimersMaxMeltingTemp ); makeWidgetTypeInt( consed.primersMaxMeltingTempForPCR, PrimersMaxMeltingTempForPCR ); makeWidgetTypeBool( consed.primersPickTemplatesForPrimers, PrimersPickTemplatesForPrimers ); makeWidgetTypeRWCString( consed.primersSubcloneFullPathnameOfFileOfSequencesForScreening, PrimersSubcloneFullPathnameOfFileOfSequencesForScreening ); makeWidgetTypeRWCString( consed.primersCloneFullPathnameOfFileOfSequencesForScreening, PrimersCloneFullPathnameOfFileOfSequencesForScreening ); makeWidgetTypeInt( consed.primersMinMeltingTemp, PrimersMinMeltingTemp ); makeWidgetTypeInt( consed.primersMinMeltingTempForPCR, PrimersMinMeltingTempForPCR ); makeWidgetTypeBool( consed.searchFunctionsUseUnalignedEndsOfReads, SearchFunctionsUseUnalignedEndsOfReads ); makeWidgetTypeBool( consed.searchFunctionsUseLowQualityEndsOfReads, SearchFunctionsUseLowQualityEndsOfReads ); makeWidgetTypeInt( consed.inexactSearchForStringMaxPerCentMismatch, InexactSearchForStringMaxPerCentMismatch ); makeWidgetTypeBool( consed.onlyAllowOneReadWriteConsedAtATime, OnlyAllowOneReadWriteConsedAtATime ); makeWidgetTypeBool( consed.autoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair, AutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair ); makeWidgetTypeRWCString( consed.printWindowCommand, PrintWindowCommand ); makeWidgetTypeFileName( consed.fileOfTagTypes, FileOfTagTypes ); makeWidgetTypeBool( consed.assemblyViewShowConsistentFwdRevPairs, AssemblyViewShowConsistentFwdRevPairs ); makeWidgetTypeBool( consed.assemblyViewShowConsistentFwdRevPairDepth, AssemblyViewShowConsistentFwdRevPairDepth ); makeWidgetTypeBool( consed.assemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds, AssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds ); makeWidgetTypeBool( consed.assemblyViewShowLegsOnSquaresForConsistentFwdRevPairs, AssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs ); makeWidgetTypeBool( consed.assemblyViewShowGapSpanningFwdRevPairs, AssemblyViewShowGapSpanningFwdRevPairs ); makeWidgetTypeRWCString( consed.assemblyViewShowWhichInconsistentFwdRevPairs, AssemblyViewShowWhichInconsistentFwdRevPairs ); makeWidgetTypeBool( consed.assemblyViewShowReadDepth, AssemblyViewShowReadDepth ); makeWidgetTypeBool( consed.assemblyViewShowMultipleHighQualityDiscrepancies, AssemblyViewShowMultipleHighQualityDiscrepancies ); makeWidgetTypeBool( consed.assemblyViewShowRestrictionDigestCutSites, AssemblyViewShowRestrictionDigestCutSites ); makeWidgetTypeBool( consed.assemblyViewFilterSequenceMatchesBySize, AssemblyViewFilterSequenceMatchesBySize ); makeWidgetTypeInt( consed.assemblyViewSequenceMatchesMinSize, AssemblyViewSequenceMatchesMinSize ); makeWidgetTypeInt( consed.assemblyViewSequenceMatchesMaxSize, AssemblyViewSequenceMatchesMaxSize ); makeWidgetTypeBool( consed.assemblyViewAutomaticallyStartWithConsed, AssemblyViewAutomaticallyStartWithConsed ); makeWidgetTypeRWCString( consed.assemblyViewDisplayTheseTagTypesOnTheseLines, AssemblyViewDisplayTheseTagTypesOnTheseLines ); makeWidgetTypeBool( consed.assemblyViewShowTags, AssemblyViewShowTags ); makeWidgetTypeBool( consed.autoEditRecalculateHighQualitySegmentsOfReads, AutoEditRecalculateHighQualitySegmentsOfReads ); makeWidgetTypeBool( consed.autoEditConvertCloneEndBasesToXs, AutoEditConvertCloneEndBasesToXs ); makeWidgetTypeBool( consed.autoEditTellPhrapNotToOverlapMultiplyDiscrepantReads, AutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads ); makeWidgetTypeBool( consed.autoEditTagEditableLowConsensusQualityRegions, AutoEditTagEditableLowConsensusQualityRegions ); makeWidgetTypeBool( consed.autoEditMakeFakeRead, AutoEditMakeFakeRead ); makeWidgetTypeRWCString( consed.autoEditMakeFakeReadFromRead1, AutoEditMakeFakeReadFromRead1 ); makeWidgetTypeRWCString( consed.autoEditMakeFakeReadFromRead2, AutoEditMakeFakeReadFromRead2 ); makeWidgetTypeRWCString( consed.autoEditMakeFakeReadName, AutoEditMakeFakeReadName ); makeWidgetTypeFileName( consed.autoEditMakeFakeReadFastaFilename, AutoEditMakeFakeReadFastaFilename ); makeWidgetTypeBool( consed.autoEditMergeAssembly, AutoEditMergeAssembly ); makeWidgetTypeFileName( consed.autoEditSecondaryAceFile, AutoEditSecondaryAceFile ); makeWidgetTypeBool( consed.autoEditFixRunsInConsensus, AutoEditFixRunsInConsensus ); makeWidgetTypeBool( consed.showAllTracesJustShowGoodTraces, ShowAllTracesJustShowGoodTraces ); makeWidgetTypeInt( consed.addAlignedSequenceQualityOfBases, AddAlignedSequenceQualityOfBases ); makeWidgetTypeBool( consed.makeLightBackgroundInAlignedReadsWindowAndTracesWindow, MakeLightBackgroundInAlignedReadsWindowAndTracesWindow ); makeWidgetTypeBool( consed.putVerticalLineAtCursor, PutVerticalLineAtCursor ); makeWidgetTypeBool( consed.putHorizontalLineAtCursor, PutHorizontalLineAtCursor ); makeWidgetTypeFileName( consed.highlightedReadsFile, HighlightedReadsFile ); makeWidgetTypeBool( consed.autoReportPrintReadNamesInRegion, AutoReportPrintReadNamesInRegion ); makeWidgetTypeRWCString( consed.autoReportPrintReadNamesInRegionContig, AutoReportPrintReadNamesInRegionContig ); makeWidgetTypeInt( consed.autoReportPrintReadNamesInRegionLeftPos, AutoReportPrintReadNamesInRegionLeftPos ); makeWidgetTypeInt( consed.autoReportPrintReadNamesInRegionRightPos, AutoReportPrintReadNamesInRegionRightPos ); makeWidgetTypeBool( consed.autoReportPrintHighlyDiscrepantRegions, AutoReportPrintHighlyDiscrepantRegions ); makeWidgetTypeBool( consed.autoReportPrintScaffolds, AutoReportPrintScaffolds ); makeWidgetTypeBool( consed.numberUnpaddedConsensusAtUserDefined, NumberUnpaddedConsensusAtUserDefined ); makeWidgetTypeBool( consed.autoReportPrintHighQualityDiscrepancies, AutoReportPrintHighQualityDiscrepancies ); makeWidgetTypeBool( consed.autoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags, AutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags ); makeWidgetTypeBool( consed.autoReportHighQualityDiscrepanciesExcludeMostPads, AutoReportHighQualityDiscrepanciesExcludeMostPads ); makeWidgetTypeBool( consed.autoReportPrintLowConsensusQualityRegions, AutoReportPrintLowConsensusQualityRegions ); makeWidgetTypeBool( consed.autoReportPrintSingleSubcloneRegions, AutoReportPrintSingleSubcloneRegions ); makeWidgetTypeBool( consed.autoReportPrintSingleStrandedRegions, AutoReportPrintSingleStrandedRegions ); makeWidgetTypeBool( consed.autoReportPrintLinkingForwardReversePairs, AutoReportPrintLinkingForwardReversePairs ); makeWidgetTypeBool( consed.autoReportPrintFilteredInconsistentForwardReversePairs, AutoReportPrintFilteredInconsistentForwardReversePairs ); makeWidgetTypeBool( consed.autoReportPrintAssemblySummary, AutoReportPrintAssemblySummary ); makeWidgetTypeRWCString( consed.showAllTracesDoNotShowTraceIfTheseTagsPresent, ShowAllTracesDoNotShowTraceIfTheseTagsPresent ); makeWidgetTypeBool( consed.nameOfFakeJoiningReadsIncludesAceFileName, NameOfFakeJoiningReadsIncludesAceFileName ); makeWidgetTypeInt( consed.whenUserScrollsOffWindowMillisecondsBetweenScrolling, WhenUserScrollsOffWindowMillisecondsBetweenScrolling ); makeWidgetTypeInt( consed.whenUserScrollsOffWindowBasesToScrollEachTime, WhenUserScrollsOffWindowBasesToScrollEachTime ); makeWidgetTypeBool( consed.compareContigsUseBandedRatherThanFullSmithWaterman, CompareContigsUseBandedRatherThanFullSmithWaterman ); makeWidgetTypeInt( consed.compareContigsBandSize, CompareContigsBandSize ); makeWidgetTypeInt( consed.assemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany, AssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany ); makeWidgetTypeBool( consed.assemblyViewShowSequenceMatches, AssemblyViewShowSequenceMatches ); makeWidgetTypeBool( consed.assemblyViewOKToShowSequenceMatchesBetweenContigs, AssemblyViewOKToShowSequenceMatchesBetweenContigs ); makeWidgetTypeBool( consed.assemblyViewOKToShowSequenceMatchesWithinContigs, AssemblyViewOKToShowSequenceMatchesWithinContigs ); makeWidgetTypeBool( consed.assemblyViewOKToShowDirectSequenceMatches, AssemblyViewOKToShowDirectSequenceMatches ); makeWidgetTypeBool( consed.assemblyViewOKToShowInvertedSequenceMatches, AssemblyViewOKToShowInvertedSequenceMatches ); makeWidgetTypeBool( consed.assemblyViewOnlyShowSequenceMatchesToAParticularRegion, AssemblyViewOnlyShowSequenceMatchesToAParticularRegion ); makeWidgetTypeRWCString( consed.assemblyViewOnlyShowSequenceMatchesToThisContig, AssemblyViewOnlyShowSequenceMatchesToThisContig ); makeWidgetTypeInt( consed.assemblyViewOnlyShowSequenceMatchesToThisRegionLeft, AssemblyViewOnlyShowSequenceMatchesToThisRegionLeft ); makeWidgetTypeInt( consed.assemblyViewOnlyShowSequenceMatchesToThisRegionRight, AssemblyViewOnlyShowSequenceMatchesToThisRegionRight ); makeWidgetTypeBool( consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigs, AssemblyViewOnlyShowSequenceMatchesToEndsOfContigs ); makeWidgetTypeInt( consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar, AssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar ); makeWidgetTypeRWCString( consed.defaultReadPrefix, DefaultReadPrefix ); makeWidgetTypeFileName( consed.readPrefixesFile, ReadPrefixesFile ); makeWidgetTypeInt( consed.maxCharsDisplayedForReadPrefix, MaxCharsDisplayedForReadPrefix ); makeWidgetTypeInt( consed.autoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates, AutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates ); makeWidgetTypeInt( consed.autoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions, AutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions ); makeWidgetTypeInt( consed.autoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis, AutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis ); makeWidgetTypeBool( consed.autoFinishDoNotDoPCRIfEndIsExtendedByReads, AutoFinishDoNotDoPCRIfEndIsExtendedByReads ); makeWidgetTypeInt( consed.autoFinishMaxAcceptableErrorsPerMegabase, AutoFinishMaxAcceptableErrorsPerMegabase ); makeWidgetTypeInt( consed.autoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize, AutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize ); makeWidgetTypeInt( consed.primersNumberOfBasesToBackUpToStartLooking, PrimersNumberOfBasesToBackUpToStartLooking ); makeWidgetTypeInt( consed.primersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment, PrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment ); makeWidgetTypeBool( consed.primersOKToChoosePrimersInSingleSubcloneRegion, PrimersOKToChoosePrimersInSingleSubcloneRegion ); makeWidgetTypeBool( consed.primersOKToChoosePrimersWhereHighQualityDiscrepancies, PrimersOKToChoosePrimersWhereHighQualityDiscrepancies ); makeWidgetTypeBool( consed.primersOKToChoosePrimersWhereUnalignedHighQualityRegion, PrimersOKToChoosePrimersWhereUnalignedHighQualityRegion ); makeWidgetTypeBool( consed.autoFinishCallReversesToFlankGaps, AutoFinishCallReversesToFlankGaps ); makeWidgetTypeBool( consed.autoFinishAllowWholeCloneReads, AutoFinishAllowWholeCloneReads ); makeWidgetTypeBool( consed.autoFinishAllowCustomPrimerSubcloneReads, AutoFinishAllowCustomPrimerSubcloneReads ); makeWidgetTypeBool( consed.autoFinishAllowResequencingReads, AutoFinishAllowResequencingReads ); makeWidgetTypeBool( consed.autoFinishAllowResequencingReadsOnlyForRunsAndStops, AutoFinishAllowResequencingReadsOnlyForRunsAndStops ); makeWidgetTypeBool( consed.autoFinishAllowDeNovoUniversalPrimerSubcloneReads, AutoFinishAllowDeNovoUniversalPrimerSubcloneReads ); makeWidgetTypeBool( consed.autoFinishAllowMinilibraries, AutoFinishAllowMinilibraries ); makeWidgetTypeBool( consed.autoFinishAllowPCR, AutoFinishAllowPCR ); makeWidgetTypeBool( consed.autoFinishAllowUnorientedPCRReactions, AutoFinishAllowUnorientedPCRReactions ); makeWidgetTypeBool( consed.autoFinishAllowResequencingAUniversalPrimerAutofinishRead, AutoFinishAllowResequencingAUniversalPrimerAutofinishRead ); makeWidgetTypeBool( consed.autoFinishAlwaysCloseGapsUsingMinilibraries, AutoFinishAlwaysCloseGapsUsingMinilibraries ); makeWidgetTypeInt( consed.autoFinishMaximumFinishingReadLength, AutoFinishMaximumFinishingReadLength ); makeWidgetTypeInt( consed.autoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger, AutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger ); makeWidgetTypeBool( consed.autoFinishSuggestSpecialChemistryForRunsAndStops, AutoFinishSuggestSpecialChemistryForRunsAndStops ); makeWidgetTypeInt( consed.autoFinishSuggestThisManyMinilibrariesPerGap, AutoFinishSuggestThisManyMinilibrariesPerGap ); makeWidgetTypeInt( consed.primersWindowSizeInLooking, PrimersWindowSizeInLooking ); makeWidgetTypeBool( consed.primersAssumeTemplatesAreDoubleStrandedUnlessSpecified, PrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified ); makeWidgetTypeInt( consed.alignedReadsWindowInitialCharsWide, AlignedReadsWindowInitialCharsWide ); makeWidgetTypeInt( consed.alignedReadsWindowInitialCharsHigh, AlignedReadsWindowInitialCharsHigh ); makeWidgetTypeInt( consed.alignedReadsWindowMaxCharsForReadNames, AlignedReadsWindowMaxCharsForReadNames ); makeWidgetTypeBool( consed.alignedReadsWindowAutomaticallyExpandRoomForReadNames, AlignedReadsWindowAutomaticallyExpandRoomForReadNames ); makeWidgetTypeBool( consed.autoFinishAllowResequencingReadsToExtendContigs, AutoFinishAllowResequencingReadsToExtendContigs ); makeWidgetTypeInt( consed.autoFinishCallHowManyReversesToFlankGaps, AutoFinishCallHowManyReversesToFlankGaps ); makeWidgetTypeBool( consed.autoFinishCloseGaps, AutoFinishCloseGaps ); makeWidgetTypeBool( consed.autoFinishContinueEvenThoughReadInfoDoesNotMakeSense, AutoFinishContinueEvenThoughReadInfoDoesNotMakeSense ); makeWidgetTypeDouble( consed.autoFinishCostOfResequencingUniversalPrimerSubcloneReaction, AutoFinishCostOfResequencingUniversalPrimerSubcloneReaction ); makeWidgetTypeDouble( consed.autoFinishCostOfCustomPrimerSubcloneReaction, AutoFinishCostOfCustomPrimerSubcloneReaction ); makeWidgetTypeDouble( consed.autoFinishCostOfCustomPrimerCloneReaction, AutoFinishCostOfCustomPrimerCloneReaction ); makeWidgetTypeDouble( consed.autoFinishCostOfDeNovoUniversalPrimerSubcloneReaction, AutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction ); makeWidgetTypeDouble( consed.autoFinishCostOfMinilibrary, AutoFinishCostOfMinilibrary ); makeWidgetTypeBool( consed.autoFinishCoverSingleSubcloneRegions, AutoFinishCoverSingleSubcloneRegions ); makeWidgetTypeBool( consed.autoFinishCoverLowConsensusQualityRegions, AutoFinishCoverLowConsensusQualityRegions ); makeWidgetTypeFileName( consed.autoFinishDebugUniversalPrimerReadsFile, AutoFinishDebugUniversalPrimerReadsFile ); makeWidgetTypeFileName( consed.autoFinishDebugCustomPrimerReadsFile, AutoFinishDebugCustomPrimerReadsFile ); makeWidgetTypeInt( consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases, AutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases ); makeWidgetTypeInt( consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases, AutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases ); makeWidgetTypeRWCString( consed.autoFinishDoNotFinishWhereTheseTagsAre, AutoFinishDoNotFinishWhereTheseTagsAre ); makeWidgetTypeRWCString( consed.autoFinishDoNotExtendContigsWhereTheseTagsAre, AutoFinishDoNotExtendContigsWhereTheseTagsAre ); makeWidgetTypeInt( consed.autoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd, AutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd ); makeWidgetTypeFileName( consed.dumpContigOrderAndOrientationInfoToThisFile, DumpContigOrderAndOrientationInfoToThisFile ); makeWidgetTypeBool( consed.autoFinishDumpTemplates, AutoFinishDumpTemplates ); makeWidgetTypeInt( consed.autoFinishExcludeContigIfOnlyThisManyReadsOrLess, AutoFinishExcludeContigIfOnlyThisManyReadsOrLess ); makeWidgetTypeDouble( consed.autoFinishExcludeContigIfDepthOfCoverageGreaterThanThis, AutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis ); makeWidgetTypeInt( consed.autoFinishExcludeContigIfThisManyBasesOrLess, AutoFinishExcludeContigIfThisManyBasesOrLess ); makeWidgetTypeInt( consed.autoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions, AutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions ); makeWidgetTypeInt( consed.primersMinNumberOfTemplatesForPrimers, PrimersMinNumberOfTemplatesForPrimers ); makeWidgetTypeInt( consed.autoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus, AutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus ); makeWidgetTypeInt( consed.autoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead, AutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead ); makeWidgetTypeBool( consed.autoFinishCDNANotGenomic, AutoFinishCDNANotGenomic ); makeWidgetTypeInt( consed.autoFinishConfidenceThatReadWillCoverSingleSubcloneRegion, AutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion ); makeWidgetTypeBool( consed.autoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads, AutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads ); makeWidgetTypeBool( consed.autoFinishPrintMinilibrariesSummaryFile, AutoFinishPrintMinilibrariesSummaryFile ); makeWidgetTypeBool( consed.autoFinishNearGapsSuggestEachMissingReadOfReadPairs, AutoFinishNearGapsSuggestEachMissingReadOfReadPairs ); makeWidgetTypeInt( consed.autoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger, AutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger ); makeWidgetTypeBool( consed.checkIfTooManyWalks, CheckIfTooManyWalks ); makeWidgetTypeInt( consed.numberOfColumnsBeforeReadNameInAlignedReadsWindow, NumberOfColumnsBeforeReadNameInAlignedReadsWindow ); makeWidgetTypeInt( consed.compareContigsAlignsThisManyBasesMax, CompareContigsAlignsThisManyBasesMax ); makeWidgetTypeRWCString( consed.compressedChromatExtension, CompressedChromatExtension ); makeWidgetTypeBool( consed.dimLowQualityEndsOfReads, DimLowQualityEndsOfReads ); makeWidgetTypeBool( consed.dimUnalignedEndsOfReads, DimUnalignedEndsOfReads ); makeWidgetTypeBool( consed.fakeReadsSpecifiedByFilenameExtension, FakeReadsSpecifiedByFilenameExtension ); makeWidgetTypeFileName( consed.fullPathnameOfAddReads2ConsedScript, FullPathnameOfAddReads2ConsedScript ); makeWidgetTypeFileName( consed.fullPathnameOfFixContigEndScript, FullPathnameOfFixContigEndScript ); makeWidgetTypeBool( consed.fixContigEndsCleanUpTemporaryFiles, FixContigEndsCleanUpTemporaryFiles ); makeWidgetTypeInt( consed.fixContigEndsMinSmithWatermanScoreToMakeJoin, FixContigEndsMinSmithWatermanScoreToMakeJoin ); makeWidgetTypeInt( consed.fixContigEndsMinNumberOfReadsInContig, FixContigEndsMinNumberOfReadsInContig ); makeWidgetTypeFileName( consed.fullPathnameOfCrossMatch, FullPathnameOfCrossMatch ); makeWidgetTypeFileName( consed.fullPathnameOfPhred, FullPathnameOfPhred ); makeWidgetTypeFileName( consed.fullPathnameOfMiniassemblyScript, FullPathnameOfMiniassemblyScript ); makeWidgetTypeRWCString( consed.gunzipFullPath, GunzipFullPath ); makeWidgetTypeFileName( consed.fullPathnameOfFilter454ReadsScript, FullPathnameOfFilter454ReadsScript ); makeWidgetTypeFileName( consed.filter454ReadsAgainstThis, Filter454ReadsAgainstThis ); makeWidgetTypeFileName( consed.454LinkerSequences, 454LinkerSequences ); makeWidgetTypeBool( consed.hideSomeTagTypesAtStartup, HideSomeTagTypesAtStartup ); makeWidgetTypeInt( consed.maximumNumberOfTracesShown, MaximumNumberOfTracesShown ); makeWidgetTypeBool( consed.navigateAutomaticTracePopup, NavigateAutomaticTracePopup ); makeWidgetTypeBool( consed.navigateAutomaticAllTracesPopup, NavigateAutomaticAllTracesPopup ); makeWidgetTypeInt( consed.primersMinimumLengthOfAPrimer, PrimersMinimumLengthOfAPrimer ); makeWidgetTypeInt( consed.primersMaximumLengthOfAPrimer, PrimersMaximumLengthOfAPrimer ); makeWidgetTypeInt( consed.primersMinimumLengthOfAPrimerForPCR, PrimersMinimumLengthOfAPrimerForPCR ); makeWidgetTypeInt( consed.primersMaximumLengthOfAPrimerForPCR, PrimersMaximumLengthOfAPrimerForPCR ); makeWidgetTypeDouble( consed.primersMaxMeltingTempDifferenceForPCR, PrimersMaxMeltingTempDifferenceForPCR ); makeWidgetTypeInt( consed.primersMaxPCRPrimerPairsToDisplay, PrimersMaxPCRPrimerPairsToDisplay ); makeWidgetTypeBool( consed.primersCheckJustSomePCRPrimerPairsRatherThanAll, PrimersCheckJustSomePCRPrimerPairsRatherThanAll ); makeWidgetTypeInt( consed.primersNumberOfTemplatesToDisplayInFront, PrimersNumberOfTemplatesToDisplayInFront ); makeWidgetTypeInt( consed.primersMaxLengthOfMononucleotideRepeat, PrimersMaxLengthOfMononucleotideRepeat ); makeWidgetTypeFileName( consed.primersBadLibrariesFile, PrimersBadLibrariesFile ); makeWidgetTypeFileName( consed.primersLibrariesInfoFile, PrimersLibrariesInfoFile ); makeWidgetTypeFileName( consed.primersBadTemplatesFile, PrimersBadTemplatesFile ); makeWidgetTypeBool( consed.primersChooseTemplatesByPositionInsteadOfQuality, PrimersChooseTemplatesByPositionInsteadOfQuality ); makeWidgetTypeInt( consed.primersWhenChoosingATemplateMinPotentialReadLength, PrimersWhenChoosingATemplateMinPotentialReadLength ); makeWidgetTypeInt( consed.primersWindowSizeInLookingForPCR, PrimersWindowSizeInLookingForPCR ); makeWidgetTypeInt( consed.qualityThresholdForFindingHighQualityDiscrepancies, QualityThresholdForFindingHighQualityDiscrepancies ); makeWidgetTypeInt( consed.qualityThresholdForNavigateByDepthOfCoverage, QualityThresholdForNavigateByDepthOfCoverage ); makeWidgetTypeBool( consed.navigateByHighDepthOfCoverageNotLow, NavigateByHighDepthOfCoverageNotLow ); makeWidgetTypeInt( consed.MinDepthForNavigateByDepthOfCoverage, MinDepthForNavigateByDepthOfCoverage ); makeWidgetTypeFileName( consed.defaultVectorPathnameForRestrictionFragments, DefaultVectorPathnameForRestrictionFragments ); makeWidgetTypeFileName( consed.fileOfAdditionalRestrictionEnzymes, FileOfAdditionalRestrictionEnzymes ); makeWidgetTypeRWCString( consed.commonRestrictionEnzymes, CommonRestrictionEnzymes ); makeWidgetTypeRWCString( consed.defaultSelectedRestrictionEnzymes, DefaultSelectedRestrictionEnzymes ); makeWidgetTypeFileName( consed.restrictionEnzymesActualFragmentsFile, RestrictionEnzymesActualFragmentsFile ); makeWidgetTypeInt( consed.restrictionDigestInitialWindowSizeInTextRows, RestrictionDigestInitialWindowSizeInTextRows ); makeWidgetTypeInt( consed.restrictionDigestDoNoShowAreaOfFragmentsOverThisSize, RestrictionDigestDoNoShowAreaOfFragmentsOverThisSize ); makeWidgetTypeBool( consed.showReadsAlphabetically, ShowReadsAlphabetically ); makeWidgetTypeBool( consed.showReadsInAlignedReadsWindowOrderedByFile, ShowReadsInAlignedReadsWindowOrderedByFile ); makeWidgetTypeFileName( consed.showReadsInAlignedReadsWindowOrderedByThisFile, ShowReadsInAlignedReadsWindowOrderedByThisFile ); makeWidgetTypeRWCString( consed.showReadsAtCursorSortedHow, ShowReadsAtCursorSortedHow ); makeWidgetTypeBool( consed.showABIBasesInTraceWindow, ShowABIBasesInTraceWindow ); makeWidgetTypeInt( consed.tracesWindowInitialPixelHeight, TracesWindowInitialPixelHeight ); makeWidgetTypeInt( consed.assemblyViewWindowInitialPixelHeight, AssemblyViewWindowInitialPixelHeight ); makeWidgetTypeFileName( consed.assemblyViewFileOfTemplatesToNotShow, AssemblyViewFileOfTemplatesToNotShow ); makeWidgetTypeInt( consed.assemblyViewCrossMatchMinmatch, AssemblyViewCrossMatchMinmatch ); makeWidgetTypeInt( consed.assemblyViewCrossMatchMinscore, AssemblyViewCrossMatchMinscore ); makeWidgetTypeFileName( consed.assemblyViewFindSequenceMatchesForConsedScript, AssemblyViewFindSequenceMatchesForConsedScript ); makeWidgetTypeInt( consed.assemblyViewCrossmatchMinmatch, AssemblyViewCrossmatchMinmatch ); makeWidgetTypeInt( consed.assemblyViewCrossmatchMinscore, AssemblyViewCrossmatchMinscore ); makeWidgetTypeInt( consed.assemblyViewSequenceMatchesMinimumSimilarity, AssemblyViewSequenceMatchesMinimumSimilarity ); makeWidgetTypeInt( consed.tracesWindowInitialPixelWidth, TracesWindowInitialPixelWidth ); makeWidgetTypeInt( consed.assemblyViewWindowInitialPixelWidth, AssemblyViewWindowInitialPixelWidth ); makeWidgetTypeBool( consed.automaticallyScaleTraces, AutomaticallyScaleTraces ); makeWidgetTypeDouble( consed.automaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight, AutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight ); makeWidgetTypeInt( consed.automaticallyScaleTracesSamplePeakPercentile, AutomaticallyScaleTracesSamplePeakPercentile ); makeWidgetTypeInt( consed.verticalTraceMagnification, VerticalTraceMagnification ); makeWidgetTypeRWCString( consed.userDefinedKeys, UserDefinedKeys ); makeWidgetTypeRWCString( consed.programsForUserDefinedKeys, ProgramsForUserDefinedKeys ); makeWidgetTypeRWCString( consed.argumentsToPassToUserDefinedPrograms, ArgumentsToPassToUserDefinedPrograms ); makeWidgetTypeRWCString( consed.tagsToApplyWithUserDefinedKeys, TagsToApplyWithUserDefinedKeys ); makeWidgetTypeBool( consed.snpGenomeUseInsertionPolymorphisms, SnpGenomeUseInsertionPolymorphisms ); makeWidgetTypeRWCString( consed.listOfTagTypesToHide, ListOfTagTypesToHide ); makeWidgetTypeRWCString( consed.listOfOptionalWordsToSaveInListOfReadNames, ListOfOptionalWordsToSaveInListOfReadNames ); makeWidgetTypeBool( consed.extendConsensusWithHighQuality, ExtendConsensusWithHighQuality ); makeWidgetTypeBool( consed.fastStartup, FastStartup ); makeWidgetTypeFileName( consed.fastStartupFile, FastStartupFile ); makeWidgetTypeRWCString( consed.alwaysRunProgramToGetChromats, AlwaysRunProgramToGetChromats ); makeWidgetTypeFileName( consed.programToRunToGetChromats, ProgramToRunToGetChromats ); makeWidgetTypeFileName( consed.programToRunToGetChromatsOf454Reads, ProgramToRunToGetChromatsOf454Reads ); makeWidgetTypeBool( consed.createFakeChromatsForSolexaReads, CreateFakeChromatsForSolexaReads ); makeWidgetTypeBool( consed.autoFinishUseLongModelReadRatherThanShort, AutoFinishUseLongModelReadRatherThanShort ); makeWidgetTypeInt( consed.askAgainIfWantToQuitConsedIfThisManyReads, AskAgainIfWantToQuitConsedIfThisManyReads ); makeWidgetTypeRWCString( consed.printWindowInstructions, PrintWindowInstructions ); makeWidgetTypeBool( consed.allowMultipleSearchForStringWindows, AllowMultipleSearchForStringWindows ); makeWidgetTypeInt( consed.autoPCRAmplifyFalseProductsOKIfLargerThanThis, AutoPCRAmplifyFalseProductsOKIfLargerThanThis ); makeWidgetTypeBool( consed.autoPCRAmplifyMakePrimerOutOfFirstRegion, AutoPCRAmplifyMakePrimerOutOfFirstRegion ); makeWidgetTypeInt( consed.autoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct, AutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct ); makeWidgetTypeBool( consed.addNewReadsRecalculateConsensusQuality, AddNewReadsRecalculateConsensusQuality ); makeWidgetTypeRWCString( consed.addNewReadsPutReadIntoItsOwnContig, AddNewReadsPutReadIntoItsOwnContig ); makeWidgetTypeBool( consed.addNewReadsCheckThatCrossMatchRunCorrectly, AddNewReadsCheckThatCrossMatchRunCorrectly ); makeWidgetTypeInt( consed.assemblyViewNumberOfRowsOfTags, AssemblyViewNumberOfRowsOfTags ); makeWidgetTypeBool( consed.warnUserWhenTryingToEditAllReads, WarnUserWhenTryingToEditAllReads ); makeWidgetTypeFileName( consed.maybeXKEYSYMDBPath, MaybeXKEYSYMDBPath ); makeWidgetTypeFileName( consed.maybeXKEYSYMDBPath2, MaybeXKEYSYMDBPath2 ); makeWidgetTypeInt( consed.amountToMoveWithBigLeftAndRightArrows, AmountToMoveWithBigLeftAndRightArrows ); makeWidgetTypeInt( consed.navigateByHighlyDiscrepantPositionsMinDiscrepantReads, NavigateByHighlyDiscrepantPositionsMinDiscrepantReads ); makeWidgetTypeInt( consed.navigateByHighlyDiscrepantPositionsMaxDepthOfCoverage, NavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage ); makeWidgetTypeInt( consed.navigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality, NavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality ); makeWidgetTypeBool( consed.navigateByHighlyDiscrepantPositionsJustListIndels, NavigateByHighlyDiscrepantPositionsJustListIndels ); makeWidgetTypeBool( consed.navigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation, NavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation ); makeWidgetTypeBool( consed.navigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus, NavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus ); makeWidgetTypeRWCString( consed.navigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus, NavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus ); makeWidgetTypeFileName( consed.phdBallDirectory, PhdBallDirectory ); makeWidgetTypeFileName( consed.newAceFileFOF, NewAceFileFOF ); makeWidgetTypeInt( consed.navigateByHighOrLowDepthCoalesceRegionsIfThisClose, NavigateByHighOrLowDepthCoalesceRegionsIfThisClose ); makeWidgetTypeBool( consed.removeReadsDeleteNotJustPutInOwnContig, RemoveReadsDeleteNotJustPutInOwnContig ); makeWidgetTypeRWCString( consed.paired454LeftReadExtension, Paired454LeftReadExtension ); makeWidgetTypeRWCString( consed.paired454RightReadExtension, Paired454RightReadExtension ); makeWidgetTypeFileName( consed.snpGenome1MSnps, SnpGenome1MSnps ); makeWidgetTypeBool( consed.diffChromosomesExcludeDeletions, DiffChromosomesExcludeDeletions ); makeWidgetTypeBool( consed.snpGenomeFilterByWeight, SnpGenomeFilterByWeight ); makeWidgetTypeInt( consed.wantReadsUpToThisFarFromSnps, WantReadsUpToThisFarFromSnps ); makeWidgetTypeRWCString( consed.phaster2PhdBallSaveWhichMate, Phaster2PhdBallSaveWhichMate ); makeWidgetTypeBool( consed.phaster2PhdBallSaveInPhasterFormat, Phaster2PhdBallSaveInPhasterFormat ); makeWidgetTypeBool( consed.phaster2PhdBallCalculateNewLocationsFile, Phaster2PhdBallCalculateNewLocationsFile ); makeWidgetTypeBool( consed.phdBall2FastaIgnoreLowQualityReads, PhdBall2FastaIgnoreLowQualityReads ); makeWidgetTypeInt( consed.phdBall2FastaLowestAverageQuality, PhdBall2FastaLowestAverageQuality ); makeWidgetTypeFileName( consed.nextPhredPipelineControlFile, NextPhredPipelineControlFile ); makeWidgetTypeFileName( consed.nextPhredPipelineTiffPerlScript, NextPhredPipelineTiffPerlScript ); makeWidgetTypeFileName( consed.nextPhredPipelinePhasterPerlScript, NextPhredPipelinePhasterPerlScript ); makeWidgetTypeRWCString( consed.nextPhredPipelineVersion, NextPhredPipelineVersion ); makeWidgetTypeRWCString( consed.nextPhredPipelineMainDirectory, NextPhredPipelineMainDirectory ); makeWidgetTypeInt( consed.maxNumberOfReadsPerPhdBall, MaxNumberOfReadsPerPhdBall ); makeWidgetTypeFileName( consed.userWantsToSaveToThisAceFile, UserWantsToSaveToThisAceFile ); makeWidgetTypeBool( consed.autoFinishEmulate9_66Behavior, AutoFinishEmulate9_66Behavior ); makeWidgetTypeInt( consed.primersPCRPrimersGroupedIntoWindowOfThisManyBases, PrimersPCRPrimersGroupedIntoWindowOfThisManyBases ); makeWidgetTypeInt( consed.primersLookForThisManyPCRPrimerPairsPerPairOfGroups, PrimersLookForThisManyPCRPrimerPairsPerPairOfGroups ); makeWidgetTypeDouble( consed.autoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs, AutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs ); makeWidgetTypeBool( consed.autoFinishCheckThatReadsFromTheSameTemplateAreConsistent, AutoFinishCheckThatReadsFromTheSameTemplateAreConsistent ); makeWidgetTypeBool( consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether, AutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether ); makeWidgetTypeBool( consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether, AutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether ); makeWidgetTypeDouble( consed.autoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean, AutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean ); makeWidgetTypeInt( consed.autoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize, AutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize ); makeWidgetTypeDouble( consed.autoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize, AutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize ); makeWidgetTypeInt( consed.autoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead, AutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead ); makeWidgetTypeInt( consed.autoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp, AutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp ); makeWidgetTypeInt( consed.autoFinishNumberOfBasesBetweenContigsAssumed, AutoFinishNumberOfBasesBetweenContigsAssumed ); makeWidgetTypeInt( consed.autoFinishPotentialHighQualityPartOfReadStart, AutoFinishPotentialHighQualityPartOfReadStart ); makeWidgetTypeInt( consed.autoFinishPotentialHighQualityPartOfReadEnd, AutoFinishPotentialHighQualityPartOfReadEnd ); makeWidgetTypeBool( consed.autoFinishPrintCustomNavigationFileForChosenReads, AutoFinishPrintCustomNavigationFileForChosenReads ); makeWidgetTypeInt( consed.autoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch, AutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch ); makeWidgetTypeBool( consed.autoFinishTagOligosWhenDoExperiments, AutoFinishTagOligosWhenDoExperiments ); makeWidgetTypeBool( consed.countPads, CountPads ); makeWidgetTypeInt( consed.debugging, Debugging ); makeWidgetTypeInt( consed.debugging2, Debugging2 ); makeWidgetTypeInt( consed.debugging3, Debugging3 ); makeWidgetTypeRWCString( consed.debuggingString, DebuggingString ); makeWidgetTypeInt( consed.ignoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion, IgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion ); makeWidgetTypeInt( consed.ignoreUnalignedHighQualitySegmentsShorterThanThis, IgnoreUnalignedHighQualitySegmentsShorterThanThis ); makeWidgetTypeInt( consed.primersLookThisFarForForwardVectorInsertJunction, PrimersLookThisFarForForwardVectorInsertJunction ); makeWidgetTypeDouble( consed.primersDNAConcentrationNanomolar, PrimersDNAConcentrationNanomolar ); makeWidgetTypeInt( consed.primersMaxMatchElsewhereScore, PrimersMaxMatchElsewhereScore ); makeWidgetTypeInt( consed.primersMaxMatchElsewhereScoreForPCR, PrimersMaxMatchElsewhereScoreForPCR ); makeWidgetTypeInt( consed.primersMaxSelfMatchScore, PrimersMaxSelfMatchScore ); makeWidgetTypeInt( consed.primersMaxPrimerDimerScoreForPCR, PrimersMaxPrimerDimerScoreForPCR ); makeWidgetTypeInt( consed.primersMinQuality, PrimersMinQuality ); makeWidgetTypeBool( consed.primersPrintInfoOnRejectedTemplates, PrimersPrintInfoOnRejectedTemplates ); makeWidgetTypeDouble( consed.primersSaltConcentrationMillimolar, PrimersSaltConcentrationMillimolar ); makeWidgetTypeBool( consed.primersScreenForVector, PrimersScreenForVector ); makeWidgetTypeInt( consed.primersToleranceForDifferentBeginningLocationOfUniversalPrimerReads, PrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads ); makeWidgetTypeInt( consed.primersTooManyVectorBasesInWalkingRead, PrimersTooManyVectorBasesInWalkingRead ); makeWidgetTypeInt( consed.qualityThresholdForLowConsensusQuality, QualityThresholdForLowConsensusQuality ); makeWidgetTypeInt( consed.tagColorPerCentOfBase, TagColorPerCentOfBase ); makeWidgetTypeRWCString( consed.uncompressedChromatDirectory, UncompressedChromatDirectory ); makeWidgetTypeFileName( consed.454sff2scfDirectory, 454sff2scfDirectory ); makeWidgetTypeInt( consed.whenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion, WhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion ); makeWidgetTypeInt( consed.writeThisAceFormat, WriteThisAceFormat ); makeWidgetTypeBool( consed.dumpCoreIfBoundsError, DumpCoreIfBoundsError ); makeWidgetTypeInt( consed.autoFinishMinSmithWatermanScoreOfARun, AutoFinishMinSmithWatermanScoreOfARun ); makeWidgetTypeDouble( consed.autoFinishDoNotComparePCRPrimersMoreThanThisManyTimes, AutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes ); makeWidgetTypeInt( consed.restrictionDigestMaximumBasesToCompareToVector, RestrictionDigestMaximumBasesToCompareToVector ); makeWidgetTypeDouble( consed.restrictionDigestZoomFactor, RestrictionDigestZoomFactor ); makeWidgetTypeDouble( consed.restrictionDigestZoomFactorForNavigate, RestrictionDigestZoomFactorForNavigate ); makeWidgetTypeInt( consed.restrictionDigestToleranceInPositionUnits, RestrictionDigestToleranceInPositionUnits ); makeWidgetTypeInt( consed.autoPCRAmplifyTooManySeriousFalseMatches, AutoPCRAmplifyTooManySeriousFalseMatches ); makeWidgetTypeDouble( consed.assemblyViewZoomFactor, AssemblyViewZoomFactor ); makeWidgetTypeInt( consed.assemblyViewFilterInconsistentFwdRevPairsIfThisClose, AssemblyViewFilterInconsistentFwdRevPairsIfThisClose ); makeWidgetTypeDouble( consed.assemblyViewGridCellWidthInPixels, AssemblyViewGridCellWidthInPixels ); makeWidgetTypeInt( consed.assemblyViewCursorSensitivityInPixels, AssemblyViewCursorSensitivityInPixels ); makeWidgetTypeInt( consed.assemblyViewReadDepthQuality, AssemblyViewReadDepthQuality ); makeWidgetTypeInt( consed.showAllTracesMaxNumberOfTracesToShowAtOnce, ShowAllTracesMaxNumberOfTracesToShowAtOnce ); makeWidgetTypeInt( consed.allowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess, AllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess ); makeWidgetTypeBool( consed.justForPrimateProject, JustForPrimateProject ); makeWidgetTypeFileName( consed.solexaFilesAreAssumedToBeHere, SolexaFilesAreAssumedToBeHere ); makeWidgetTypeInt( consed.solexaAlignmentFilesPerInsertingPadsCycle, SolexaAlignmentFilesPerInsertingPadsCycle ); makeWidgetTypeInt( consed.solexaAlignmentsPerAlignmentFile, SolexaAlignmentsPerAlignmentFile ); makeWidgetTypeBool( consed.solexaFastqFilesArePhredQualityNotSolexaQuality, SolexaFastqFilesArePhredQualityNotSolexaQuality ); makeWidgetTypeRWCString( consed.solexa64FastqOrSanger33Fastq, Solexa64FastqOrSanger33Fastq ); makeWidgetTypeInt( consed.maximumReadsInReadList, MaximumReadsInReadList ); makeWidgetTypeInt( consed.maxLengthOfReadsInapLocatedFragment2, MaxLengthOfReadsInapLocatedFragment2 ); makeWidgetTypeInt( consed.maximumStartupErrorsToReport, MaximumStartupErrorsToReport ); makeWidgetTypeInt( consed.454LinkerAlignmentMatchScore, 454LinkerAlignmentMatchScore ); makeWidgetTypeInt( consed.454LinkerAlignmentMismatchScore, 454LinkerAlignmentMismatchScore ); makeWidgetTypeInt( consed.454LinkerAlignmentIndelScore, 454LinkerAlignmentIndelScore ); makeWidgetTypeBool( consed.filter454ReadsDeleteCrossMatchOutput, Filter454ReadsDeleteCrossMatchOutput ); makeWidgetTypeInt( consed.autoReportAllNeededSpeciesCode, AutoReportAllNeededSpeciesCode ); makeWidgetTypeBool( consed.autoReportUseCommasInBigNumbers, AutoReportUseCommasInBigNumbers ); makeWidgetTypeBool( consed.autoReportPrintToCompareToReich, AutoReportPrintToCompareToReich ); makeWidgetTypeBool( consed.autoReportOnlyAllowSitesThatAreBetweenAcceptableSites, AutoReportOnlyAllowSitesThatAreBetweenAcceptableSites ); makeWidgetTypeBool( consed.autoReportDeaminationMutationsDeterminedByMoreAccurateMethod, AutoReportDeaminationMutationsDeterminedByMoreAccurateMethod ); makeWidgetTypeBool( consed.autoReportChooseTreesUsingBadData, AutoReportChooseTreesUsingBadData ); makeWidgetTypeBool( consed.autoReportChooseTreesByCountingDeaminationMutations, AutoReportChooseTreesByCountingDeaminationMutations ); makeWidgetTypeBool( consed.autoReportChooseTreesUsingKimura, AutoReportChooseTreesUsingKimura ); makeWidgetTypeBool( consed.autoReportPrintCrudeChimpHumanMutations, AutoReportPrintCrudeChimpHumanMutations ); makeWidgetTypeBool( consed.autoReportPrintPositionsForGraham, AutoReportPrintPositionsForGraham ); makeWidgetTypeBool( consed.autoReportPrintAncestralCpGs, AutoReportPrintAncestralCpGs ); makeWidgetTypeBool( consed.autoReportPrintCpGMutations, AutoReportPrintCpGMutations ); makeWidgetTypeBool( consed.autoReportPrintMutationsWithContext, AutoReportPrintMutationsWithContext ); makeWidgetTypeBool( consed.autoReportCountAllMutationsML, AutoReportCountAllMutationsML ); makeWidgetTypeBool( consed.autoReportCountAllMutations, AutoReportCountAllMutations ); makeWidgetTypeBool( consed.autoReportIgnoreMultipleTrees, AutoReportIgnoreMultipleTrees ); makeWidgetTypeBool( consed.autoReportCountAcceptableColumnsWithNoneOnLeft, AutoReportCountAcceptableColumnsWithNoneOnLeft ); makeWidgetTypeBool( consed.autoReportPrintFlankedColumns4, AutoReportPrintFlankedColumns4 ); makeWidgetTypeBool( consed.autoReportUseAnnotationFormat, AutoReportUseAnnotationFormat ); makeWidgetTypeBool( consed.autoReportPrintFlankedColumns3, AutoReportPrintFlankedColumns3 ); makeWidgetTypeBool( consed.autoReportPrintFlankedColumns2, AutoReportPrintFlankedColumns2 ); makeWidgetTypeBool( consed.autoReportPrintFlankedColumns, AutoReportPrintFlankedColumns ); makeWidgetTypeBool( consed.autoReportHighQualitySegmentData, AutoReportHighQualitySegmentData ); makeWidgetTypeBool( consed.autoReportGoodReadsBug, AutoReportGoodReadsBug ); makeWidgetTypeBool( consed.autoReportDiscrepancyRateInFlankedRegions, AutoReportDiscrepancyRateInFlankedRegions ); makeWidgetTypeBool( consed.autoReportDiscrepancyRateInFlankedRegions2, AutoReportDiscrepancyRateInFlankedRegions2 ); makeWidgetTypeBool( consed.autoReportDiscrepancyRateInFlankedRegions4, AutoReportDiscrepancyRateInFlankedRegions4 ); makeWidgetTypeBool( consed.autoReportDiscrepancyRateInFlankedRegions5, AutoReportDiscrepancyRateInFlankedRegions5 ); makeWidgetTypeBool( consed.autoReportSingleSignalOrQuality, AutoReportSingleSignalOrQuality ); makeWidgetTypeBool( consed.autoReportLowQualityBasesInHQS, AutoReportLowQualityBasesInHQS ); makeWidgetTypeBool( consed.autoReportCompareHQSWithLQS, AutoReportCompareHQSWithLQS ); makeWidgetTypeBool( consed.autoReportCountColumnsForGroupsOfSpecies, AutoReportCountColumnsForGroupsOfSpecies ); makeWidgetTypeBool( consed.autoReportSingleSignalInfo, AutoReportSingleSignalInfo ); makeWidgetTypeBool( consed.autoReportSingleSignalInfo2, AutoReportSingleSignalInfo2 ); makeWidgetTypeBool( consed.autoReportCompareTopAndBottomStrands, AutoReportCompareTopAndBottomStrands ); makeWidgetTypeBool( consed.autoReportCompareTopAndBottomStrandsNoHuman, AutoReportCompareTopAndBottomStrandsNoHuman ); makeWidgetTypeBool( consed.autoReportCompareTopAndBottomStrands2, AutoReportCompareTopAndBottomStrands2 ); makeWidgetTypeBool( consed.autoReportCompareTopAndBottomStrands3, AutoReportCompareTopAndBottomStrands3 ); makeWidgetTypeBool( consed.autoReportCompareTopAndBottomStrands4, AutoReportCompareTopAndBottomStrands4 ); makeWidgetTypeInt( consed.autoReportTopStrandPinnedPosition, AutoReportTopStrandPinnedPosition ); makeWidgetTypeInt( consed.autoReportBottomStrandPinnedPosition, AutoReportBottomStrandPinnedPosition ); makeWidgetTypeBool( consed.autoReportCompareTopAndBottomStrandsWithHuman, AutoReportCompareTopAndBottomStrandsWithHuman ); makeWidgetTypeBool( consed.autoReportPrintLengthsOfAlignedSegmentsOfReads, AutoReportPrintLengthsOfAlignedSegmentsOfReads ); makeWidgetTypeBool( consed.autoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads, AutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads ); makeWidgetTypeBool( consed.autoReportPrintIfReadsAreCorrectlyAligned, AutoReportPrintIfReadsAreCorrectlyAligned ); makeWidgetTypeBool( consed.autoReportCalculateErrorProbabilitiesByComparingPTroPPan, AutoReportCalculateErrorProbabilitiesByComparingPTroPPan ); makeWidgetTypeBool( consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies, AutoReportPrintAgreeDisagreeBetweenPairsOfSpecies ); makeWidgetTypeBool( consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies2, AutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2 ); makeWidgetTypeBool( consed.autoReportFilterSingleSignal, AutoReportFilterSingleSignal ); makeWidgetTypeFileName( consed.autoReportGoodHitReads, AutoReportGoodHitReads ); makeWidgetTypeInt( consed.autoReportQualityWindowLow, AutoReportQualityWindowLow ); makeWidgetTypeInt( consed.autoReportQualityWindowHigh, AutoReportQualityWindowHigh ); makeWidgetTypeBool( consed.autoReportPrintNumberOfIsolatedPadsForEachSpecies, AutoReportPrintNumberOfIsolatedPadsForEachSpecies ); makeWidgetTypeBool( consed.autoReportPrintNumberOfIsolatedPads, AutoReportPrintNumberOfIsolatedPads ); makeWidgetTypeRWCString( consed.autoReportIsolatedPadsOfReadsWithThisPattern, AutoReportIsolatedPadsOfReadsWithThisPattern ); makeWidgetTypeInt( consed.autoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy, AutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy ); makeWidgetTypeInt( consed.autoReportMaxSizeOfDiscrepantRegion, AutoReportMaxSizeOfDiscrepantRegion ); makeWidgetTypeInt( consed.autoReportSizeOfDiscrepantRegion, AutoReportSizeOfDiscrepantRegion ); makeWidgetTypeBool( consed.autoReportPrintMinimumQualityHistogram, AutoReportPrintMinimumQualityHistogram ); makeWidgetTypeBool( consed.autoReportPrintDiscrepantRegions, AutoReportPrintDiscrepantRegions ); makeWidgetTypeBool( consed.autoReportPrintBasesInDiscrepantRegions, AutoReportPrintBasesInDiscrepantRegions ); makeWidgetTypeRWCString( consed.autoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis, AutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis ); makeWidgetTypeRWCString( consed.autoReportBackboneReadHasThisStringInIt, AutoReportBackboneReadHasThisStringInIt ); makeWidgetTypeBool( consed.autoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold, AutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold ); makeWidgetTypeBool( consed.autoReportPrintSpeciesAlignment, AutoReportPrintSpeciesAlignment ); makeWidgetTypeBool( consed.autoReportPrintReadAlignment, AutoReportPrintReadAlignment ); makeWidgetTypeFileName( consed.autoReportPrintTheseReads, AutoReportPrintTheseReads ); makeWidgetTypeBool( consed.autoReportPrintReadPositions, AutoReportPrintReadPositions ); makeWidgetTypeBool( consed.autoReportPrintChosenReadName, AutoReportPrintChosenReadName ); makeWidgetTypeInt( consed.autoReportNumbersOfCharactersOfChosenReadNameToBePrinted, AutoReportNumbersOfCharactersOfChosenReadNameToBePrinted ); makeWidgetTypeRWCString( consed.autoReportPrefix, AutoReportPrefix ); makeWidgetTypeBool( consed.autoReportUseOldCriteriaForDeletingColumnsOfPads, AutoReportUseOldCriteriaForDeletingColumnsOfPads ); makeWidgetTypeBool( consed.autoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues, AutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues ); makeWidgetTypeBool( consed.autoReportFlankingBasesMustBeSingleSignal, AutoReportFlankingBasesMustBeSingleSignal ); makeWidgetTypeInt( consed.autoReportMinimumQualityOfFlankingBases, AutoReportMinimumQualityOfFlankingBases ); makeWidgetTypeBool( consed.autoReportFlankingBasesMustBeInHighQualitySegment, AutoReportFlankingBasesMustBeInHighQualitySegment ); makeWidgetTypeRWCString( consed.autoReportSpecies, AutoReportSpecies ); // guiEditResources.cpp.part5 // this needs to be saved for use in the resize callback widPrimersSubcloneFullPathnameForm_ = widPrimersSubcloneFullPathnameOfFileOfSequencesForScreeningForm; if ( !bStandAlone_ ) XtPopup( widPopupShell_, XtGrabNone ); delete pPleaseWait; createResourceArray(); waitUntilDialogIsVisible( widPopupShell_ ); windowCameUp(); bAllTheWayUp_ = true; } guiEditResources :: ~guiEditResources() { // segmentation fault without this because cbResize gets called // after popping down the window XtRemoveCallback( widClipWindow_, XmNresizeCallback, cbResize, this ); XtPopdown( widPopupShell_ ); XtDestroyWidget( widPopupShell_ ); if ( bStandAlone_ ) _exit( 0 ); } void guiEditResources :: userPushedSave() { checkEverything(); // open the appropriate file and check with the user that this // is really the one they want--put up a Motif file dialog box. FileName filToWrite; if ( XmToggleButtonGetState( widUserRadioButton_ ) == True ) { // thus we want to write to $HOME/.consedrc // translate $HOME char* pHOME = getenv( "HOME" ); if ( !pHOME ) { popupErrorMessage( "something is really screwed up because $HOME is not set. Thus no user-defined parameters can be set" ); return; } filToWrite = pHOME; filToWrite += "/.consedrc"; } else if ( XmToggleButtonGetState( widProjectRadioButton_ ) == True ) { const int nBigNumber = 1000; char szCurrentDirectory[ nBigNumber + 1 ]; getcwd( szCurrentDirectory, nBigNumber ); filToWrite = szCurrentDirectory; filToWrite += "/.consedrc"; } else if ( XmToggleButtonGetState( widAllUsersAllProjectsRadioButton_ ) ) { char* pConsedParameters = getenv( "CONSED_PARAMETERS" ); if ( !pConsedParameters ) { popupErrorMessage( "environment variable CONSED_PARAMETERS is not set so I don't know where to write the parameters: you will have to tell me" ); filToWrite = "./.consedrc"; } else { filToWrite = pConsedParameters; } } else assert( false ); int nArgs = 0; Arg aArg[50]; // XtSetArg( aArg[ nArgs ], XmNdialogTitle, xmsTitle ); ++nArgs; Widget widFileSelectionBox = XmCreateFileSelectionDialog( widPopupShell_, "Parameter Filename", NULL, 0 ); XtAddCallback( widFileSelectionBox, XmNokCallback, cbFileSelectionOK, this ); XtAddCallback( widFileSelectionBox, XmNcancelCallback, cbFileSelectionCancel, this ); XmString xmsTitle = XmStringCreateSimple( "Name of parameter file to write" ); RWCString soDirMask = filToWrite.soGetDirectory() + "*.*"; XmString xmsDirMask = XmStringCreateSimple( soDirMask.data() ); XmString xmsDirSpec = XmStringCreateSimple( filToWrite.data() ); XmString xmsDirectory = XmStringCreateSimple( filToWrite.soGetDirectory().data() ); XtVaSetValues( widFileSelectionBox, XmNdialogTitle, xmsTitle, XmNselectionLabelString, xmsTitle, XmNdirMask, xmsDirMask, XmNdirectory, xmsDirectory, NULL ); XtVaSetValues( widFileSelectionBox, XmNdirSpec, xmsDirSpec, NULL ); XtManageChild( widFileSelectionBox ); XmStringFree( xmsDirSpec ); XmStringFree( xmsTitle ); XmStringFree( xmsDirMask ); } void guiEditResources :: userChoseFileAndPushedOK( const Widget wid, XmFileSelectionBoxCallbackStruct* pCallbackStruct ) { char* szFullPath; assert( XmStringGetLtoR( pCallbackStruct->value, XmSTRING_DEFAULT_CHARSET, &szFullPath ) ); FileName filToWrite( szFullPath ); cerr << "user selected file" << filToWrite << endl; if ( filToWrite.bFileByThisNameExists() ) { bool bGoAhead = GuiApp::popupDecisionMessage( "File %s exists. Save anyway?", filToWrite.data() ); if ( !bGoAhead ) { return; } } // no more user input below here // this might throw an exception checkEverything(); // once more // since the user is satisfied with this file, we don't need the // file dialog box any longer: XtUnmanageChild( wid ); XtDestroyWidget( wid ); FILE* pFileToWrite = fopen( szFullPath, "w" ); // now write the changed resources // guiEditResources.cpp.part6 // consed.printPS if ( resources_.bPrintPS_ != CONDEF->bPrintPS_ ) { fprintf( pFileToWrite, "consed.printPS: %s\n", ( resources_.bPrintPS_ ? "true" : "false" ) ); } // consed.defaultTagType if ( resources_.soDefaultTagType_ != CONDEF->soDefaultTagType_ ) { fprintf( pFileToWrite, "consed.defaultTagType: %s\n", resources_.soDefaultTagType_.data() ); } // consed.defaultTagOnConsensusNotReads if ( resources_.bDefaultTagOnConsensusNotReads_ != CONDEF->bDefaultTagOnConsensusNotReads_ ) { fprintf( pFileToWrite, "consed.defaultTagOnConsensusNotReads: %s\n", ( resources_.bDefaultTagOnConsensusNotReads_ ? "true" : "false" ) ); } // consed.autoFinishMinNumberOfErrorsFixedByAnExp if ( resources_.dAutoFinishMinNumberOfErrorsFixedByAnExp_ != CONDEF->dAutoFinishMinNumberOfErrorsFixedByAnExp_ ) { fprintf( pFileToWrite, "consed.autoFinishMinNumberOfErrorsFixedByAnExp: %f\n", resources_.dAutoFinishMinNumberOfErrorsFixedByAnExp_ ); } // consed.autoFinishRedundancy if ( resources_.dAutoFinishRedundancy_ != CONDEF->dAutoFinishRedundancy_ ) { fprintf( pFileToWrite, "consed.autoFinishRedundancy: %f\n", resources_.dAutoFinishRedundancy_ ); } // consed.autoFinishAverageInsertSize if ( resources_.nAutoFinishAverageInsertSize_ != CONDEF->nAutoFinishAverageInsertSize_ ) { fprintf( pFileToWrite, "consed.autoFinishAverageInsertSize: %d\n", resources_.nAutoFinishAverageInsertSize_ ); } // consed.primersMaxInsertSizeOfASubclone if ( resources_.nPrimersMaxInsertSizeOfASubclone_ != CONDEF->nPrimersMaxInsertSizeOfASubclone_ ) { fprintf( pFileToWrite, "consed.primersMaxInsertSizeOfASubclone: %d\n", resources_.nPrimersMaxInsertSizeOfASubclone_ ); } // consed.primersMaxMeltingTemp if ( resources_.nPrimersMaxMeltingTemp_ != CONDEF->nPrimersMaxMeltingTemp_ ) { fprintf( pFileToWrite, "consed.primersMaxMeltingTemp: %d\n", resources_.nPrimersMaxMeltingTemp_ ); } // consed.primersMaxMeltingTempForPCR if ( resources_.nPrimersMaxMeltingTempForPCR_ != CONDEF->nPrimersMaxMeltingTempForPCR_ ) { fprintf( pFileToWrite, "consed.primersMaxMeltingTempForPCR: %d\n", resources_.nPrimersMaxMeltingTempForPCR_ ); } // consed.primersPickTemplatesForPrimers if ( resources_.bPrimersPickTemplatesForPrimers_ != CONDEF->bPrimersPickTemplatesForPrimers_ ) { fprintf( pFileToWrite, "consed.primersPickTemplatesForPrimers: %s\n", ( resources_.bPrimersPickTemplatesForPrimers_ ? "true" : "false" ) ); } // consed.primersSubcloneFullPathnameOfFileOfSequencesForScreening if ( resources_.soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_ != CONDEF->soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_ ) { fprintf( pFileToWrite, "consed.primersSubcloneFullPathnameOfFileOfSequencesForScreening: %s\n", resources_.soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_.data() ); } // consed.primersCloneFullPathnameOfFileOfSequencesForScreening if ( resources_.soPrimersCloneFullPathnameOfFileOfSequencesForScreening_ != CONDEF->soPrimersCloneFullPathnameOfFileOfSequencesForScreening_ ) { fprintf( pFileToWrite, "consed.primersCloneFullPathnameOfFileOfSequencesForScreening: %s\n", resources_.soPrimersCloneFullPathnameOfFileOfSequencesForScreening_.data() ); } // consed.primersMinMeltingTemp if ( resources_.nPrimersMinMeltingTemp_ != CONDEF->nPrimersMinMeltingTemp_ ) { fprintf( pFileToWrite, "consed.primersMinMeltingTemp: %d\n", resources_.nPrimersMinMeltingTemp_ ); } // consed.primersMinMeltingTempForPCR if ( resources_.nPrimersMinMeltingTempForPCR_ != CONDEF->nPrimersMinMeltingTempForPCR_ ) { fprintf( pFileToWrite, "consed.primersMinMeltingTempForPCR: %d\n", resources_.nPrimersMinMeltingTempForPCR_ ); } // consed.searchFunctionsUseUnalignedEndsOfReads if ( resources_.bSearchFunctionsUseUnalignedEndsOfReads_ != CONDEF->bSearchFunctionsUseUnalignedEndsOfReads_ ) { fprintf( pFileToWrite, "consed.searchFunctionsUseUnalignedEndsOfReads: %s\n", ( resources_.bSearchFunctionsUseUnalignedEndsOfReads_ ? "true" : "false" ) ); } // consed.searchFunctionsUseLowQualityEndsOfReads if ( resources_.bSearchFunctionsUseLowQualityEndsOfReads_ != CONDEF->bSearchFunctionsUseLowQualityEndsOfReads_ ) { fprintf( pFileToWrite, "consed.searchFunctionsUseLowQualityEndsOfReads: %s\n", ( resources_.bSearchFunctionsUseLowQualityEndsOfReads_ ? "true" : "false" ) ); } // consed.inexactSearchForStringMaxPerCentMismatch if ( resources_.nInexactSearchForStringMaxPerCentMismatch_ != CONDEF->nInexactSearchForStringMaxPerCentMismatch_ ) { fprintf( pFileToWrite, "consed.inexactSearchForStringMaxPerCentMismatch: %d\n", resources_.nInexactSearchForStringMaxPerCentMismatch_ ); } // consed.onlyAllowOneReadWriteConsedAtATime if ( resources_.bOnlyAllowOneReadWriteConsedAtATime_ != CONDEF->bOnlyAllowOneReadWriteConsedAtATime_ ) { fprintf( pFileToWrite, "consed.onlyAllowOneReadWriteConsedAtATime: %s\n", ( resources_.bOnlyAllowOneReadWriteConsedAtATime_ ? "true" : "false" ) ); } // consed.autoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair if ( resources_.bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_ != CONDEF->bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair: %s\n", ( resources_.bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_ ? "true" : "false" ) ); } // consed.printWindowCommand if ( resources_.soPrintWindowCommand_ != CONDEF->soPrintWindowCommand_ ) { fprintf( pFileToWrite, "consed.printWindowCommand: %s\n", resources_.soPrintWindowCommand_.data() ); } // consed.fileOfTagTypes if ( resources_.filFileOfTagTypes_ != CONDEF->filFileOfTagTypes_ ) { fprintf( pFileToWrite, "consed.fileOfTagTypes: %s\n", resources_.filFileOfTagTypes_.data() ); } // consed.assemblyViewShowConsistentFwdRevPairs if ( resources_.bAssemblyViewShowConsistentFwdRevPairs_ != CONDEF->bAssemblyViewShowConsistentFwdRevPairs_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowConsistentFwdRevPairs: %s\n", ( resources_.bAssemblyViewShowConsistentFwdRevPairs_ ? "true" : "false" ) ); } // consed.assemblyViewShowConsistentFwdRevPairDepth if ( resources_.bAssemblyViewShowConsistentFwdRevPairDepth_ != CONDEF->bAssemblyViewShowConsistentFwdRevPairDepth_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowConsistentFwdRevPairDepth: %s\n", ( resources_.bAssemblyViewShowConsistentFwdRevPairDepth_ ? "true" : "false" ) ); } // consed.assemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds if ( resources_.bAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds_ != CONDEF->bAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds: %s\n", ( resources_.bAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds_ ? "true" : "false" ) ); } // consed.assemblyViewShowLegsOnSquaresForConsistentFwdRevPairs if ( resources_.bAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs_ != CONDEF->bAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowLegsOnSquaresForConsistentFwdRevPairs: %s\n", ( resources_.bAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs_ ? "true" : "false" ) ); } // consed.assemblyViewShowGapSpanningFwdRevPairs if ( resources_.bAssemblyViewShowGapSpanningFwdRevPairs_ != CONDEF->bAssemblyViewShowGapSpanningFwdRevPairs_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowGapSpanningFwdRevPairs: %s\n", ( resources_.bAssemblyViewShowGapSpanningFwdRevPairs_ ? "true" : "false" ) ); } // consed.assemblyViewShowWhichInconsistentFwdRevPairs if ( resources_.soAssemblyViewShowWhichInconsistentFwdRevPairs_ != CONDEF->soAssemblyViewShowWhichInconsistentFwdRevPairs_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowWhichInconsistentFwdRevPairs: %s\n", resources_.soAssemblyViewShowWhichInconsistentFwdRevPairs_.data() ); } // consed.assemblyViewShowReadDepth if ( resources_.bAssemblyViewShowReadDepth_ != CONDEF->bAssemblyViewShowReadDepth_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowReadDepth: %s\n", ( resources_.bAssemblyViewShowReadDepth_ ? "true" : "false" ) ); } // consed.assemblyViewShowMultipleHighQualityDiscrepancies if ( resources_.bAssemblyViewShowMultipleHighQualityDiscrepancies_ != CONDEF->bAssemblyViewShowMultipleHighQualityDiscrepancies_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowMultipleHighQualityDiscrepancies: %s\n", ( resources_.bAssemblyViewShowMultipleHighQualityDiscrepancies_ ? "true" : "false" ) ); } // consed.assemblyViewShowRestrictionDigestCutSites if ( resources_.bAssemblyViewShowRestrictionDigestCutSites_ != CONDEF->bAssemblyViewShowRestrictionDigestCutSites_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowRestrictionDigestCutSites: %s\n", ( resources_.bAssemblyViewShowRestrictionDigestCutSites_ ? "true" : "false" ) ); } // consed.assemblyViewFilterSequenceMatchesBySize if ( resources_.bAssemblyViewFilterSequenceMatchesBySize_ != CONDEF->bAssemblyViewFilterSequenceMatchesBySize_ ) { fprintf( pFileToWrite, "consed.assemblyViewFilterSequenceMatchesBySize: %s\n", ( resources_.bAssemblyViewFilterSequenceMatchesBySize_ ? "true" : "false" ) ); } // consed.assemblyViewSequenceMatchesMinSize if ( resources_.nAssemblyViewSequenceMatchesMinSize_ != CONDEF->nAssemblyViewSequenceMatchesMinSize_ ) { fprintf( pFileToWrite, "consed.assemblyViewSequenceMatchesMinSize: %d\n", resources_.nAssemblyViewSequenceMatchesMinSize_ ); } // consed.assemblyViewSequenceMatchesMaxSize if ( resources_.nAssemblyViewSequenceMatchesMaxSize_ != CONDEF->nAssemblyViewSequenceMatchesMaxSize_ ) { fprintf( pFileToWrite, "consed.assemblyViewSequenceMatchesMaxSize: %d\n", resources_.nAssemblyViewSequenceMatchesMaxSize_ ); } // consed.assemblyViewAutomaticallyStartWithConsed if ( resources_.bAssemblyViewAutomaticallyStartWithConsed_ != CONDEF->bAssemblyViewAutomaticallyStartWithConsed_ ) { fprintf( pFileToWrite, "consed.assemblyViewAutomaticallyStartWithConsed: %s\n", ( resources_.bAssemblyViewAutomaticallyStartWithConsed_ ? "true" : "false" ) ); } // consed.assemblyViewDisplayTheseTagTypesOnTheseLines if ( resources_.soAssemblyViewDisplayTheseTagTypesOnTheseLines_ != CONDEF->soAssemblyViewDisplayTheseTagTypesOnTheseLines_ ) { fprintf( pFileToWrite, "consed.assemblyViewDisplayTheseTagTypesOnTheseLines: %s\n", resources_.soAssemblyViewDisplayTheseTagTypesOnTheseLines_.data() ); } // consed.assemblyViewShowTags if ( resources_.bAssemblyViewShowTags_ != CONDEF->bAssemblyViewShowTags_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowTags: %s\n", ( resources_.bAssemblyViewShowTags_ ? "true" : "false" ) ); } // consed.autoEditRecalculateHighQualitySegmentsOfReads if ( resources_.bAutoEditRecalculateHighQualitySegmentsOfReads_ != CONDEF->bAutoEditRecalculateHighQualitySegmentsOfReads_ ) { fprintf( pFileToWrite, "consed.autoEditRecalculateHighQualitySegmentsOfReads: %s\n", ( resources_.bAutoEditRecalculateHighQualitySegmentsOfReads_ ? "true" : "false" ) ); } // consed.autoEditConvertCloneEndBasesToXs if ( resources_.bAutoEditConvertCloneEndBasesToXs_ != CONDEF->bAutoEditConvertCloneEndBasesToXs_ ) { fprintf( pFileToWrite, "consed.autoEditConvertCloneEndBasesToXs: %s\n", ( resources_.bAutoEditConvertCloneEndBasesToXs_ ? "true" : "false" ) ); } // consed.autoEditTellPhrapNotToOverlapMultiplyDiscrepantReads if ( resources_.bAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads_ != CONDEF->bAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads_ ) { fprintf( pFileToWrite, "consed.autoEditTellPhrapNotToOverlapMultiplyDiscrepantReads: %s\n", ( resources_.bAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads_ ? "true" : "false" ) ); } // consed.autoEditTagEditableLowConsensusQualityRegions if ( resources_.bAutoEditTagEditableLowConsensusQualityRegions_ != CONDEF->bAutoEditTagEditableLowConsensusQualityRegions_ ) { fprintf( pFileToWrite, "consed.autoEditTagEditableLowConsensusQualityRegions: %s\n", ( resources_.bAutoEditTagEditableLowConsensusQualityRegions_ ? "true" : "false" ) ); } // consed.autoEditMakeFakeRead if ( resources_.bAutoEditMakeFakeRead_ != CONDEF->bAutoEditMakeFakeRead_ ) { fprintf( pFileToWrite, "consed.autoEditMakeFakeRead: %s\n", ( resources_.bAutoEditMakeFakeRead_ ? "true" : "false" ) ); } // consed.autoEditMakeFakeReadFromRead1 if ( resources_.soAutoEditMakeFakeReadFromRead1_ != CONDEF->soAutoEditMakeFakeReadFromRead1_ ) { fprintf( pFileToWrite, "consed.autoEditMakeFakeReadFromRead1: %s\n", resources_.soAutoEditMakeFakeReadFromRead1_.data() ); } // consed.autoEditMakeFakeReadFromRead2 if ( resources_.soAutoEditMakeFakeReadFromRead2_ != CONDEF->soAutoEditMakeFakeReadFromRead2_ ) { fprintf( pFileToWrite, "consed.autoEditMakeFakeReadFromRead2: %s\n", resources_.soAutoEditMakeFakeReadFromRead2_.data() ); } // consed.autoEditMakeFakeReadName if ( resources_.soAutoEditMakeFakeReadName_ != CONDEF->soAutoEditMakeFakeReadName_ ) { fprintf( pFileToWrite, "consed.autoEditMakeFakeReadName: %s\n", resources_.soAutoEditMakeFakeReadName_.data() ); } // consed.autoEditMakeFakeReadFastaFilename if ( resources_.filAutoEditMakeFakeReadFastaFilename_ != CONDEF->filAutoEditMakeFakeReadFastaFilename_ ) { fprintf( pFileToWrite, "consed.autoEditMakeFakeReadFastaFilename: %s\n", resources_.filAutoEditMakeFakeReadFastaFilename_.data() ); } // consed.autoEditMergeAssembly if ( resources_.bAutoEditMergeAssembly_ != CONDEF->bAutoEditMergeAssembly_ ) { fprintf( pFileToWrite, "consed.autoEditMergeAssembly: %s\n", ( resources_.bAutoEditMergeAssembly_ ? "true" : "false" ) ); } // consed.autoEditSecondaryAceFile if ( resources_.filAutoEditSecondaryAceFile_ != CONDEF->filAutoEditSecondaryAceFile_ ) { fprintf( pFileToWrite, "consed.autoEditSecondaryAceFile: %s\n", resources_.filAutoEditSecondaryAceFile_.data() ); } // consed.autoEditFixRunsInConsensus if ( resources_.bAutoEditFixRunsInConsensus_ != CONDEF->bAutoEditFixRunsInConsensus_ ) { fprintf( pFileToWrite, "consed.autoEditFixRunsInConsensus: %s\n", ( resources_.bAutoEditFixRunsInConsensus_ ? "true" : "false" ) ); } // consed.showAllTracesJustShowGoodTraces if ( resources_.bShowAllTracesJustShowGoodTraces_ != CONDEF->bShowAllTracesJustShowGoodTraces_ ) { fprintf( pFileToWrite, "consed.showAllTracesJustShowGoodTraces: %s\n", ( resources_.bShowAllTracesJustShowGoodTraces_ ? "true" : "false" ) ); } // consed.addAlignedSequenceQualityOfBases if ( resources_.nAddAlignedSequenceQualityOfBases_ != CONDEF->nAddAlignedSequenceQualityOfBases_ ) { fprintf( pFileToWrite, "consed.addAlignedSequenceQualityOfBases: %d\n", resources_.nAddAlignedSequenceQualityOfBases_ ); } // consed.makeLightBackgroundInAlignedReadsWindowAndTracesWindow if ( resources_.bMakeLightBackgroundInAlignedReadsWindowAndTracesWindow_ != CONDEF->bMakeLightBackgroundInAlignedReadsWindowAndTracesWindow_ ) { fprintf( pFileToWrite, "consed.makeLightBackgroundInAlignedReadsWindowAndTracesWindow: %s\n", ( resources_.bMakeLightBackgroundInAlignedReadsWindowAndTracesWindow_ ? "true" : "false" ) ); } // consed.putVerticalLineAtCursor if ( resources_.bPutVerticalLineAtCursor_ != CONDEF->bPutVerticalLineAtCursor_ ) { fprintf( pFileToWrite, "consed.putVerticalLineAtCursor: %s\n", ( resources_.bPutVerticalLineAtCursor_ ? "true" : "false" ) ); } // consed.putHorizontalLineAtCursor if ( resources_.bPutHorizontalLineAtCursor_ != CONDEF->bPutHorizontalLineAtCursor_ ) { fprintf( pFileToWrite, "consed.putHorizontalLineAtCursor: %s\n", ( resources_.bPutHorizontalLineAtCursor_ ? "true" : "false" ) ); } // consed.highlightedReadsFile if ( resources_.filHighlightedReadsFile_ != CONDEF->filHighlightedReadsFile_ ) { fprintf( pFileToWrite, "consed.highlightedReadsFile: %s\n", resources_.filHighlightedReadsFile_.data() ); } // consed.autoReportPrintReadNamesInRegion if ( resources_.bAutoReportPrintReadNamesInRegion_ != CONDEF->bAutoReportPrintReadNamesInRegion_ ) { fprintf( pFileToWrite, "consed.autoReportPrintReadNamesInRegion: %s\n", ( resources_.bAutoReportPrintReadNamesInRegion_ ? "true" : "false" ) ); } // consed.autoReportPrintReadNamesInRegionContig if ( resources_.soAutoReportPrintReadNamesInRegionContig_ != CONDEF->soAutoReportPrintReadNamesInRegionContig_ ) { fprintf( pFileToWrite, "consed.autoReportPrintReadNamesInRegionContig: %s\n", resources_.soAutoReportPrintReadNamesInRegionContig_.data() ); } // consed.autoReportPrintReadNamesInRegionLeftPos if ( resources_.nAutoReportPrintReadNamesInRegionLeftPos_ != CONDEF->nAutoReportPrintReadNamesInRegionLeftPos_ ) { fprintf( pFileToWrite, "consed.autoReportPrintReadNamesInRegionLeftPos: %d\n", resources_.nAutoReportPrintReadNamesInRegionLeftPos_ ); } // consed.autoReportPrintReadNamesInRegionRightPos if ( resources_.nAutoReportPrintReadNamesInRegionRightPos_ != CONDEF->nAutoReportPrintReadNamesInRegionRightPos_ ) { fprintf( pFileToWrite, "consed.autoReportPrintReadNamesInRegionRightPos: %d\n", resources_.nAutoReportPrintReadNamesInRegionRightPos_ ); } // consed.autoReportPrintHighlyDiscrepantRegions if ( resources_.bAutoReportPrintHighlyDiscrepantRegions_ != CONDEF->bAutoReportPrintHighlyDiscrepantRegions_ ) { fprintf( pFileToWrite, "consed.autoReportPrintHighlyDiscrepantRegions: %s\n", ( resources_.bAutoReportPrintHighlyDiscrepantRegions_ ? "true" : "false" ) ); } // consed.autoReportPrintScaffolds if ( resources_.bAutoReportPrintScaffolds_ != CONDEF->bAutoReportPrintScaffolds_ ) { fprintf( pFileToWrite, "consed.autoReportPrintScaffolds: %s\n", ( resources_.bAutoReportPrintScaffolds_ ? "true" : "false" ) ); } // consed.numberUnpaddedConsensusAtUserDefined if ( resources_.bNumberUnpaddedConsensusAtUserDefined_ != CONDEF->bNumberUnpaddedConsensusAtUserDefined_ ) { fprintf( pFileToWrite, "consed.numberUnpaddedConsensusAtUserDefined: %s\n", ( resources_.bNumberUnpaddedConsensusAtUserDefined_ ? "true" : "false" ) ); } // consed.autoReportPrintHighQualityDiscrepancies if ( resources_.bAutoReportPrintHighQualityDiscrepancies_ != CONDEF->bAutoReportPrintHighQualityDiscrepancies_ ) { fprintf( pFileToWrite, "consed.autoReportPrintHighQualityDiscrepancies: %s\n", ( resources_.bAutoReportPrintHighQualityDiscrepancies_ ? "true" : "false" ) ); } // consed.autoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags if ( resources_.bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_ != CONDEF->bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_ ) { fprintf( pFileToWrite, "consed.autoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags: %s\n", ( resources_.bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_ ? "true" : "false" ) ); } // consed.autoReportHighQualityDiscrepanciesExcludeMostPads if ( resources_.bAutoReportHighQualityDiscrepanciesExcludeMostPads_ != CONDEF->bAutoReportHighQualityDiscrepanciesExcludeMostPads_ ) { fprintf( pFileToWrite, "consed.autoReportHighQualityDiscrepanciesExcludeMostPads: %s\n", ( resources_.bAutoReportHighQualityDiscrepanciesExcludeMostPads_ ? "true" : "false" ) ); } // consed.autoReportPrintLowConsensusQualityRegions if ( resources_.bAutoReportPrintLowConsensusQualityRegions_ != CONDEF->bAutoReportPrintLowConsensusQualityRegions_ ) { fprintf( pFileToWrite, "consed.autoReportPrintLowConsensusQualityRegions: %s\n", ( resources_.bAutoReportPrintLowConsensusQualityRegions_ ? "true" : "false" ) ); } // consed.autoReportPrintSingleSubcloneRegions if ( resources_.bAutoReportPrintSingleSubcloneRegions_ != CONDEF->bAutoReportPrintSingleSubcloneRegions_ ) { fprintf( pFileToWrite, "consed.autoReportPrintSingleSubcloneRegions: %s\n", ( resources_.bAutoReportPrintSingleSubcloneRegions_ ? "true" : "false" ) ); } // consed.autoReportPrintSingleStrandedRegions if ( resources_.bAutoReportPrintSingleStrandedRegions_ != CONDEF->bAutoReportPrintSingleStrandedRegions_ ) { fprintf( pFileToWrite, "consed.autoReportPrintSingleStrandedRegions: %s\n", ( resources_.bAutoReportPrintSingleStrandedRegions_ ? "true" : "false" ) ); } // consed.autoReportPrintLinkingForwardReversePairs if ( resources_.bAutoReportPrintLinkingForwardReversePairs_ != CONDEF->bAutoReportPrintLinkingForwardReversePairs_ ) { fprintf( pFileToWrite, "consed.autoReportPrintLinkingForwardReversePairs: %s\n", ( resources_.bAutoReportPrintLinkingForwardReversePairs_ ? "true" : "false" ) ); } // consed.autoReportPrintFilteredInconsistentForwardReversePairs if ( resources_.bAutoReportPrintFilteredInconsistentForwardReversePairs_ != CONDEF->bAutoReportPrintFilteredInconsistentForwardReversePairs_ ) { fprintf( pFileToWrite, "consed.autoReportPrintFilteredInconsistentForwardReversePairs: %s\n", ( resources_.bAutoReportPrintFilteredInconsistentForwardReversePairs_ ? "true" : "false" ) ); } // consed.autoReportPrintAssemblySummary if ( resources_.bAutoReportPrintAssemblySummary_ != CONDEF->bAutoReportPrintAssemblySummary_ ) { fprintf( pFileToWrite, "consed.autoReportPrintAssemblySummary: %s\n", ( resources_.bAutoReportPrintAssemblySummary_ ? "true" : "false" ) ); } // consed.showAllTracesDoNotShowTraceIfTheseTagsPresent if ( resources_.soShowAllTracesDoNotShowTraceIfTheseTagsPresent_ != CONDEF->soShowAllTracesDoNotShowTraceIfTheseTagsPresent_ ) { fprintf( pFileToWrite, "consed.showAllTracesDoNotShowTraceIfTheseTagsPresent: %s\n", resources_.soShowAllTracesDoNotShowTraceIfTheseTagsPresent_.data() ); } // consed.nameOfFakeJoiningReadsIncludesAceFileName if ( resources_.bNameOfFakeJoiningReadsIncludesAceFileName_ != CONDEF->bNameOfFakeJoiningReadsIncludesAceFileName_ ) { fprintf( pFileToWrite, "consed.nameOfFakeJoiningReadsIncludesAceFileName: %s\n", ( resources_.bNameOfFakeJoiningReadsIncludesAceFileName_ ? "true" : "false" ) ); } // consed.whenUserScrollsOffWindowMillisecondsBetweenScrolling if ( resources_.nWhenUserScrollsOffWindowMillisecondsBetweenScrolling_ != CONDEF->nWhenUserScrollsOffWindowMillisecondsBetweenScrolling_ ) { fprintf( pFileToWrite, "consed.whenUserScrollsOffWindowMillisecondsBetweenScrolling: %d\n", resources_.nWhenUserScrollsOffWindowMillisecondsBetweenScrolling_ ); } // consed.whenUserScrollsOffWindowBasesToScrollEachTime if ( resources_.nWhenUserScrollsOffWindowBasesToScrollEachTime_ != CONDEF->nWhenUserScrollsOffWindowBasesToScrollEachTime_ ) { fprintf( pFileToWrite, "consed.whenUserScrollsOffWindowBasesToScrollEachTime: %d\n", resources_.nWhenUserScrollsOffWindowBasesToScrollEachTime_ ); } // consed.compareContigsUseBandedRatherThanFullSmithWaterman if ( resources_.bCompareContigsUseBandedRatherThanFullSmithWaterman_ != CONDEF->bCompareContigsUseBandedRatherThanFullSmithWaterman_ ) { fprintf( pFileToWrite, "consed.compareContigsUseBandedRatherThanFullSmithWaterman: %s\n", ( resources_.bCompareContigsUseBandedRatherThanFullSmithWaterman_ ? "true" : "false" ) ); } // consed.compareContigsBandSize if ( resources_.nCompareContigsBandSize_ != CONDEF->nCompareContigsBandSize_ ) { fprintf( pFileToWrite, "consed.compareContigsBandSize: %d\n", resources_.nCompareContigsBandSize_ ); } // consed.assemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany if ( resources_.nAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany_ != CONDEF->nAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany: %d\n", resources_.nAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany_ ); } // consed.assemblyViewShowSequenceMatches if ( resources_.bAssemblyViewShowSequenceMatches_ != CONDEF->bAssemblyViewShowSequenceMatches_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowSequenceMatches: %s\n", ( resources_.bAssemblyViewShowSequenceMatches_ ? "true" : "false" ) ); } // consed.assemblyViewOKToShowSequenceMatchesBetweenContigs if ( resources_.bAssemblyViewOKToShowSequenceMatchesBetweenContigs_ != CONDEF->bAssemblyViewOKToShowSequenceMatchesBetweenContigs_ ) { fprintf( pFileToWrite, "consed.assemblyViewOKToShowSequenceMatchesBetweenContigs: %s\n", ( resources_.bAssemblyViewOKToShowSequenceMatchesBetweenContigs_ ? "true" : "false" ) ); } // consed.assemblyViewOKToShowSequenceMatchesWithinContigs if ( resources_.bAssemblyViewOKToShowSequenceMatchesWithinContigs_ != CONDEF->bAssemblyViewOKToShowSequenceMatchesWithinContigs_ ) { fprintf( pFileToWrite, "consed.assemblyViewOKToShowSequenceMatchesWithinContigs: %s\n", ( resources_.bAssemblyViewOKToShowSequenceMatchesWithinContigs_ ? "true" : "false" ) ); } // consed.assemblyViewOKToShowDirectSequenceMatches if ( resources_.bAssemblyViewOKToShowDirectSequenceMatches_ != CONDEF->bAssemblyViewOKToShowDirectSequenceMatches_ ) { fprintf( pFileToWrite, "consed.assemblyViewOKToShowDirectSequenceMatches: %s\n", ( resources_.bAssemblyViewOKToShowDirectSequenceMatches_ ? "true" : "false" ) ); } // consed.assemblyViewOKToShowInvertedSequenceMatches if ( resources_.bAssemblyViewOKToShowInvertedSequenceMatches_ != CONDEF->bAssemblyViewOKToShowInvertedSequenceMatches_ ) { fprintf( pFileToWrite, "consed.assemblyViewOKToShowInvertedSequenceMatches: %s\n", ( resources_.bAssemblyViewOKToShowInvertedSequenceMatches_ ? "true" : "false" ) ); } // consed.assemblyViewOnlyShowSequenceMatchesToAParticularRegion if ( resources_.bAssemblyViewOnlyShowSequenceMatchesToAParticularRegion_ != CONDEF->bAssemblyViewOnlyShowSequenceMatchesToAParticularRegion_ ) { fprintf( pFileToWrite, "consed.assemblyViewOnlyShowSequenceMatchesToAParticularRegion: %s\n", ( resources_.bAssemblyViewOnlyShowSequenceMatchesToAParticularRegion_ ? "true" : "false" ) ); } // consed.assemblyViewOnlyShowSequenceMatchesToThisContig if ( resources_.soAssemblyViewOnlyShowSequenceMatchesToThisContig_ != CONDEF->soAssemblyViewOnlyShowSequenceMatchesToThisContig_ ) { fprintf( pFileToWrite, "consed.assemblyViewOnlyShowSequenceMatchesToThisContig: %s\n", resources_.soAssemblyViewOnlyShowSequenceMatchesToThisContig_.data() ); } // consed.assemblyViewOnlyShowSequenceMatchesToThisRegionLeft if ( resources_.nAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft_ != CONDEF->nAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft_ ) { fprintf( pFileToWrite, "consed.assemblyViewOnlyShowSequenceMatchesToThisRegionLeft: %d\n", resources_.nAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft_ ); } // consed.assemblyViewOnlyShowSequenceMatchesToThisRegionRight if ( resources_.nAssemblyViewOnlyShowSequenceMatchesToThisRegionRight_ != CONDEF->nAssemblyViewOnlyShowSequenceMatchesToThisRegionRight_ ) { fprintf( pFileToWrite, "consed.assemblyViewOnlyShowSequenceMatchesToThisRegionRight: %d\n", resources_.nAssemblyViewOnlyShowSequenceMatchesToThisRegionRight_ ); } // consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigs if ( resources_.bAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs_ != CONDEF->bAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs_ ) { fprintf( pFileToWrite, "consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigs: %s\n", ( resources_.bAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs_ ? "true" : "false" ) ); } // consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar if ( resources_.nAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar_ != CONDEF->nAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar_ ) { fprintf( pFileToWrite, "consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar: %d\n", resources_.nAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar_ ); } // consed.defaultReadPrefix if ( resources_.soDefaultReadPrefix_ != CONDEF->soDefaultReadPrefix_ ) { fprintf( pFileToWrite, "consed.defaultReadPrefix: %s\n", resources_.soDefaultReadPrefix_.data() ); } // consed.readPrefixesFile if ( resources_.filReadPrefixesFile_ != CONDEF->filReadPrefixesFile_ ) { fprintf( pFileToWrite, "consed.readPrefixesFile: %s\n", resources_.filReadPrefixesFile_.data() ); } // consed.maxCharsDisplayedForReadPrefix if ( resources_.nMaxCharsDisplayedForReadPrefix_ != CONDEF->nMaxCharsDisplayedForReadPrefix_ ) { fprintf( pFileToWrite, "consed.maxCharsDisplayedForReadPrefix: %d\n", resources_.nMaxCharsDisplayedForReadPrefix_ ); } // consed.autoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates if ( resources_.nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_ != CONDEF->nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates: %d\n", resources_.nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_ ); } // consed.autoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions if ( resources_.nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_ != CONDEF->nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions: %d\n", resources_.nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_ ); } // consed.autoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis if ( resources_.nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_ != CONDEF->nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis: %d\n", resources_.nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_ ); } // consed.autoFinishDoNotDoPCRIfEndIsExtendedByReads if ( resources_.bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_ != CONDEF->bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotDoPCRIfEndIsExtendedByReads: %s\n", ( resources_.bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_ ? "true" : "false" ) ); } // consed.autoFinishMaxAcceptableErrorsPerMegabase if ( resources_.nAutoFinishMaxAcceptableErrorsPerMegabase_ != CONDEF->nAutoFinishMaxAcceptableErrorsPerMegabase_ ) { fprintf( pFileToWrite, "consed.autoFinishMaxAcceptableErrorsPerMegabase: %d\n", resources_.nAutoFinishMaxAcceptableErrorsPerMegabase_ ); } // consed.autoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize if ( resources_.nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_ != CONDEF->nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_ ) { fprintf( pFileToWrite, "consed.autoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize: %d\n", resources_.nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_ ); } // consed.primersNumberOfBasesToBackUpToStartLooking if ( resources_.nPrimersNumberOfBasesToBackUpToStartLooking_ != CONDEF->nPrimersNumberOfBasesToBackUpToStartLooking_ ) { fprintf( pFileToWrite, "consed.primersNumberOfBasesToBackUpToStartLooking: %d\n", resources_.nPrimersNumberOfBasesToBackUpToStartLooking_ ); } // consed.primersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment if ( resources_.nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_ != CONDEF->nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_ ) { fprintf( pFileToWrite, "consed.primersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment: %d\n", resources_.nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_ ); } // consed.primersOKToChoosePrimersInSingleSubcloneRegion if ( resources_.bPrimersOKToChoosePrimersInSingleSubcloneRegion_ != CONDEF->bPrimersOKToChoosePrimersInSingleSubcloneRegion_ ) { fprintf( pFileToWrite, "consed.primersOKToChoosePrimersInSingleSubcloneRegion: %s\n", ( resources_.bPrimersOKToChoosePrimersInSingleSubcloneRegion_ ? "true" : "false" ) ); } // consed.primersOKToChoosePrimersWhereHighQualityDiscrepancies if ( resources_.bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_ != CONDEF->bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_ ) { fprintf( pFileToWrite, "consed.primersOKToChoosePrimersWhereHighQualityDiscrepancies: %s\n", ( resources_.bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_ ? "true" : "false" ) ); } // consed.primersOKToChoosePrimersWhereUnalignedHighQualityRegion if ( resources_.bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_ != CONDEF->bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_ ) { fprintf( pFileToWrite, "consed.primersOKToChoosePrimersWhereUnalignedHighQualityRegion: %s\n", ( resources_.bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_ ? "true" : "false" ) ); } // consed.autoFinishCallReversesToFlankGaps if ( resources_.bAutoFinishCallReversesToFlankGaps_ != CONDEF->bAutoFinishCallReversesToFlankGaps_ ) { fprintf( pFileToWrite, "consed.autoFinishCallReversesToFlankGaps: %s\n", ( resources_.bAutoFinishCallReversesToFlankGaps_ ? "true" : "false" ) ); } // consed.autoFinishAllowWholeCloneReads if ( resources_.bAutoFinishAllowWholeCloneReads_ != CONDEF->bAutoFinishAllowWholeCloneReads_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowWholeCloneReads: %s\n", ( resources_.bAutoFinishAllowWholeCloneReads_ ? "true" : "false" ) ); } // consed.autoFinishAllowCustomPrimerSubcloneReads if ( resources_.bAutoFinishAllowCustomPrimerSubcloneReads_ != CONDEF->bAutoFinishAllowCustomPrimerSubcloneReads_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowCustomPrimerSubcloneReads: %s\n", ( resources_.bAutoFinishAllowCustomPrimerSubcloneReads_ ? "true" : "false" ) ); } // consed.autoFinishAllowResequencingReads if ( resources_.bAutoFinishAllowResequencingReads_ != CONDEF->bAutoFinishAllowResequencingReads_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowResequencingReads: %s\n", ( resources_.bAutoFinishAllowResequencingReads_ ? "true" : "false" ) ); } // consed.autoFinishAllowResequencingReadsOnlyForRunsAndStops if ( resources_.bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_ != CONDEF->bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowResequencingReadsOnlyForRunsAndStops: %s\n", ( resources_.bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_ ? "true" : "false" ) ); } // consed.autoFinishAllowDeNovoUniversalPrimerSubcloneReads if ( resources_.bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_ != CONDEF->bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowDeNovoUniversalPrimerSubcloneReads: %s\n", ( resources_.bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_ ? "true" : "false" ) ); } // consed.autoFinishAllowMinilibraries if ( resources_.bAutoFinishAllowMinilibraries_ != CONDEF->bAutoFinishAllowMinilibraries_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowMinilibraries: %s\n", ( resources_.bAutoFinishAllowMinilibraries_ ? "true" : "false" ) ); } // consed.autoFinishAllowPCR if ( resources_.bAutoFinishAllowPCR_ != CONDEF->bAutoFinishAllowPCR_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowPCR: %s\n", ( resources_.bAutoFinishAllowPCR_ ? "true" : "false" ) ); } // consed.autoFinishAllowUnorientedPCRReactions if ( resources_.bAutoFinishAllowUnorientedPCRReactions_ != CONDEF->bAutoFinishAllowUnorientedPCRReactions_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowUnorientedPCRReactions: %s\n", ( resources_.bAutoFinishAllowUnorientedPCRReactions_ ? "true" : "false" ) ); } // consed.autoFinishAllowResequencingAUniversalPrimerAutofinishRead if ( resources_.bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_ != CONDEF->bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowResequencingAUniversalPrimerAutofinishRead: %s\n", ( resources_.bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_ ? "true" : "false" ) ); } // consed.autoFinishAlwaysCloseGapsUsingMinilibraries if ( resources_.bAutoFinishAlwaysCloseGapsUsingMinilibraries_ != CONDEF->bAutoFinishAlwaysCloseGapsUsingMinilibraries_ ) { fprintf( pFileToWrite, "consed.autoFinishAlwaysCloseGapsUsingMinilibraries: %s\n", ( resources_.bAutoFinishAlwaysCloseGapsUsingMinilibraries_ ? "true" : "false" ) ); } // consed.autoFinishMaximumFinishingReadLength if ( resources_.nAutoFinishMaximumFinishingReadLength_ != CONDEF->nAutoFinishMaximumFinishingReadLength_ ) { fprintf( pFileToWrite, "consed.autoFinishMaximumFinishingReadLength: %d\n", resources_.nAutoFinishMaximumFinishingReadLength_ ); } // consed.autoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger if ( resources_.nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_ != CONDEF->nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_ ) { fprintf( pFileToWrite, "consed.autoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger: %d\n", resources_.nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_ ); } // consed.autoFinishSuggestSpecialChemistryForRunsAndStops if ( resources_.bAutoFinishSuggestSpecialChemistryForRunsAndStops_ != CONDEF->bAutoFinishSuggestSpecialChemistryForRunsAndStops_ ) { fprintf( pFileToWrite, "consed.autoFinishSuggestSpecialChemistryForRunsAndStops: %s\n", ( resources_.bAutoFinishSuggestSpecialChemistryForRunsAndStops_ ? "true" : "false" ) ); } // consed.autoFinishSuggestThisManyMinilibrariesPerGap if ( resources_.nAutoFinishSuggestThisManyMinilibrariesPerGap_ != CONDEF->nAutoFinishSuggestThisManyMinilibrariesPerGap_ ) { fprintf( pFileToWrite, "consed.autoFinishSuggestThisManyMinilibrariesPerGap: %d\n", resources_.nAutoFinishSuggestThisManyMinilibrariesPerGap_ ); } // consed.primersWindowSizeInLooking if ( resources_.nPrimersWindowSizeInLooking_ != CONDEF->nPrimersWindowSizeInLooking_ ) { fprintf( pFileToWrite, "consed.primersWindowSizeInLooking: %d\n", resources_.nPrimersWindowSizeInLooking_ ); } // consed.primersAssumeTemplatesAreDoubleStrandedUnlessSpecified if ( resources_.bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_ != CONDEF->bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_ ) { fprintf( pFileToWrite, "consed.primersAssumeTemplatesAreDoubleStrandedUnlessSpecified: %s\n", ( resources_.bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_ ? "true" : "false" ) ); } // consed.alignedReadsWindowInitialCharsWide if ( resources_.nAlignedReadsWindowInitialCharsWide_ != CONDEF->nAlignedReadsWindowInitialCharsWide_ ) { fprintf( pFileToWrite, "consed.alignedReadsWindowInitialCharsWide: %d\n", resources_.nAlignedReadsWindowInitialCharsWide_ ); } // consed.alignedReadsWindowInitialCharsHigh if ( resources_.nAlignedReadsWindowInitialCharsHigh_ != CONDEF->nAlignedReadsWindowInitialCharsHigh_ ) { fprintf( pFileToWrite, "consed.alignedReadsWindowInitialCharsHigh: %d\n", resources_.nAlignedReadsWindowInitialCharsHigh_ ); } // consed.alignedReadsWindowMaxCharsForReadNames if ( resources_.nAlignedReadsWindowMaxCharsForReadNames_ != CONDEF->nAlignedReadsWindowMaxCharsForReadNames_ ) { fprintf( pFileToWrite, "consed.alignedReadsWindowMaxCharsForReadNames: %d\n", resources_.nAlignedReadsWindowMaxCharsForReadNames_ ); } // consed.alignedReadsWindowAutomaticallyExpandRoomForReadNames if ( resources_.bAlignedReadsWindowAutomaticallyExpandRoomForReadNames_ != CONDEF->bAlignedReadsWindowAutomaticallyExpandRoomForReadNames_ ) { fprintf( pFileToWrite, "consed.alignedReadsWindowAutomaticallyExpandRoomForReadNames: %s\n", ( resources_.bAlignedReadsWindowAutomaticallyExpandRoomForReadNames_ ? "true" : "false" ) ); } // consed.autoFinishAllowResequencingReadsToExtendContigs if ( resources_.bAutoFinishAllowResequencingReadsToExtendContigs_ != CONDEF->bAutoFinishAllowResequencingReadsToExtendContigs_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowResequencingReadsToExtendContigs: %s\n", ( resources_.bAutoFinishAllowResequencingReadsToExtendContigs_ ? "true" : "false" ) ); } // consed.autoFinishCallHowManyReversesToFlankGaps if ( resources_.nAutoFinishCallHowManyReversesToFlankGaps_ != CONDEF->nAutoFinishCallHowManyReversesToFlankGaps_ ) { fprintf( pFileToWrite, "consed.autoFinishCallHowManyReversesToFlankGaps: %d\n", resources_.nAutoFinishCallHowManyReversesToFlankGaps_ ); } // consed.autoFinishCloseGaps if ( resources_.bAutoFinishCloseGaps_ != CONDEF->bAutoFinishCloseGaps_ ) { fprintf( pFileToWrite, "consed.autoFinishCloseGaps: %s\n", ( resources_.bAutoFinishCloseGaps_ ? "true" : "false" ) ); } // consed.autoFinishContinueEvenThoughReadInfoDoesNotMakeSense if ( resources_.bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_ != CONDEF->bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_ ) { fprintf( pFileToWrite, "consed.autoFinishContinueEvenThoughReadInfoDoesNotMakeSense: %s\n", ( resources_.bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_ ? "true" : "false" ) ); } // consed.autoFinishCostOfResequencingUniversalPrimerSubcloneReaction if ( resources_.dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_ != CONDEF->dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_ ) { fprintf( pFileToWrite, "consed.autoFinishCostOfResequencingUniversalPrimerSubcloneReaction: %f\n", resources_.dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_ ); } // consed.autoFinishCostOfCustomPrimerSubcloneReaction if ( resources_.dAutoFinishCostOfCustomPrimerSubcloneReaction_ != CONDEF->dAutoFinishCostOfCustomPrimerSubcloneReaction_ ) { fprintf( pFileToWrite, "consed.autoFinishCostOfCustomPrimerSubcloneReaction: %f\n", resources_.dAutoFinishCostOfCustomPrimerSubcloneReaction_ ); } // consed.autoFinishCostOfCustomPrimerCloneReaction if ( resources_.dAutoFinishCostOfCustomPrimerCloneReaction_ != CONDEF->dAutoFinishCostOfCustomPrimerCloneReaction_ ) { fprintf( pFileToWrite, "consed.autoFinishCostOfCustomPrimerCloneReaction: %f\n", resources_.dAutoFinishCostOfCustomPrimerCloneReaction_ ); } // consed.autoFinishCostOfDeNovoUniversalPrimerSubcloneReaction if ( resources_.dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_ != CONDEF->dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_ ) { fprintf( pFileToWrite, "consed.autoFinishCostOfDeNovoUniversalPrimerSubcloneReaction: %f\n", resources_.dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_ ); } // consed.autoFinishCostOfMinilibrary if ( resources_.dAutoFinishCostOfMinilibrary_ != CONDEF->dAutoFinishCostOfMinilibrary_ ) { fprintf( pFileToWrite, "consed.autoFinishCostOfMinilibrary: %f\n", resources_.dAutoFinishCostOfMinilibrary_ ); } // consed.autoFinishCoverSingleSubcloneRegions if ( resources_.bAutoFinishCoverSingleSubcloneRegions_ != CONDEF->bAutoFinishCoverSingleSubcloneRegions_ ) { fprintf( pFileToWrite, "consed.autoFinishCoverSingleSubcloneRegions: %s\n", ( resources_.bAutoFinishCoverSingleSubcloneRegions_ ? "true" : "false" ) ); } // consed.autoFinishCoverLowConsensusQualityRegions if ( resources_.bAutoFinishCoverLowConsensusQualityRegions_ != CONDEF->bAutoFinishCoverLowConsensusQualityRegions_ ) { fprintf( pFileToWrite, "consed.autoFinishCoverLowConsensusQualityRegions: %s\n", ( resources_.bAutoFinishCoverLowConsensusQualityRegions_ ? "true" : "false" ) ); } // consed.autoFinishDebugUniversalPrimerReadsFile if ( resources_.filAutoFinishDebugUniversalPrimerReadsFile_ != CONDEF->filAutoFinishDebugUniversalPrimerReadsFile_ ) { fprintf( pFileToWrite, "consed.autoFinishDebugUniversalPrimerReadsFile: %s\n", resources_.filAutoFinishDebugUniversalPrimerReadsFile_.data() ); } // consed.autoFinishDebugCustomPrimerReadsFile if ( resources_.filAutoFinishDebugCustomPrimerReadsFile_ != CONDEF->filAutoFinishDebugCustomPrimerReadsFile_ ) { fprintf( pFileToWrite, "consed.autoFinishDebugCustomPrimerReadsFile: %s\n", resources_.filAutoFinishDebugCustomPrimerReadsFile_.data() ); } // consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases if ( resources_.nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_ != CONDEF->nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases: %d\n", resources_.nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_ ); } // consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases if ( resources_.nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_ != CONDEF->nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases: %d\n", resources_.nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_ ); } // consed.autoFinishDoNotFinishWhereTheseTagsAre if ( resources_.soAutoFinishDoNotFinishWhereTheseTagsAre_ != CONDEF->soAutoFinishDoNotFinishWhereTheseTagsAre_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotFinishWhereTheseTagsAre: %s\n", resources_.soAutoFinishDoNotFinishWhereTheseTagsAre_.data() ); } // consed.autoFinishDoNotExtendContigsWhereTheseTagsAre if ( resources_.soAutoFinishDoNotExtendContigsWhereTheseTagsAre_ != CONDEF->soAutoFinishDoNotExtendContigsWhereTheseTagsAre_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotExtendContigsWhereTheseTagsAre: %s\n", resources_.soAutoFinishDoNotExtendContigsWhereTheseTagsAre_.data() ); } // consed.autoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd if ( resources_.nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_ != CONDEF->nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd: %d\n", resources_.nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_ ); } // consed.dumpContigOrderAndOrientationInfoToThisFile if ( resources_.filDumpContigOrderAndOrientationInfoToThisFile_ != CONDEF->filDumpContigOrderAndOrientationInfoToThisFile_ ) { fprintf( pFileToWrite, "consed.dumpContigOrderAndOrientationInfoToThisFile: %s\n", resources_.filDumpContigOrderAndOrientationInfoToThisFile_.data() ); } // consed.autoFinishDumpTemplates if ( resources_.bAutoFinishDumpTemplates_ != CONDEF->bAutoFinishDumpTemplates_ ) { fprintf( pFileToWrite, "consed.autoFinishDumpTemplates: %s\n", ( resources_.bAutoFinishDumpTemplates_ ? "true" : "false" ) ); } // consed.autoFinishExcludeContigIfOnlyThisManyReadsOrLess if ( resources_.nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_ != CONDEF->nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_ ) { fprintf( pFileToWrite, "consed.autoFinishExcludeContigIfOnlyThisManyReadsOrLess: %d\n", resources_.nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_ ); } // consed.autoFinishExcludeContigIfDepthOfCoverageGreaterThanThis if ( resources_.dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_ != CONDEF->dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_ ) { fprintf( pFileToWrite, "consed.autoFinishExcludeContigIfDepthOfCoverageGreaterThanThis: %f\n", resources_.dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_ ); } // consed.autoFinishExcludeContigIfThisManyBasesOrLess if ( resources_.nAutoFinishExcludeContigIfThisManyBasesOrLess_ != CONDEF->nAutoFinishExcludeContigIfThisManyBasesOrLess_ ) { fprintf( pFileToWrite, "consed.autoFinishExcludeContigIfThisManyBasesOrLess: %d\n", resources_.nAutoFinishExcludeContigIfThisManyBasesOrLess_ ); } // consed.autoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions if ( resources_.nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_ != CONDEF->nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_ ) { fprintf( pFileToWrite, "consed.autoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions: %d\n", resources_.nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_ ); } // consed.primersMinNumberOfTemplatesForPrimers if ( resources_.nPrimersMinNumberOfTemplatesForPrimers_ != CONDEF->nPrimersMinNumberOfTemplatesForPrimers_ ) { fprintf( pFileToWrite, "consed.primersMinNumberOfTemplatesForPrimers: %d\n", resources_.nPrimersMinNumberOfTemplatesForPrimers_ ); } // consed.autoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus if ( resources_.nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_ != CONDEF->nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_ ) { fprintf( pFileToWrite, "consed.autoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus: %d\n", resources_.nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_ ); } // consed.autoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead if ( resources_.nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_ != CONDEF->nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_ ) { fprintf( pFileToWrite, "consed.autoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead: %d\n", resources_.nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_ ); } // consed.autoFinishCDNANotGenomic if ( resources_.bAutoFinishCDNANotGenomic_ != CONDEF->bAutoFinishCDNANotGenomic_ ) { fprintf( pFileToWrite, "consed.autoFinishCDNANotGenomic: %s\n", ( resources_.bAutoFinishCDNANotGenomic_ ? "true" : "false" ) ); } // consed.autoFinishConfidenceThatReadWillCoverSingleSubcloneRegion if ( resources_.nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ != CONDEF->nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ ) { fprintf( pFileToWrite, "consed.autoFinishConfidenceThatReadWillCoverSingleSubcloneRegion: %d\n", resources_.nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ ); } // consed.autoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads if ( resources_.bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_ != CONDEF->bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_ ) { fprintf( pFileToWrite, "consed.autoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads: %s\n", ( resources_.bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_ ? "true" : "false" ) ); } // consed.autoFinishPrintMinilibrariesSummaryFile if ( resources_.bAutoFinishPrintMinilibrariesSummaryFile_ != CONDEF->bAutoFinishPrintMinilibrariesSummaryFile_ ) { fprintf( pFileToWrite, "consed.autoFinishPrintMinilibrariesSummaryFile: %s\n", ( resources_.bAutoFinishPrintMinilibrariesSummaryFile_ ? "true" : "false" ) ); } // consed.autoFinishNearGapsSuggestEachMissingReadOfReadPairs if ( resources_.bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_ != CONDEF->bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_ ) { fprintf( pFileToWrite, "consed.autoFinishNearGapsSuggestEachMissingReadOfReadPairs: %s\n", ( resources_.bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_ ? "true" : "false" ) ); } // consed.autoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger if ( resources_.nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_ != CONDEF->nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger: %d\n", resources_.nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_ ); } // consed.checkIfTooManyWalks if ( resources_.bCheckIfTooManyWalks_ != CONDEF->bCheckIfTooManyWalks_ ) { fprintf( pFileToWrite, "consed.checkIfTooManyWalks: %s\n", ( resources_.bCheckIfTooManyWalks_ ? "true" : "false" ) ); } // consed.numberOfColumnsBeforeReadNameInAlignedReadsWindow if ( resources_.nNumberOfColumnsBeforeReadNameInAlignedReadsWindow_ != CONDEF->nNumberOfColumnsBeforeReadNameInAlignedReadsWindow_ ) { fprintf( pFileToWrite, "consed.numberOfColumnsBeforeReadNameInAlignedReadsWindow: %d\n", resources_.nNumberOfColumnsBeforeReadNameInAlignedReadsWindow_ ); } // consed.compareContigsAlignsThisManyBasesMax if ( resources_.nCompareContigsAlignsThisManyBasesMax_ != CONDEF->nCompareContigsAlignsThisManyBasesMax_ ) { fprintf( pFileToWrite, "consed.compareContigsAlignsThisManyBasesMax: %d\n", resources_.nCompareContigsAlignsThisManyBasesMax_ ); } // consed.compressedChromatExtension if ( resources_.soCompressedChromatExtension_ != CONDEF->soCompressedChromatExtension_ ) { fprintf( pFileToWrite, "consed.compressedChromatExtension: %s\n", resources_.soCompressedChromatExtension_.data() ); } // consed.dimLowQualityEndsOfReads if ( resources_.bDimLowQualityEndsOfReads_ != CONDEF->bDimLowQualityEndsOfReads_ ) { fprintf( pFileToWrite, "consed.dimLowQualityEndsOfReads: %s\n", ( resources_.bDimLowQualityEndsOfReads_ ? "true" : "false" ) ); } // consed.dimUnalignedEndsOfReads if ( resources_.bDimUnalignedEndsOfReads_ != CONDEF->bDimUnalignedEndsOfReads_ ) { fprintf( pFileToWrite, "consed.dimUnalignedEndsOfReads: %s\n", ( resources_.bDimUnalignedEndsOfReads_ ? "true" : "false" ) ); } // consed.fakeReadsSpecifiedByFilenameExtension if ( resources_.bFakeReadsSpecifiedByFilenameExtension_ != CONDEF->bFakeReadsSpecifiedByFilenameExtension_ ) { fprintf( pFileToWrite, "consed.fakeReadsSpecifiedByFilenameExtension: %s\n", ( resources_.bFakeReadsSpecifiedByFilenameExtension_ ? "true" : "false" ) ); } // consed.fullPathnameOfAddReads2ConsedScript if ( resources_.filFullPathnameOfAddReads2ConsedScript_ != CONDEF->filFullPathnameOfAddReads2ConsedScript_ ) { fprintf( pFileToWrite, "consed.fullPathnameOfAddReads2ConsedScript: %s\n", resources_.filFullPathnameOfAddReads2ConsedScript_.data() ); } // consed.fullPathnameOfFixContigEndScript if ( resources_.filFullPathnameOfFixContigEndScript_ != CONDEF->filFullPathnameOfFixContigEndScript_ ) { fprintf( pFileToWrite, "consed.fullPathnameOfFixContigEndScript: %s\n", resources_.filFullPathnameOfFixContigEndScript_.data() ); } // consed.fixContigEndsCleanUpTemporaryFiles if ( resources_.bFixContigEndsCleanUpTemporaryFiles_ != CONDEF->bFixContigEndsCleanUpTemporaryFiles_ ) { fprintf( pFileToWrite, "consed.fixContigEndsCleanUpTemporaryFiles: %s\n", ( resources_.bFixContigEndsCleanUpTemporaryFiles_ ? "true" : "false" ) ); } // consed.fixContigEndsMinSmithWatermanScoreToMakeJoin if ( resources_.nFixContigEndsMinSmithWatermanScoreToMakeJoin_ != CONDEF->nFixContigEndsMinSmithWatermanScoreToMakeJoin_ ) { fprintf( pFileToWrite, "consed.fixContigEndsMinSmithWatermanScoreToMakeJoin: %d\n", resources_.nFixContigEndsMinSmithWatermanScoreToMakeJoin_ ); } // consed.fixContigEndsMinNumberOfReadsInContig if ( resources_.nFixContigEndsMinNumberOfReadsInContig_ != CONDEF->nFixContigEndsMinNumberOfReadsInContig_ ) { fprintf( pFileToWrite, "consed.fixContigEndsMinNumberOfReadsInContig: %d\n", resources_.nFixContigEndsMinNumberOfReadsInContig_ ); } // consed.fullPathnameOfCrossMatch if ( resources_.filFullPathnameOfCrossMatch_ != CONDEF->filFullPathnameOfCrossMatch_ ) { fprintf( pFileToWrite, "consed.fullPathnameOfCrossMatch: %s\n", resources_.filFullPathnameOfCrossMatch_.data() ); } // consed.fullPathnameOfPhred if ( resources_.filFullPathnameOfPhred_ != CONDEF->filFullPathnameOfPhred_ ) { fprintf( pFileToWrite, "consed.fullPathnameOfPhred: %s\n", resources_.filFullPathnameOfPhred_.data() ); } // consed.fullPathnameOfMiniassemblyScript if ( resources_.filFullPathnameOfMiniassemblyScript_ != CONDEF->filFullPathnameOfMiniassemblyScript_ ) { fprintf( pFileToWrite, "consed.fullPathnameOfMiniassemblyScript: %s\n", resources_.filFullPathnameOfMiniassemblyScript_.data() ); } // consed.gunzipFullPath if ( resources_.soGunzipFullPath_ != CONDEF->soGunzipFullPath_ ) { fprintf( pFileToWrite, "consed.gunzipFullPath: %s\n", resources_.soGunzipFullPath_.data() ); } // consed.fullPathnameOfFilter454ReadsScript if ( resources_.filFullPathnameOfFilter454ReadsScript_ != CONDEF->filFullPathnameOfFilter454ReadsScript_ ) { fprintf( pFileToWrite, "consed.fullPathnameOfFilter454ReadsScript: %s\n", resources_.filFullPathnameOfFilter454ReadsScript_.data() ); } // consed.filter454ReadsAgainstThis if ( resources_.filFilter454ReadsAgainstThis_ != CONDEF->filFilter454ReadsAgainstThis_ ) { fprintf( pFileToWrite, "consed.filter454ReadsAgainstThis: %s\n", resources_.filFilter454ReadsAgainstThis_.data() ); } // consed.454LinkerSequences if ( resources_.fil454LinkerSequences_ != CONDEF->fil454LinkerSequences_ ) { fprintf( pFileToWrite, "consed.454LinkerSequences: %s\n", resources_.fil454LinkerSequences_.data() ); } // consed.hideSomeTagTypesAtStartup if ( resources_.bHideSomeTagTypesAtStartup_ != CONDEF->bHideSomeTagTypesAtStartup_ ) { fprintf( pFileToWrite, "consed.hideSomeTagTypesAtStartup: %s\n", ( resources_.bHideSomeTagTypesAtStartup_ ? "true" : "false" ) ); } // consed.maximumNumberOfTracesShown if ( resources_.nMaximumNumberOfTracesShown_ != CONDEF->nMaximumNumberOfTracesShown_ ) { fprintf( pFileToWrite, "consed.maximumNumberOfTracesShown: %d\n", resources_.nMaximumNumberOfTracesShown_ ); } // consed.navigateAutomaticTracePopup if ( resources_.bNavigateAutomaticTracePopup_ != CONDEF->bNavigateAutomaticTracePopup_ ) { fprintf( pFileToWrite, "consed.navigateAutomaticTracePopup: %s\n", ( resources_.bNavigateAutomaticTracePopup_ ? "true" : "false" ) ); } // consed.navigateAutomaticAllTracesPopup if ( resources_.bNavigateAutomaticAllTracesPopup_ != CONDEF->bNavigateAutomaticAllTracesPopup_ ) { fprintf( pFileToWrite, "consed.navigateAutomaticAllTracesPopup: %s\n", ( resources_.bNavigateAutomaticAllTracesPopup_ ? "true" : "false" ) ); } // consed.primersMinimumLengthOfAPrimer if ( resources_.nPrimersMinimumLengthOfAPrimer_ != CONDEF->nPrimersMinimumLengthOfAPrimer_ ) { fprintf( pFileToWrite, "consed.primersMinimumLengthOfAPrimer: %d\n", resources_.nPrimersMinimumLengthOfAPrimer_ ); } // consed.primersMaximumLengthOfAPrimer if ( resources_.nPrimersMaximumLengthOfAPrimer_ != CONDEF->nPrimersMaximumLengthOfAPrimer_ ) { fprintf( pFileToWrite, "consed.primersMaximumLengthOfAPrimer: %d\n", resources_.nPrimersMaximumLengthOfAPrimer_ ); } // consed.primersMinimumLengthOfAPrimerForPCR if ( resources_.nPrimersMinimumLengthOfAPrimerForPCR_ != CONDEF->nPrimersMinimumLengthOfAPrimerForPCR_ ) { fprintf( pFileToWrite, "consed.primersMinimumLengthOfAPrimerForPCR: %d\n", resources_.nPrimersMinimumLengthOfAPrimerForPCR_ ); } // consed.primersMaximumLengthOfAPrimerForPCR if ( resources_.nPrimersMaximumLengthOfAPrimerForPCR_ != CONDEF->nPrimersMaximumLengthOfAPrimerForPCR_ ) { fprintf( pFileToWrite, "consed.primersMaximumLengthOfAPrimerForPCR: %d\n", resources_.nPrimersMaximumLengthOfAPrimerForPCR_ ); } // consed.primersMaxMeltingTempDifferenceForPCR if ( resources_.dPrimersMaxMeltingTempDifferenceForPCR_ != CONDEF->dPrimersMaxMeltingTempDifferenceForPCR_ ) { fprintf( pFileToWrite, "consed.primersMaxMeltingTempDifferenceForPCR: %f\n", resources_.dPrimersMaxMeltingTempDifferenceForPCR_ ); } // consed.primersMaxPCRPrimerPairsToDisplay if ( resources_.nPrimersMaxPCRPrimerPairsToDisplay_ != CONDEF->nPrimersMaxPCRPrimerPairsToDisplay_ ) { fprintf( pFileToWrite, "consed.primersMaxPCRPrimerPairsToDisplay: %d\n", resources_.nPrimersMaxPCRPrimerPairsToDisplay_ ); } // consed.primersCheckJustSomePCRPrimerPairsRatherThanAll if ( resources_.bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_ != CONDEF->bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_ ) { fprintf( pFileToWrite, "consed.primersCheckJustSomePCRPrimerPairsRatherThanAll: %s\n", ( resources_.bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_ ? "true" : "false" ) ); } // consed.primersNumberOfTemplatesToDisplayInFront if ( resources_.nPrimersNumberOfTemplatesToDisplayInFront_ != CONDEF->nPrimersNumberOfTemplatesToDisplayInFront_ ) { fprintf( pFileToWrite, "consed.primersNumberOfTemplatesToDisplayInFront: %d\n", resources_.nPrimersNumberOfTemplatesToDisplayInFront_ ); } // consed.primersMaxLengthOfMononucleotideRepeat if ( resources_.nPrimersMaxLengthOfMononucleotideRepeat_ != CONDEF->nPrimersMaxLengthOfMononucleotideRepeat_ ) { fprintf( pFileToWrite, "consed.primersMaxLengthOfMononucleotideRepeat: %d\n", resources_.nPrimersMaxLengthOfMononucleotideRepeat_ ); } // consed.primersBadLibrariesFile if ( resources_.filPrimersBadLibrariesFile_ != CONDEF->filPrimersBadLibrariesFile_ ) { fprintf( pFileToWrite, "consed.primersBadLibrariesFile: %s\n", resources_.filPrimersBadLibrariesFile_.data() ); } // consed.primersLibrariesInfoFile if ( resources_.filPrimersLibrariesInfoFile_ != CONDEF->filPrimersLibrariesInfoFile_ ) { fprintf( pFileToWrite, "consed.primersLibrariesInfoFile: %s\n", resources_.filPrimersLibrariesInfoFile_.data() ); } // consed.primersBadTemplatesFile if ( resources_.filPrimersBadTemplatesFile_ != CONDEF->filPrimersBadTemplatesFile_ ) { fprintf( pFileToWrite, "consed.primersBadTemplatesFile: %s\n", resources_.filPrimersBadTemplatesFile_.data() ); } // consed.primersChooseTemplatesByPositionInsteadOfQuality if ( resources_.bPrimersChooseTemplatesByPositionInsteadOfQuality_ != CONDEF->bPrimersChooseTemplatesByPositionInsteadOfQuality_ ) { fprintf( pFileToWrite, "consed.primersChooseTemplatesByPositionInsteadOfQuality: %s\n", ( resources_.bPrimersChooseTemplatesByPositionInsteadOfQuality_ ? "true" : "false" ) ); } // consed.primersWhenChoosingATemplateMinPotentialReadLength if ( resources_.nPrimersWhenChoosingATemplateMinPotentialReadLength_ != CONDEF->nPrimersWhenChoosingATemplateMinPotentialReadLength_ ) { fprintf( pFileToWrite, "consed.primersWhenChoosingATemplateMinPotentialReadLength: %d\n", resources_.nPrimersWhenChoosingATemplateMinPotentialReadLength_ ); } // consed.primersWindowSizeInLookingForPCR if ( resources_.nPrimersWindowSizeInLookingForPCR_ != CONDEF->nPrimersWindowSizeInLookingForPCR_ ) { fprintf( pFileToWrite, "consed.primersWindowSizeInLookingForPCR: %d\n", resources_.nPrimersWindowSizeInLookingForPCR_ ); } // consed.qualityThresholdForFindingHighQualityDiscrepancies if ( resources_.nQualityThresholdForFindingHighQualityDiscrepancies_ != CONDEF->nQualityThresholdForFindingHighQualityDiscrepancies_ ) { fprintf( pFileToWrite, "consed.qualityThresholdForFindingHighQualityDiscrepancies: %d\n", resources_.nQualityThresholdForFindingHighQualityDiscrepancies_ ); } // consed.qualityThresholdForNavigateByDepthOfCoverage if ( resources_.nQualityThresholdForNavigateByDepthOfCoverage_ != CONDEF->nQualityThresholdForNavigateByDepthOfCoverage_ ) { fprintf( pFileToWrite, "consed.qualityThresholdForNavigateByDepthOfCoverage: %d\n", resources_.nQualityThresholdForNavigateByDepthOfCoverage_ ); } // consed.navigateByHighDepthOfCoverageNotLow if ( resources_.bNavigateByHighDepthOfCoverageNotLow_ != CONDEF->bNavigateByHighDepthOfCoverageNotLow_ ) { fprintf( pFileToWrite, "consed.navigateByHighDepthOfCoverageNotLow: %s\n", ( resources_.bNavigateByHighDepthOfCoverageNotLow_ ? "true" : "false" ) ); } // consed.MinDepthForNavigateByDepthOfCoverage if ( resources_.nMinDepthForNavigateByDepthOfCoverage_ != CONDEF->nMinDepthForNavigateByDepthOfCoverage_ ) { fprintf( pFileToWrite, "consed.MinDepthForNavigateByDepthOfCoverage: %d\n", resources_.nMinDepthForNavigateByDepthOfCoverage_ ); } // consed.defaultVectorPathnameForRestrictionFragments if ( resources_.filDefaultVectorPathnameForRestrictionFragments_ != CONDEF->filDefaultVectorPathnameForRestrictionFragments_ ) { fprintf( pFileToWrite, "consed.defaultVectorPathnameForRestrictionFragments: %s\n", resources_.filDefaultVectorPathnameForRestrictionFragments_.data() ); } // consed.fileOfAdditionalRestrictionEnzymes if ( resources_.filFileOfAdditionalRestrictionEnzymes_ != CONDEF->filFileOfAdditionalRestrictionEnzymes_ ) { fprintf( pFileToWrite, "consed.fileOfAdditionalRestrictionEnzymes: %s\n", resources_.filFileOfAdditionalRestrictionEnzymes_.data() ); } // consed.commonRestrictionEnzymes if ( resources_.soCommonRestrictionEnzymes_ != CONDEF->soCommonRestrictionEnzymes_ ) { fprintf( pFileToWrite, "consed.commonRestrictionEnzymes: %s\n", resources_.soCommonRestrictionEnzymes_.data() ); } // consed.defaultSelectedRestrictionEnzymes if ( resources_.soDefaultSelectedRestrictionEnzymes_ != CONDEF->soDefaultSelectedRestrictionEnzymes_ ) { fprintf( pFileToWrite, "consed.defaultSelectedRestrictionEnzymes: %s\n", resources_.soDefaultSelectedRestrictionEnzymes_.data() ); } // consed.restrictionEnzymesActualFragmentsFile if ( resources_.filRestrictionEnzymesActualFragmentsFile_ != CONDEF->filRestrictionEnzymesActualFragmentsFile_ ) { fprintf( pFileToWrite, "consed.restrictionEnzymesActualFragmentsFile: %s\n", resources_.filRestrictionEnzymesActualFragmentsFile_.data() ); } // consed.restrictionDigestInitialWindowSizeInTextRows if ( resources_.nRestrictionDigestInitialWindowSizeInTextRows_ != CONDEF->nRestrictionDigestInitialWindowSizeInTextRows_ ) { fprintf( pFileToWrite, "consed.restrictionDigestInitialWindowSizeInTextRows: %d\n", resources_.nRestrictionDigestInitialWindowSizeInTextRows_ ); } // consed.restrictionDigestDoNoShowAreaOfFragmentsOverThisSize if ( resources_.nRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize_ != CONDEF->nRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize_ ) { fprintf( pFileToWrite, "consed.restrictionDigestDoNoShowAreaOfFragmentsOverThisSize: %d\n", resources_.nRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize_ ); } // consed.showReadsAlphabetically if ( resources_.bShowReadsAlphabetically_ != CONDEF->bShowReadsAlphabetically_ ) { fprintf( pFileToWrite, "consed.showReadsAlphabetically: %s\n", ( resources_.bShowReadsAlphabetically_ ? "true" : "false" ) ); } // consed.showReadsInAlignedReadsWindowOrderedByFile if ( resources_.bShowReadsInAlignedReadsWindowOrderedByFile_ != CONDEF->bShowReadsInAlignedReadsWindowOrderedByFile_ ) { fprintf( pFileToWrite, "consed.showReadsInAlignedReadsWindowOrderedByFile: %s\n", ( resources_.bShowReadsInAlignedReadsWindowOrderedByFile_ ? "true" : "false" ) ); } // consed.showReadsInAlignedReadsWindowOrderedByThisFile if ( resources_.filShowReadsInAlignedReadsWindowOrderedByThisFile_ != CONDEF->filShowReadsInAlignedReadsWindowOrderedByThisFile_ ) { fprintf( pFileToWrite, "consed.showReadsInAlignedReadsWindowOrderedByThisFile: %s\n", resources_.filShowReadsInAlignedReadsWindowOrderedByThisFile_.data() ); } // consed.showReadsAtCursorSortedHow if ( resources_.soShowReadsAtCursorSortedHow_ != CONDEF->soShowReadsAtCursorSortedHow_ ) { fprintf( pFileToWrite, "consed.showReadsAtCursorSortedHow: %s\n", resources_.soShowReadsAtCursorSortedHow_.data() ); } // consed.showABIBasesInTraceWindow if ( resources_.bShowABIBasesInTraceWindow_ != CONDEF->bShowABIBasesInTraceWindow_ ) { fprintf( pFileToWrite, "consed.showABIBasesInTraceWindow: %s\n", ( resources_.bShowABIBasesInTraceWindow_ ? "true" : "false" ) ); } // consed.tracesWindowInitialPixelHeight if ( resources_.nTracesWindowInitialPixelHeight_ != CONDEF->nTracesWindowInitialPixelHeight_ ) { fprintf( pFileToWrite, "consed.tracesWindowInitialPixelHeight: %d\n", resources_.nTracesWindowInitialPixelHeight_ ); } // consed.assemblyViewWindowInitialPixelHeight if ( resources_.nAssemblyViewWindowInitialPixelHeight_ != CONDEF->nAssemblyViewWindowInitialPixelHeight_ ) { fprintf( pFileToWrite, "consed.assemblyViewWindowInitialPixelHeight: %d\n", resources_.nAssemblyViewWindowInitialPixelHeight_ ); } // consed.assemblyViewFileOfTemplatesToNotShow if ( resources_.filAssemblyViewFileOfTemplatesToNotShow_ != CONDEF->filAssemblyViewFileOfTemplatesToNotShow_ ) { fprintf( pFileToWrite, "consed.assemblyViewFileOfTemplatesToNotShow: %s\n", resources_.filAssemblyViewFileOfTemplatesToNotShow_.data() ); } // consed.assemblyViewCrossMatchMinmatch if ( resources_.nAssemblyViewCrossMatchMinmatch_ != CONDEF->nAssemblyViewCrossMatchMinmatch_ ) { fprintf( pFileToWrite, "consed.assemblyViewCrossMatchMinmatch: %d\n", resources_.nAssemblyViewCrossMatchMinmatch_ ); } // consed.assemblyViewCrossMatchMinscore if ( resources_.nAssemblyViewCrossMatchMinscore_ != CONDEF->nAssemblyViewCrossMatchMinscore_ ) { fprintf( pFileToWrite, "consed.assemblyViewCrossMatchMinscore: %d\n", resources_.nAssemblyViewCrossMatchMinscore_ ); } // consed.assemblyViewFindSequenceMatchesForConsedScript if ( resources_.filAssemblyViewFindSequenceMatchesForConsedScript_ != CONDEF->filAssemblyViewFindSequenceMatchesForConsedScript_ ) { fprintf( pFileToWrite, "consed.assemblyViewFindSequenceMatchesForConsedScript: %s\n", resources_.filAssemblyViewFindSequenceMatchesForConsedScript_.data() ); } // consed.assemblyViewCrossmatchMinmatch if ( resources_.nAssemblyViewCrossmatchMinmatch_ != CONDEF->nAssemblyViewCrossmatchMinmatch_ ) { fprintf( pFileToWrite, "consed.assemblyViewCrossmatchMinmatch: %d\n", resources_.nAssemblyViewCrossmatchMinmatch_ ); } // consed.assemblyViewCrossmatchMinscore if ( resources_.nAssemblyViewCrossmatchMinscore_ != CONDEF->nAssemblyViewCrossmatchMinscore_ ) { fprintf( pFileToWrite, "consed.assemblyViewCrossmatchMinscore: %d\n", resources_.nAssemblyViewCrossmatchMinscore_ ); } // consed.assemblyViewSequenceMatchesMinimumSimilarity if ( resources_.nAssemblyViewSequenceMatchesMinimumSimilarity_ != CONDEF->nAssemblyViewSequenceMatchesMinimumSimilarity_ ) { fprintf( pFileToWrite, "consed.assemblyViewSequenceMatchesMinimumSimilarity: %d\n", resources_.nAssemblyViewSequenceMatchesMinimumSimilarity_ ); } // consed.tracesWindowInitialPixelWidth if ( resources_.nTracesWindowInitialPixelWidth_ != CONDEF->nTracesWindowInitialPixelWidth_ ) { fprintf( pFileToWrite, "consed.tracesWindowInitialPixelWidth: %d\n", resources_.nTracesWindowInitialPixelWidth_ ); } // consed.assemblyViewWindowInitialPixelWidth if ( resources_.nAssemblyViewWindowInitialPixelWidth_ != CONDEF->nAssemblyViewWindowInitialPixelWidth_ ) { fprintf( pFileToWrite, "consed.assemblyViewWindowInitialPixelWidth: %d\n", resources_.nAssemblyViewWindowInitialPixelWidth_ ); } // consed.automaticallyScaleTraces if ( resources_.bAutomaticallyScaleTraces_ != CONDEF->bAutomaticallyScaleTraces_ ) { fprintf( pFileToWrite, "consed.automaticallyScaleTraces: %s\n", ( resources_.bAutomaticallyScaleTraces_ ? "true" : "false" ) ); } // consed.automaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight if ( resources_.dAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight_ != CONDEF->dAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight_ ) { fprintf( pFileToWrite, "consed.automaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight: %f\n", resources_.dAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight_ ); } // consed.automaticallyScaleTracesSamplePeakPercentile if ( resources_.nAutomaticallyScaleTracesSamplePeakPercentile_ != CONDEF->nAutomaticallyScaleTracesSamplePeakPercentile_ ) { fprintf( pFileToWrite, "consed.automaticallyScaleTracesSamplePeakPercentile: %d\n", resources_.nAutomaticallyScaleTracesSamplePeakPercentile_ ); } // consed.verticalTraceMagnification if ( resources_.nVerticalTraceMagnification_ != CONDEF->nVerticalTraceMagnification_ ) { fprintf( pFileToWrite, "consed.verticalTraceMagnification: %d\n", resources_.nVerticalTraceMagnification_ ); } // consed.userDefinedKeys if ( resources_.soUserDefinedKeys_ != CONDEF->soUserDefinedKeys_ ) { fprintf( pFileToWrite, "consed.userDefinedKeys: %s\n", resources_.soUserDefinedKeys_.data() ); } // consed.programsForUserDefinedKeys if ( resources_.soProgramsForUserDefinedKeys_ != CONDEF->soProgramsForUserDefinedKeys_ ) { fprintf( pFileToWrite, "consed.programsForUserDefinedKeys: %s\n", resources_.soProgramsForUserDefinedKeys_.data() ); } // consed.argumentsToPassToUserDefinedPrograms if ( resources_.soArgumentsToPassToUserDefinedPrograms_ != CONDEF->soArgumentsToPassToUserDefinedPrograms_ ) { fprintf( pFileToWrite, "consed.argumentsToPassToUserDefinedPrograms: %s\n", resources_.soArgumentsToPassToUserDefinedPrograms_.data() ); } // consed.tagsToApplyWithUserDefinedKeys if ( resources_.soTagsToApplyWithUserDefinedKeys_ != CONDEF->soTagsToApplyWithUserDefinedKeys_ ) { fprintf( pFileToWrite, "consed.tagsToApplyWithUserDefinedKeys: %s\n", resources_.soTagsToApplyWithUserDefinedKeys_.data() ); } // consed.snpGenomeUseInsertionPolymorphisms if ( resources_.bSnpGenomeUseInsertionPolymorphisms_ != CONDEF->bSnpGenomeUseInsertionPolymorphisms_ ) { fprintf( pFileToWrite, "consed.snpGenomeUseInsertionPolymorphisms: %s\n", ( resources_.bSnpGenomeUseInsertionPolymorphisms_ ? "true" : "false" ) ); } // consed.listOfTagTypesToHide if ( resources_.soListOfTagTypesToHide_ != CONDEF->soListOfTagTypesToHide_ ) { fprintf( pFileToWrite, "consed.listOfTagTypesToHide: %s\n", resources_.soListOfTagTypesToHide_.data() ); } // consed.listOfOptionalWordsToSaveInListOfReadNames if ( resources_.soListOfOptionalWordsToSaveInListOfReadNames_ != CONDEF->soListOfOptionalWordsToSaveInListOfReadNames_ ) { fprintf( pFileToWrite, "consed.listOfOptionalWordsToSaveInListOfReadNames: %s\n", resources_.soListOfOptionalWordsToSaveInListOfReadNames_.data() ); } // consed.extendConsensusWithHighQuality if ( resources_.bExtendConsensusWithHighQuality_ != CONDEF->bExtendConsensusWithHighQuality_ ) { fprintf( pFileToWrite, "consed.extendConsensusWithHighQuality: %s\n", ( resources_.bExtendConsensusWithHighQuality_ ? "true" : "false" ) ); } // consed.fastStartup if ( resources_.bFastStartup_ != CONDEF->bFastStartup_ ) { fprintf( pFileToWrite, "consed.fastStartup: %s\n", ( resources_.bFastStartup_ ? "true" : "false" ) ); } // consed.fastStartupFile if ( resources_.filFastStartupFile_ != CONDEF->filFastStartupFile_ ) { fprintf( pFileToWrite, "consed.fastStartupFile: %s\n", resources_.filFastStartupFile_.data() ); } // consed.alwaysRunProgramToGetChromats if ( resources_.soAlwaysRunProgramToGetChromats_ != CONDEF->soAlwaysRunProgramToGetChromats_ ) { fprintf( pFileToWrite, "consed.alwaysRunProgramToGetChromats: %s\n", resources_.soAlwaysRunProgramToGetChromats_.data() ); } // consed.programToRunToGetChromats if ( resources_.filProgramToRunToGetChromats_ != CONDEF->filProgramToRunToGetChromats_ ) { fprintf( pFileToWrite, "consed.programToRunToGetChromats: %s\n", resources_.filProgramToRunToGetChromats_.data() ); } // consed.programToRunToGetChromatsOf454Reads if ( resources_.filProgramToRunToGetChromatsOf454Reads_ != CONDEF->filProgramToRunToGetChromatsOf454Reads_ ) { fprintf( pFileToWrite, "consed.programToRunToGetChromatsOf454Reads: %s\n", resources_.filProgramToRunToGetChromatsOf454Reads_.data() ); } // consed.createFakeChromatsForSolexaReads if ( resources_.bCreateFakeChromatsForSolexaReads_ != CONDEF->bCreateFakeChromatsForSolexaReads_ ) { fprintf( pFileToWrite, "consed.createFakeChromatsForSolexaReads: %s\n", ( resources_.bCreateFakeChromatsForSolexaReads_ ? "true" : "false" ) ); } // consed.autoFinishUseLongModelReadRatherThanShort if ( resources_.bAutoFinishUseLongModelReadRatherThanShort_ != CONDEF->bAutoFinishUseLongModelReadRatherThanShort_ ) { fprintf( pFileToWrite, "consed.autoFinishUseLongModelReadRatherThanShort: %s\n", ( resources_.bAutoFinishUseLongModelReadRatherThanShort_ ? "true" : "false" ) ); } // consed.askAgainIfWantToQuitConsedIfThisManyReads if ( resources_.nAskAgainIfWantToQuitConsedIfThisManyReads_ != CONDEF->nAskAgainIfWantToQuitConsedIfThisManyReads_ ) { fprintf( pFileToWrite, "consed.askAgainIfWantToQuitConsedIfThisManyReads: %d\n", resources_.nAskAgainIfWantToQuitConsedIfThisManyReads_ ); } // consed.printWindowInstructions if ( resources_.soPrintWindowInstructions_ != CONDEF->soPrintWindowInstructions_ ) { fprintf( pFileToWrite, "consed.printWindowInstructions: %s\n", resources_.soPrintWindowInstructions_.data() ); } // consed.allowMultipleSearchForStringWindows if ( resources_.bAllowMultipleSearchForStringWindows_ != CONDEF->bAllowMultipleSearchForStringWindows_ ) { fprintf( pFileToWrite, "consed.allowMultipleSearchForStringWindows: %s\n", ( resources_.bAllowMultipleSearchForStringWindows_ ? "true" : "false" ) ); } // consed.autoPCRAmplifyFalseProductsOKIfLargerThanThis if ( resources_.nAutoPCRAmplifyFalseProductsOKIfLargerThanThis_ != CONDEF->nAutoPCRAmplifyFalseProductsOKIfLargerThanThis_ ) { fprintf( pFileToWrite, "consed.autoPCRAmplifyFalseProductsOKIfLargerThanThis: %d\n", resources_.nAutoPCRAmplifyFalseProductsOKIfLargerThanThis_ ); } // consed.autoPCRAmplifyMakePrimerOutOfFirstRegion if ( resources_.bAutoPCRAmplifyMakePrimerOutOfFirstRegion_ != CONDEF->bAutoPCRAmplifyMakePrimerOutOfFirstRegion_ ) { fprintf( pFileToWrite, "consed.autoPCRAmplifyMakePrimerOutOfFirstRegion: %s\n", ( resources_.bAutoPCRAmplifyMakePrimerOutOfFirstRegion_ ? "true" : "false" ) ); } // consed.autoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct if ( resources_.nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_ != CONDEF->nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_ ) { fprintf( pFileToWrite, "consed.autoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct: %d\n", resources_.nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_ ); } // consed.addNewReadsRecalculateConsensusQuality if ( resources_.bAddNewReadsRecalculateConsensusQuality_ != CONDEF->bAddNewReadsRecalculateConsensusQuality_ ) { fprintf( pFileToWrite, "consed.addNewReadsRecalculateConsensusQuality: %s\n", ( resources_.bAddNewReadsRecalculateConsensusQuality_ ? "true" : "false" ) ); } // consed.addNewReadsPutReadIntoItsOwnContig if ( resources_.soAddNewReadsPutReadIntoItsOwnContig_ != CONDEF->soAddNewReadsPutReadIntoItsOwnContig_ ) { fprintf( pFileToWrite, "consed.addNewReadsPutReadIntoItsOwnContig: %s\n", resources_.soAddNewReadsPutReadIntoItsOwnContig_.data() ); } // consed.addNewReadsCheckThatCrossMatchRunCorrectly if ( resources_.bAddNewReadsCheckThatCrossMatchRunCorrectly_ != CONDEF->bAddNewReadsCheckThatCrossMatchRunCorrectly_ ) { fprintf( pFileToWrite, "consed.addNewReadsCheckThatCrossMatchRunCorrectly: %s\n", ( resources_.bAddNewReadsCheckThatCrossMatchRunCorrectly_ ? "true" : "false" ) ); } // consed.assemblyViewNumberOfRowsOfTags if ( resources_.nAssemblyViewNumberOfRowsOfTags_ != CONDEF->nAssemblyViewNumberOfRowsOfTags_ ) { fprintf( pFileToWrite, "consed.assemblyViewNumberOfRowsOfTags: %d\n", resources_.nAssemblyViewNumberOfRowsOfTags_ ); } // consed.warnUserWhenTryingToEditAllReads if ( resources_.bWarnUserWhenTryingToEditAllReads_ != CONDEF->bWarnUserWhenTryingToEditAllReads_ ) { fprintf( pFileToWrite, "consed.warnUserWhenTryingToEditAllReads: %s\n", ( resources_.bWarnUserWhenTryingToEditAllReads_ ? "true" : "false" ) ); } // consed.maybeXKEYSYMDBPath if ( resources_.filMaybeXKEYSYMDBPath_ != CONDEF->filMaybeXKEYSYMDBPath_ ) { fprintf( pFileToWrite, "consed.maybeXKEYSYMDBPath: %s\n", resources_.filMaybeXKEYSYMDBPath_.data() ); } // consed.maybeXKEYSYMDBPath2 if ( resources_.filMaybeXKEYSYMDBPath2_ != CONDEF->filMaybeXKEYSYMDBPath2_ ) { fprintf( pFileToWrite, "consed.maybeXKEYSYMDBPath2: %s\n", resources_.filMaybeXKEYSYMDBPath2_.data() ); } // consed.amountToMoveWithBigLeftAndRightArrows if ( resources_.nAmountToMoveWithBigLeftAndRightArrows_ != CONDEF->nAmountToMoveWithBigLeftAndRightArrows_ ) { fprintf( pFileToWrite, "consed.amountToMoveWithBigLeftAndRightArrows: %d\n", resources_.nAmountToMoveWithBigLeftAndRightArrows_ ); } // consed.navigateByHighlyDiscrepantPositionsMinDiscrepantReads if ( resources_.nNavigateByHighlyDiscrepantPositionsMinDiscrepantReads_ != CONDEF->nNavigateByHighlyDiscrepantPositionsMinDiscrepantReads_ ) { fprintf( pFileToWrite, "consed.navigateByHighlyDiscrepantPositionsMinDiscrepantReads: %d\n", resources_.nNavigateByHighlyDiscrepantPositionsMinDiscrepantReads_ ); } // consed.navigateByHighlyDiscrepantPositionsMaxDepthOfCoverage if ( resources_.nNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage_ != CONDEF->nNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage_ ) { fprintf( pFileToWrite, "consed.navigateByHighlyDiscrepantPositionsMaxDepthOfCoverage: %d\n", resources_.nNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage_ ); } // consed.navigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality if ( resources_.nNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality_ != CONDEF->nNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality_ ) { fprintf( pFileToWrite, "consed.navigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality: %d\n", resources_.nNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality_ ); } // consed.navigateByHighlyDiscrepantPositionsJustListIndels if ( resources_.bNavigateByHighlyDiscrepantPositionsJustListIndels_ != CONDEF->bNavigateByHighlyDiscrepantPositionsJustListIndels_ ) { fprintf( pFileToWrite, "consed.navigateByHighlyDiscrepantPositionsJustListIndels: %s\n", ( resources_.bNavigateByHighlyDiscrepantPositionsJustListIndels_ ? "true" : "false" ) ); } // consed.navigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation if ( resources_.bNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation_ != CONDEF->bNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation_ ) { fprintf( pFileToWrite, "consed.navigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation: %s\n", ( resources_.bNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation_ ? "true" : "false" ) ); } // consed.navigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus if ( resources_.bNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus_ != CONDEF->bNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus_ ) { fprintf( pFileToWrite, "consed.navigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus: %s\n", ( resources_.bNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus_ ? "true" : "false" ) ); } // consed.navigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus if ( resources_.soNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus_ != CONDEF->soNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus_ ) { fprintf( pFileToWrite, "consed.navigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus: %s\n", resources_.soNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus_.data() ); } // consed.phdBallDirectory if ( resources_.filPhdBallDirectory_ != CONDEF->filPhdBallDirectory_ ) { fprintf( pFileToWrite, "consed.phdBallDirectory: %s\n", resources_.filPhdBallDirectory_.data() ); } // consed.newAceFileFOF if ( resources_.filNewAceFileFOF_ != CONDEF->filNewAceFileFOF_ ) { fprintf( pFileToWrite, "consed.newAceFileFOF: %s\n", resources_.filNewAceFileFOF_.data() ); } // consed.navigateByHighOrLowDepthCoalesceRegionsIfThisClose if ( resources_.nNavigateByHighOrLowDepthCoalesceRegionsIfThisClose_ != CONDEF->nNavigateByHighOrLowDepthCoalesceRegionsIfThisClose_ ) { fprintf( pFileToWrite, "consed.navigateByHighOrLowDepthCoalesceRegionsIfThisClose: %d\n", resources_.nNavigateByHighOrLowDepthCoalesceRegionsIfThisClose_ ); } // consed.removeReadsDeleteNotJustPutInOwnContig if ( resources_.bRemoveReadsDeleteNotJustPutInOwnContig_ != CONDEF->bRemoveReadsDeleteNotJustPutInOwnContig_ ) { fprintf( pFileToWrite, "consed.removeReadsDeleteNotJustPutInOwnContig: %s\n", ( resources_.bRemoveReadsDeleteNotJustPutInOwnContig_ ? "true" : "false" ) ); } // consed.paired454LeftReadExtension if ( resources_.soPaired454LeftReadExtension_ != CONDEF->soPaired454LeftReadExtension_ ) { fprintf( pFileToWrite, "consed.paired454LeftReadExtension: %s\n", resources_.soPaired454LeftReadExtension_.data() ); } // consed.paired454RightReadExtension if ( resources_.soPaired454RightReadExtension_ != CONDEF->soPaired454RightReadExtension_ ) { fprintf( pFileToWrite, "consed.paired454RightReadExtension: %s\n", resources_.soPaired454RightReadExtension_.data() ); } // consed.snpGenome1MSnps if ( resources_.filSnpGenome1MSnps_ != CONDEF->filSnpGenome1MSnps_ ) { fprintf( pFileToWrite, "consed.snpGenome1MSnps: %s\n", resources_.filSnpGenome1MSnps_.data() ); } // consed.diffChromosomesExcludeDeletions if ( resources_.bDiffChromosomesExcludeDeletions_ != CONDEF->bDiffChromosomesExcludeDeletions_ ) { fprintf( pFileToWrite, "consed.diffChromosomesExcludeDeletions: %s\n", ( resources_.bDiffChromosomesExcludeDeletions_ ? "true" : "false" ) ); } // consed.snpGenomeFilterByWeight if ( resources_.bSnpGenomeFilterByWeight_ != CONDEF->bSnpGenomeFilterByWeight_ ) { fprintf( pFileToWrite, "consed.snpGenomeFilterByWeight: %s\n", ( resources_.bSnpGenomeFilterByWeight_ ? "true" : "false" ) ); } // consed.wantReadsUpToThisFarFromSnps if ( resources_.nWantReadsUpToThisFarFromSnps_ != CONDEF->nWantReadsUpToThisFarFromSnps_ ) { fprintf( pFileToWrite, "consed.wantReadsUpToThisFarFromSnps: %d\n", resources_.nWantReadsUpToThisFarFromSnps_ ); } // consed.phaster2PhdBallSaveWhichMate if ( resources_.soPhaster2PhdBallSaveWhichMate_ != CONDEF->soPhaster2PhdBallSaveWhichMate_ ) { fprintf( pFileToWrite, "consed.phaster2PhdBallSaveWhichMate: %s\n", resources_.soPhaster2PhdBallSaveWhichMate_.data() ); } // consed.phaster2PhdBallSaveInPhasterFormat if ( resources_.bPhaster2PhdBallSaveInPhasterFormat_ != CONDEF->bPhaster2PhdBallSaveInPhasterFormat_ ) { fprintf( pFileToWrite, "consed.phaster2PhdBallSaveInPhasterFormat: %s\n", ( resources_.bPhaster2PhdBallSaveInPhasterFormat_ ? "true" : "false" ) ); } // consed.phaster2PhdBallCalculateNewLocationsFile if ( resources_.bPhaster2PhdBallCalculateNewLocationsFile_ != CONDEF->bPhaster2PhdBallCalculateNewLocationsFile_ ) { fprintf( pFileToWrite, "consed.phaster2PhdBallCalculateNewLocationsFile: %s\n", ( resources_.bPhaster2PhdBallCalculateNewLocationsFile_ ? "true" : "false" ) ); } // consed.phdBall2FastaIgnoreLowQualityReads if ( resources_.bPhdBall2FastaIgnoreLowQualityReads_ != CONDEF->bPhdBall2FastaIgnoreLowQualityReads_ ) { fprintf( pFileToWrite, "consed.phdBall2FastaIgnoreLowQualityReads: %s\n", ( resources_.bPhdBall2FastaIgnoreLowQualityReads_ ? "true" : "false" ) ); } // consed.phdBall2FastaLowestAverageQuality if ( resources_.nPhdBall2FastaLowestAverageQuality_ != CONDEF->nPhdBall2FastaLowestAverageQuality_ ) { fprintf( pFileToWrite, "consed.phdBall2FastaLowestAverageQuality: %d\n", resources_.nPhdBall2FastaLowestAverageQuality_ ); } // consed.nextPhredPipelineControlFile if ( resources_.filNextPhredPipelineControlFile_ != CONDEF->filNextPhredPipelineControlFile_ ) { fprintf( pFileToWrite, "consed.nextPhredPipelineControlFile: %s\n", resources_.filNextPhredPipelineControlFile_.data() ); } // consed.nextPhredPipelineTiffPerlScript if ( resources_.filNextPhredPipelineTiffPerlScript_ != CONDEF->filNextPhredPipelineTiffPerlScript_ ) { fprintf( pFileToWrite, "consed.nextPhredPipelineTiffPerlScript: %s\n", resources_.filNextPhredPipelineTiffPerlScript_.data() ); } // consed.nextPhredPipelinePhasterPerlScript if ( resources_.filNextPhredPipelinePhasterPerlScript_ != CONDEF->filNextPhredPipelinePhasterPerlScript_ ) { fprintf( pFileToWrite, "consed.nextPhredPipelinePhasterPerlScript: %s\n", resources_.filNextPhredPipelinePhasterPerlScript_.data() ); } // consed.nextPhredPipelineVersion if ( resources_.soNextPhredPipelineVersion_ != CONDEF->soNextPhredPipelineVersion_ ) { fprintf( pFileToWrite, "consed.nextPhredPipelineVersion: %s\n", resources_.soNextPhredPipelineVersion_.data() ); } // consed.nextPhredPipelineMainDirectory if ( resources_.soNextPhredPipelineMainDirectory_ != CONDEF->soNextPhredPipelineMainDirectory_ ) { fprintf( pFileToWrite, "consed.nextPhredPipelineMainDirectory: %s\n", resources_.soNextPhredPipelineMainDirectory_.data() ); } // consed.maxNumberOfReadsPerPhdBall if ( resources_.nMaxNumberOfReadsPerPhdBall_ != CONDEF->nMaxNumberOfReadsPerPhdBall_ ) { fprintf( pFileToWrite, "consed.maxNumberOfReadsPerPhdBall: %d\n", resources_.nMaxNumberOfReadsPerPhdBall_ ); } // consed.userWantsToSaveToThisAceFile if ( resources_.filUserWantsToSaveToThisAceFile_ != CONDEF->filUserWantsToSaveToThisAceFile_ ) { fprintf( pFileToWrite, "consed.userWantsToSaveToThisAceFile: %s\n", resources_.filUserWantsToSaveToThisAceFile_.data() ); } // consed.autoFinishEmulate9_66Behavior if ( resources_.bAutoFinishEmulate9_66Behavior_ != CONDEF->bAutoFinishEmulate9_66Behavior_ ) { fprintf( pFileToWrite, "consed.autoFinishEmulate9_66Behavior: %s\n", ( resources_.bAutoFinishEmulate9_66Behavior_ ? "true" : "false" ) ); } // consed.primersPCRPrimersGroupedIntoWindowOfThisManyBases if ( resources_.nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_ != CONDEF->nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_ ) { fprintf( pFileToWrite, "consed.primersPCRPrimersGroupedIntoWindowOfThisManyBases: %d\n", resources_.nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_ ); } // consed.primersLookForThisManyPCRPrimerPairsPerPairOfGroups if ( resources_.nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_ != CONDEF->nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_ ) { fprintf( pFileToWrite, "consed.primersLookForThisManyPCRPrimerPairsPerPairOfGroups: %d\n", resources_.nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_ ); } // consed.autoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs if ( resources_.dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_ != CONDEF->dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_ ) { fprintf( pFileToWrite, "consed.autoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs: %f\n", resources_.dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_ ); } // consed.autoFinishCheckThatReadsFromTheSameTemplateAreConsistent if ( resources_.bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_ != CONDEF->bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_ ) { fprintf( pFileToWrite, "consed.autoFinishCheckThatReadsFromTheSameTemplateAreConsistent: %s\n", ( resources_.bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_ ? "true" : "false" ) ); } // consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether if ( resources_.bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_ != CONDEF->bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether: %s\n", ( resources_.bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_ ? "true" : "false" ) ); } // consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether if ( resources_.bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_ != CONDEF->bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether: %s\n", ( resources_.bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_ ? "true" : "false" ) ); } // consed.autoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean if ( resources_.dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_ != CONDEF->dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_ ) { fprintf( pFileToWrite, "consed.autoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean: %f\n", resources_.dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_ ); } // consed.autoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize if ( resources_.nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_ != CONDEF->nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_ ) { fprintf( pFileToWrite, "consed.autoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize: %d\n", resources_.nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_ ); } // consed.autoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize if ( resources_.dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_ != CONDEF->dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_ ) { fprintf( pFileToWrite, "consed.autoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize: %f\n", resources_.dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_ ); } // consed.autoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead if ( resources_.nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_ != CONDEF->nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_ ) { fprintf( pFileToWrite, "consed.autoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead: %d\n", resources_.nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_ ); } // consed.autoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp if ( resources_.nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_ != CONDEF->nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_ ) { fprintf( pFileToWrite, "consed.autoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp: %d\n", resources_.nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_ ); } // consed.autoFinishNumberOfBasesBetweenContigsAssumed if ( resources_.nAutoFinishNumberOfBasesBetweenContigsAssumed_ != CONDEF->nAutoFinishNumberOfBasesBetweenContigsAssumed_ ) { fprintf( pFileToWrite, "consed.autoFinishNumberOfBasesBetweenContigsAssumed: %d\n", resources_.nAutoFinishNumberOfBasesBetweenContigsAssumed_ ); } // consed.autoFinishPotentialHighQualityPartOfReadStart if ( resources_.nAutoFinishPotentialHighQualityPartOfReadStart_ != CONDEF->nAutoFinishPotentialHighQualityPartOfReadStart_ ) { fprintf( pFileToWrite, "consed.autoFinishPotentialHighQualityPartOfReadStart: %d\n", resources_.nAutoFinishPotentialHighQualityPartOfReadStart_ ); } // consed.autoFinishPotentialHighQualityPartOfReadEnd if ( resources_.nAutoFinishPotentialHighQualityPartOfReadEnd_ != CONDEF->nAutoFinishPotentialHighQualityPartOfReadEnd_ ) { fprintf( pFileToWrite, "consed.autoFinishPotentialHighQualityPartOfReadEnd: %d\n", resources_.nAutoFinishPotentialHighQualityPartOfReadEnd_ ); } // consed.autoFinishPrintCustomNavigationFileForChosenReads if ( resources_.bAutoFinishPrintCustomNavigationFileForChosenReads_ != CONDEF->bAutoFinishPrintCustomNavigationFileForChosenReads_ ) { fprintf( pFileToWrite, "consed.autoFinishPrintCustomNavigationFileForChosenReads: %s\n", ( resources_.bAutoFinishPrintCustomNavigationFileForChosenReads_ ? "true" : "false" ) ); } // consed.autoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch if ( resources_.nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_ != CONDEF->nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_ ) { fprintf( pFileToWrite, "consed.autoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch: %d\n", resources_.nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_ ); } // consed.autoFinishTagOligosWhenDoExperiments if ( resources_.bAutoFinishTagOligosWhenDoExperiments_ != CONDEF->bAutoFinishTagOligosWhenDoExperiments_ ) { fprintf( pFileToWrite, "consed.autoFinishTagOligosWhenDoExperiments: %s\n", ( resources_.bAutoFinishTagOligosWhenDoExperiments_ ? "true" : "false" ) ); } // consed.countPads if ( resources_.bCountPads_ != CONDEF->bCountPads_ ) { fprintf( pFileToWrite, "consed.countPads: %s\n", ( resources_.bCountPads_ ? "true" : "false" ) ); } // consed.debugging if ( resources_.nDebugging_ != CONDEF->nDebugging_ ) { fprintf( pFileToWrite, "consed.debugging: %d\n", resources_.nDebugging_ ); } // consed.debugging2 if ( resources_.nDebugging2_ != CONDEF->nDebugging2_ ) { fprintf( pFileToWrite, "consed.debugging2: %d\n", resources_.nDebugging2_ ); } // consed.debugging3 if ( resources_.nDebugging3_ != CONDEF->nDebugging3_ ) { fprintf( pFileToWrite, "consed.debugging3: %d\n", resources_.nDebugging3_ ); } // consed.debuggingString if ( resources_.soDebuggingString_ != CONDEF->soDebuggingString_ ) { fprintf( pFileToWrite, "consed.debuggingString: %s\n", resources_.soDebuggingString_.data() ); } // consed.ignoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion if ( resources_.nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_ != CONDEF->nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_ ) { fprintf( pFileToWrite, "consed.ignoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion: %d\n", resources_.nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_ ); } // consed.ignoreUnalignedHighQualitySegmentsShorterThanThis if ( resources_.nIgnoreUnalignedHighQualitySegmentsShorterThanThis_ != CONDEF->nIgnoreUnalignedHighQualitySegmentsShorterThanThis_ ) { fprintf( pFileToWrite, "consed.ignoreUnalignedHighQualitySegmentsShorterThanThis: %d\n", resources_.nIgnoreUnalignedHighQualitySegmentsShorterThanThis_ ); } // consed.primersLookThisFarForForwardVectorInsertJunction if ( resources_.nPrimersLookThisFarForForwardVectorInsertJunction_ != CONDEF->nPrimersLookThisFarForForwardVectorInsertJunction_ ) { fprintf( pFileToWrite, "consed.primersLookThisFarForForwardVectorInsertJunction: %d\n", resources_.nPrimersLookThisFarForForwardVectorInsertJunction_ ); } // consed.primersDNAConcentrationNanomolar if ( resources_.dPrimersDNAConcentrationNanomolar_ != CONDEF->dPrimersDNAConcentrationNanomolar_ ) { fprintf( pFileToWrite, "consed.primersDNAConcentrationNanomolar: %f\n", resources_.dPrimersDNAConcentrationNanomolar_ ); } // consed.primersMaxMatchElsewhereScore if ( resources_.nPrimersMaxMatchElsewhereScore_ != CONDEF->nPrimersMaxMatchElsewhereScore_ ) { fprintf( pFileToWrite, "consed.primersMaxMatchElsewhereScore: %d\n", resources_.nPrimersMaxMatchElsewhereScore_ ); } // consed.primersMaxMatchElsewhereScoreForPCR if ( resources_.nPrimersMaxMatchElsewhereScoreForPCR_ != CONDEF->nPrimersMaxMatchElsewhereScoreForPCR_ ) { fprintf( pFileToWrite, "consed.primersMaxMatchElsewhereScoreForPCR: %d\n", resources_.nPrimersMaxMatchElsewhereScoreForPCR_ ); } // consed.primersMaxSelfMatchScore if ( resources_.nPrimersMaxSelfMatchScore_ != CONDEF->nPrimersMaxSelfMatchScore_ ) { fprintf( pFileToWrite, "consed.primersMaxSelfMatchScore: %d\n", resources_.nPrimersMaxSelfMatchScore_ ); } // consed.primersMaxPrimerDimerScoreForPCR if ( resources_.nPrimersMaxPrimerDimerScoreForPCR_ != CONDEF->nPrimersMaxPrimerDimerScoreForPCR_ ) { fprintf( pFileToWrite, "consed.primersMaxPrimerDimerScoreForPCR: %d\n", resources_.nPrimersMaxPrimerDimerScoreForPCR_ ); } // consed.primersMinQuality if ( resources_.nPrimersMinQuality_ != CONDEF->nPrimersMinQuality_ ) { fprintf( pFileToWrite, "consed.primersMinQuality: %d\n", resources_.nPrimersMinQuality_ ); } // consed.primersPrintInfoOnRejectedTemplates if ( resources_.bPrimersPrintInfoOnRejectedTemplates_ != CONDEF->bPrimersPrintInfoOnRejectedTemplates_ ) { fprintf( pFileToWrite, "consed.primersPrintInfoOnRejectedTemplates: %s\n", ( resources_.bPrimersPrintInfoOnRejectedTemplates_ ? "true" : "false" ) ); } // consed.primersSaltConcentrationMillimolar if ( resources_.dPrimersSaltConcentrationMillimolar_ != CONDEF->dPrimersSaltConcentrationMillimolar_ ) { fprintf( pFileToWrite, "consed.primersSaltConcentrationMillimolar: %f\n", resources_.dPrimersSaltConcentrationMillimolar_ ); } // consed.primersScreenForVector if ( resources_.bPrimersScreenForVector_ != CONDEF->bPrimersScreenForVector_ ) { fprintf( pFileToWrite, "consed.primersScreenForVector: %s\n", ( resources_.bPrimersScreenForVector_ ? "true" : "false" ) ); } // consed.primersToleranceForDifferentBeginningLocationOfUniversalPrimerReads if ( resources_.nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_ != CONDEF->nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_ ) { fprintf( pFileToWrite, "consed.primersToleranceForDifferentBeginningLocationOfUniversalPrimerReads: %d\n", resources_.nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_ ); } // consed.primersTooManyVectorBasesInWalkingRead if ( resources_.nPrimersTooManyVectorBasesInWalkingRead_ != CONDEF->nPrimersTooManyVectorBasesInWalkingRead_ ) { fprintf( pFileToWrite, "consed.primersTooManyVectorBasesInWalkingRead: %d\n", resources_.nPrimersTooManyVectorBasesInWalkingRead_ ); } // consed.qualityThresholdForLowConsensusQuality if ( resources_.nQualityThresholdForLowConsensusQuality_ != CONDEF->nQualityThresholdForLowConsensusQuality_ ) { fprintf( pFileToWrite, "consed.qualityThresholdForLowConsensusQuality: %d\n", resources_.nQualityThresholdForLowConsensusQuality_ ); } // consed.tagColorPerCentOfBase if ( resources_.nTagColorPerCentOfBase_ != CONDEF->nTagColorPerCentOfBase_ ) { fprintf( pFileToWrite, "consed.tagColorPerCentOfBase: %d\n", resources_.nTagColorPerCentOfBase_ ); } // consed.uncompressedChromatDirectory if ( resources_.soUncompressedChromatDirectory_ != CONDEF->soUncompressedChromatDirectory_ ) { fprintf( pFileToWrite, "consed.uncompressedChromatDirectory: %s\n", resources_.soUncompressedChromatDirectory_.data() ); } // consed.454sff2scfDirectory if ( resources_.fil454sff2scfDirectory_ != CONDEF->fil454sff2scfDirectory_ ) { fprintf( pFileToWrite, "consed.454sff2scfDirectory: %s\n", resources_.fil454sff2scfDirectory_.data() ); } // consed.whenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion if ( resources_.nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion_ != CONDEF->nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion_ ) { fprintf( pFileToWrite, "consed.whenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion: %d\n", resources_.nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion_ ); } // consed.writeThisAceFormat if ( resources_.nWriteThisAceFormat_ != CONDEF->nWriteThisAceFormat_ ) { fprintf( pFileToWrite, "consed.writeThisAceFormat: %d\n", resources_.nWriteThisAceFormat_ ); } // consed.dumpCoreIfBoundsError if ( resources_.bDumpCoreIfBoundsError_ != CONDEF->bDumpCoreIfBoundsError_ ) { fprintf( pFileToWrite, "consed.dumpCoreIfBoundsError: %s\n", ( resources_.bDumpCoreIfBoundsError_ ? "true" : "false" ) ); } // consed.autoFinishMinSmithWatermanScoreOfARun if ( resources_.nAutoFinishMinSmithWatermanScoreOfARun_ != CONDEF->nAutoFinishMinSmithWatermanScoreOfARun_ ) { fprintf( pFileToWrite, "consed.autoFinishMinSmithWatermanScoreOfARun: %d\n", resources_.nAutoFinishMinSmithWatermanScoreOfARun_ ); } // consed.autoFinishDoNotComparePCRPrimersMoreThanThisManyTimes if ( resources_.dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_ != CONDEF->dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotComparePCRPrimersMoreThanThisManyTimes: %f\n", resources_.dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_ ); } // consed.restrictionDigestMaximumBasesToCompareToVector if ( resources_.nRestrictionDigestMaximumBasesToCompareToVector_ != CONDEF->nRestrictionDigestMaximumBasesToCompareToVector_ ) { fprintf( pFileToWrite, "consed.restrictionDigestMaximumBasesToCompareToVector: %d\n", resources_.nRestrictionDigestMaximumBasesToCompareToVector_ ); } // consed.restrictionDigestZoomFactor if ( resources_.dRestrictionDigestZoomFactor_ != CONDEF->dRestrictionDigestZoomFactor_ ) { fprintf( pFileToWrite, "consed.restrictionDigestZoomFactor: %f\n", resources_.dRestrictionDigestZoomFactor_ ); } // consed.restrictionDigestZoomFactorForNavigate if ( resources_.dRestrictionDigestZoomFactorForNavigate_ != CONDEF->dRestrictionDigestZoomFactorForNavigate_ ) { fprintf( pFileToWrite, "consed.restrictionDigestZoomFactorForNavigate: %f\n", resources_.dRestrictionDigestZoomFactorForNavigate_ ); } // consed.restrictionDigestToleranceInPositionUnits if ( resources_.nRestrictionDigestToleranceInPositionUnits_ != CONDEF->nRestrictionDigestToleranceInPositionUnits_ ) { fprintf( pFileToWrite, "consed.restrictionDigestToleranceInPositionUnits: %d\n", resources_.nRestrictionDigestToleranceInPositionUnits_ ); } // consed.autoPCRAmplifyTooManySeriousFalseMatches if ( resources_.nAutoPCRAmplifyTooManySeriousFalseMatches_ != CONDEF->nAutoPCRAmplifyTooManySeriousFalseMatches_ ) { fprintf( pFileToWrite, "consed.autoPCRAmplifyTooManySeriousFalseMatches: %d\n", resources_.nAutoPCRAmplifyTooManySeriousFalseMatches_ ); } // consed.assemblyViewZoomFactor if ( resources_.dAssemblyViewZoomFactor_ != CONDEF->dAssemblyViewZoomFactor_ ) { fprintf( pFileToWrite, "consed.assemblyViewZoomFactor: %f\n", resources_.dAssemblyViewZoomFactor_ ); } // consed.assemblyViewFilterInconsistentFwdRevPairsIfThisClose if ( resources_.nAssemblyViewFilterInconsistentFwdRevPairsIfThisClose_ != CONDEF->nAssemblyViewFilterInconsistentFwdRevPairsIfThisClose_ ) { fprintf( pFileToWrite, "consed.assemblyViewFilterInconsistentFwdRevPairsIfThisClose: %d\n", resources_.nAssemblyViewFilterInconsistentFwdRevPairsIfThisClose_ ); } // consed.assemblyViewGridCellWidthInPixels if ( resources_.dAssemblyViewGridCellWidthInPixels_ != CONDEF->dAssemblyViewGridCellWidthInPixels_ ) { fprintf( pFileToWrite, "consed.assemblyViewGridCellWidthInPixels: %f\n", resources_.dAssemblyViewGridCellWidthInPixels_ ); } // consed.assemblyViewCursorSensitivityInPixels if ( resources_.nAssemblyViewCursorSensitivityInPixels_ != CONDEF->nAssemblyViewCursorSensitivityInPixels_ ) { fprintf( pFileToWrite, "consed.assemblyViewCursorSensitivityInPixels: %d\n", resources_.nAssemblyViewCursorSensitivityInPixels_ ); } // consed.assemblyViewReadDepthQuality if ( resources_.nAssemblyViewReadDepthQuality_ != CONDEF->nAssemblyViewReadDepthQuality_ ) { fprintf( pFileToWrite, "consed.assemblyViewReadDepthQuality: %d\n", resources_.nAssemblyViewReadDepthQuality_ ); } // consed.showAllTracesMaxNumberOfTracesToShowAtOnce if ( resources_.nShowAllTracesMaxNumberOfTracesToShowAtOnce_ != CONDEF->nShowAllTracesMaxNumberOfTracesToShowAtOnce_ ) { fprintf( pFileToWrite, "consed.showAllTracesMaxNumberOfTracesToShowAtOnce: %d\n", resources_.nShowAllTracesMaxNumberOfTracesToShowAtOnce_ ); } // consed.allowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess if ( resources_.nAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess_ != CONDEF->nAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess_ ) { fprintf( pFileToWrite, "consed.allowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess: %d\n", resources_.nAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess_ ); } // consed.justForPrimateProject if ( resources_.bJustForPrimateProject_ != CONDEF->bJustForPrimateProject_ ) { fprintf( pFileToWrite, "consed.justForPrimateProject: %s\n", ( resources_.bJustForPrimateProject_ ? "true" : "false" ) ); } // consed.solexaFilesAreAssumedToBeHere if ( resources_.filSolexaFilesAreAssumedToBeHere_ != CONDEF->filSolexaFilesAreAssumedToBeHere_ ) { fprintf( pFileToWrite, "consed.solexaFilesAreAssumedToBeHere: %s\n", resources_.filSolexaFilesAreAssumedToBeHere_.data() ); } // consed.solexaAlignmentFilesPerInsertingPadsCycle if ( resources_.nSolexaAlignmentFilesPerInsertingPadsCycle_ != CONDEF->nSolexaAlignmentFilesPerInsertingPadsCycle_ ) { fprintf( pFileToWrite, "consed.solexaAlignmentFilesPerInsertingPadsCycle: %d\n", resources_.nSolexaAlignmentFilesPerInsertingPadsCycle_ ); } // consed.solexaAlignmentsPerAlignmentFile if ( resources_.nSolexaAlignmentsPerAlignmentFile_ != CONDEF->nSolexaAlignmentsPerAlignmentFile_ ) { fprintf( pFileToWrite, "consed.solexaAlignmentsPerAlignmentFile: %d\n", resources_.nSolexaAlignmentsPerAlignmentFile_ ); } // consed.solexaFastqFilesArePhredQualityNotSolexaQuality if ( resources_.bSolexaFastqFilesArePhredQualityNotSolexaQuality_ != CONDEF->bSolexaFastqFilesArePhredQualityNotSolexaQuality_ ) { fprintf( pFileToWrite, "consed.solexaFastqFilesArePhredQualityNotSolexaQuality: %s\n", ( resources_.bSolexaFastqFilesArePhredQualityNotSolexaQuality_ ? "true" : "false" ) ); } // consed.solexa64FastqOrSanger33Fastq if ( resources_.soSolexa64FastqOrSanger33Fastq_ != CONDEF->soSolexa64FastqOrSanger33Fastq_ ) { fprintf( pFileToWrite, "consed.solexa64FastqOrSanger33Fastq: %s\n", resources_.soSolexa64FastqOrSanger33Fastq_.data() ); } // consed.maximumReadsInReadList if ( resources_.nMaximumReadsInReadList_ != CONDEF->nMaximumReadsInReadList_ ) { fprintf( pFileToWrite, "consed.maximumReadsInReadList: %d\n", resources_.nMaximumReadsInReadList_ ); } // consed.maxLengthOfReadsInapLocatedFragment2 if ( resources_.nMaxLengthOfReadsInapLocatedFragment2_ != CONDEF->nMaxLengthOfReadsInapLocatedFragment2_ ) { fprintf( pFileToWrite, "consed.maxLengthOfReadsInapLocatedFragment2: %d\n", resources_.nMaxLengthOfReadsInapLocatedFragment2_ ); } // consed.maximumStartupErrorsToReport if ( resources_.nMaximumStartupErrorsToReport_ != CONDEF->nMaximumStartupErrorsToReport_ ) { fprintf( pFileToWrite, "consed.maximumStartupErrorsToReport: %d\n", resources_.nMaximumStartupErrorsToReport_ ); } // consed.454LinkerAlignmentMatchScore if ( resources_.n454LinkerAlignmentMatchScore_ != CONDEF->n454LinkerAlignmentMatchScore_ ) { fprintf( pFileToWrite, "consed.454LinkerAlignmentMatchScore: %d\n", resources_.n454LinkerAlignmentMatchScore_ ); } // consed.454LinkerAlignmentMismatchScore if ( resources_.n454LinkerAlignmentMismatchScore_ != CONDEF->n454LinkerAlignmentMismatchScore_ ) { fprintf( pFileToWrite, "consed.454LinkerAlignmentMismatchScore: %d\n", resources_.n454LinkerAlignmentMismatchScore_ ); } // consed.454LinkerAlignmentIndelScore if ( resources_.n454LinkerAlignmentIndelScore_ != CONDEF->n454LinkerAlignmentIndelScore_ ) { fprintf( pFileToWrite, "consed.454LinkerAlignmentIndelScore: %d\n", resources_.n454LinkerAlignmentIndelScore_ ); } // consed.filter454ReadsDeleteCrossMatchOutput if ( resources_.bFilter454ReadsDeleteCrossMatchOutput_ != CONDEF->bFilter454ReadsDeleteCrossMatchOutput_ ) { fprintf( pFileToWrite, "consed.filter454ReadsDeleteCrossMatchOutput: %s\n", ( resources_.bFilter454ReadsDeleteCrossMatchOutput_ ? "true" : "false" ) ); } // consed.autoReportAllNeededSpeciesCode if ( resources_.nAutoReportAllNeededSpeciesCode_ != CONDEF->nAutoReportAllNeededSpeciesCode_ ) { fprintf( pFileToWrite, "consed.autoReportAllNeededSpeciesCode: %d\n", resources_.nAutoReportAllNeededSpeciesCode_ ); } // consed.autoReportUseCommasInBigNumbers if ( resources_.bAutoReportUseCommasInBigNumbers_ != CONDEF->bAutoReportUseCommasInBigNumbers_ ) { fprintf( pFileToWrite, "consed.autoReportUseCommasInBigNumbers: %s\n", ( resources_.bAutoReportUseCommasInBigNumbers_ ? "true" : "false" ) ); } // consed.autoReportPrintToCompareToReich if ( resources_.bAutoReportPrintToCompareToReich_ != CONDEF->bAutoReportPrintToCompareToReich_ ) { fprintf( pFileToWrite, "consed.autoReportPrintToCompareToReich: %s\n", ( resources_.bAutoReportPrintToCompareToReich_ ? "true" : "false" ) ); } // consed.autoReportOnlyAllowSitesThatAreBetweenAcceptableSites if ( resources_.bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_ != CONDEF->bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_ ) { fprintf( pFileToWrite, "consed.autoReportOnlyAllowSitesThatAreBetweenAcceptableSites: %s\n", ( resources_.bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_ ? "true" : "false" ) ); } // consed.autoReportDeaminationMutationsDeterminedByMoreAccurateMethod if ( resources_.bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_ != CONDEF->bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_ ) { fprintf( pFileToWrite, "consed.autoReportDeaminationMutationsDeterminedByMoreAccurateMethod: %s\n", ( resources_.bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_ ? "true" : "false" ) ); } // consed.autoReportChooseTreesUsingBadData if ( resources_.bAutoReportChooseTreesUsingBadData_ != CONDEF->bAutoReportChooseTreesUsingBadData_ ) { fprintf( pFileToWrite, "consed.autoReportChooseTreesUsingBadData: %s\n", ( resources_.bAutoReportChooseTreesUsingBadData_ ? "true" : "false" ) ); } // consed.autoReportChooseTreesByCountingDeaminationMutations if ( resources_.bAutoReportChooseTreesByCountingDeaminationMutations_ != CONDEF->bAutoReportChooseTreesByCountingDeaminationMutations_ ) { fprintf( pFileToWrite, "consed.autoReportChooseTreesByCountingDeaminationMutations: %s\n", ( resources_.bAutoReportChooseTreesByCountingDeaminationMutations_ ? "true" : "false" ) ); } // consed.autoReportChooseTreesUsingKimura if ( resources_.bAutoReportChooseTreesUsingKimura_ != CONDEF->bAutoReportChooseTreesUsingKimura_ ) { fprintf( pFileToWrite, "consed.autoReportChooseTreesUsingKimura: %s\n", ( resources_.bAutoReportChooseTreesUsingKimura_ ? "true" : "false" ) ); } // consed.autoReportPrintCrudeChimpHumanMutations if ( resources_.bAutoReportPrintCrudeChimpHumanMutations_ != CONDEF->bAutoReportPrintCrudeChimpHumanMutations_ ) { fprintf( pFileToWrite, "consed.autoReportPrintCrudeChimpHumanMutations: %s\n", ( resources_.bAutoReportPrintCrudeChimpHumanMutations_ ? "true" : "false" ) ); } // consed.autoReportPrintPositionsForGraham if ( resources_.bAutoReportPrintPositionsForGraham_ != CONDEF->bAutoReportPrintPositionsForGraham_ ) { fprintf( pFileToWrite, "consed.autoReportPrintPositionsForGraham: %s\n", ( resources_.bAutoReportPrintPositionsForGraham_ ? "true" : "false" ) ); } // consed.autoReportPrintAncestralCpGs if ( resources_.bAutoReportPrintAncestralCpGs_ != CONDEF->bAutoReportPrintAncestralCpGs_ ) { fprintf( pFileToWrite, "consed.autoReportPrintAncestralCpGs: %s\n", ( resources_.bAutoReportPrintAncestralCpGs_ ? "true" : "false" ) ); } // consed.autoReportPrintCpGMutations if ( resources_.bAutoReportPrintCpGMutations_ != CONDEF->bAutoReportPrintCpGMutations_ ) { fprintf( pFileToWrite, "consed.autoReportPrintCpGMutations: %s\n", ( resources_.bAutoReportPrintCpGMutations_ ? "true" : "false" ) ); } // consed.autoReportPrintMutationsWithContext if ( resources_.bAutoReportPrintMutationsWithContext_ != CONDEF->bAutoReportPrintMutationsWithContext_ ) { fprintf( pFileToWrite, "consed.autoReportPrintMutationsWithContext: %s\n", ( resources_.bAutoReportPrintMutationsWithContext_ ? "true" : "false" ) ); } // consed.autoReportCountAllMutationsML if ( resources_.bAutoReportCountAllMutationsML_ != CONDEF->bAutoReportCountAllMutationsML_ ) { fprintf( pFileToWrite, "consed.autoReportCountAllMutationsML: %s\n", ( resources_.bAutoReportCountAllMutationsML_ ? "true" : "false" ) ); } // consed.autoReportCountAllMutations if ( resources_.bAutoReportCountAllMutations_ != CONDEF->bAutoReportCountAllMutations_ ) { fprintf( pFileToWrite, "consed.autoReportCountAllMutations: %s\n", ( resources_.bAutoReportCountAllMutations_ ? "true" : "false" ) ); } // consed.autoReportIgnoreMultipleTrees if ( resources_.bAutoReportIgnoreMultipleTrees_ != CONDEF->bAutoReportIgnoreMultipleTrees_ ) { fprintf( pFileToWrite, "consed.autoReportIgnoreMultipleTrees: %s\n", ( resources_.bAutoReportIgnoreMultipleTrees_ ? "true" : "false" ) ); } // consed.autoReportCountAcceptableColumnsWithNoneOnLeft if ( resources_.bAutoReportCountAcceptableColumnsWithNoneOnLeft_ != CONDEF->bAutoReportCountAcceptableColumnsWithNoneOnLeft_ ) { fprintf( pFileToWrite, "consed.autoReportCountAcceptableColumnsWithNoneOnLeft: %s\n", ( resources_.bAutoReportCountAcceptableColumnsWithNoneOnLeft_ ? "true" : "false" ) ); } // consed.autoReportPrintFlankedColumns4 if ( resources_.bAutoReportPrintFlankedColumns4_ != CONDEF->bAutoReportPrintFlankedColumns4_ ) { fprintf( pFileToWrite, "consed.autoReportPrintFlankedColumns4: %s\n", ( resources_.bAutoReportPrintFlankedColumns4_ ? "true" : "false" ) ); } // consed.autoReportUseAnnotationFormat if ( resources_.bAutoReportUseAnnotationFormat_ != CONDEF->bAutoReportUseAnnotationFormat_ ) { fprintf( pFileToWrite, "consed.autoReportUseAnnotationFormat: %s\n", ( resources_.bAutoReportUseAnnotationFormat_ ? "true" : "false" ) ); } // consed.autoReportPrintFlankedColumns3 if ( resources_.bAutoReportPrintFlankedColumns3_ != CONDEF->bAutoReportPrintFlankedColumns3_ ) { fprintf( pFileToWrite, "consed.autoReportPrintFlankedColumns3: %s\n", ( resources_.bAutoReportPrintFlankedColumns3_ ? "true" : "false" ) ); } // consed.autoReportPrintFlankedColumns2 if ( resources_.bAutoReportPrintFlankedColumns2_ != CONDEF->bAutoReportPrintFlankedColumns2_ ) { fprintf( pFileToWrite, "consed.autoReportPrintFlankedColumns2: %s\n", ( resources_.bAutoReportPrintFlankedColumns2_ ? "true" : "false" ) ); } // consed.autoReportPrintFlankedColumns if ( resources_.bAutoReportPrintFlankedColumns_ != CONDEF->bAutoReportPrintFlankedColumns_ ) { fprintf( pFileToWrite, "consed.autoReportPrintFlankedColumns: %s\n", ( resources_.bAutoReportPrintFlankedColumns_ ? "true" : "false" ) ); } // consed.autoReportHighQualitySegmentData if ( resources_.bAutoReportHighQualitySegmentData_ != CONDEF->bAutoReportHighQualitySegmentData_ ) { fprintf( pFileToWrite, "consed.autoReportHighQualitySegmentData: %s\n", ( resources_.bAutoReportHighQualitySegmentData_ ? "true" : "false" ) ); } // consed.autoReportGoodReadsBug if ( resources_.bAutoReportGoodReadsBug_ != CONDEF->bAutoReportGoodReadsBug_ ) { fprintf( pFileToWrite, "consed.autoReportGoodReadsBug: %s\n", ( resources_.bAutoReportGoodReadsBug_ ? "true" : "false" ) ); } // consed.autoReportDiscrepancyRateInFlankedRegions if ( resources_.bAutoReportDiscrepancyRateInFlankedRegions_ != CONDEF->bAutoReportDiscrepancyRateInFlankedRegions_ ) { fprintf( pFileToWrite, "consed.autoReportDiscrepancyRateInFlankedRegions: %s\n", ( resources_.bAutoReportDiscrepancyRateInFlankedRegions_ ? "true" : "false" ) ); } // consed.autoReportDiscrepancyRateInFlankedRegions2 if ( resources_.bAutoReportDiscrepancyRateInFlankedRegions2_ != CONDEF->bAutoReportDiscrepancyRateInFlankedRegions2_ ) { fprintf( pFileToWrite, "consed.autoReportDiscrepancyRateInFlankedRegions2: %s\n", ( resources_.bAutoReportDiscrepancyRateInFlankedRegions2_ ? "true" : "false" ) ); } // consed.autoReportDiscrepancyRateInFlankedRegions4 if ( resources_.bAutoReportDiscrepancyRateInFlankedRegions4_ != CONDEF->bAutoReportDiscrepancyRateInFlankedRegions4_ ) { fprintf( pFileToWrite, "consed.autoReportDiscrepancyRateInFlankedRegions4: %s\n", ( resources_.bAutoReportDiscrepancyRateInFlankedRegions4_ ? "true" : "false" ) ); } // consed.autoReportDiscrepancyRateInFlankedRegions5 if ( resources_.bAutoReportDiscrepancyRateInFlankedRegions5_ != CONDEF->bAutoReportDiscrepancyRateInFlankedRegions5_ ) { fprintf( pFileToWrite, "consed.autoReportDiscrepancyRateInFlankedRegions5: %s\n", ( resources_.bAutoReportDiscrepancyRateInFlankedRegions5_ ? "true" : "false" ) ); } // consed.autoReportSingleSignalOrQuality if ( resources_.bAutoReportSingleSignalOrQuality_ != CONDEF->bAutoReportSingleSignalOrQuality_ ) { fprintf( pFileToWrite, "consed.autoReportSingleSignalOrQuality: %s\n", ( resources_.bAutoReportSingleSignalOrQuality_ ? "true" : "false" ) ); } // consed.autoReportLowQualityBasesInHQS if ( resources_.bAutoReportLowQualityBasesInHQS_ != CONDEF->bAutoReportLowQualityBasesInHQS_ ) { fprintf( pFileToWrite, "consed.autoReportLowQualityBasesInHQS: %s\n", ( resources_.bAutoReportLowQualityBasesInHQS_ ? "true" : "false" ) ); } // consed.autoReportCompareHQSWithLQS if ( resources_.bAutoReportCompareHQSWithLQS_ != CONDEF->bAutoReportCompareHQSWithLQS_ ) { fprintf( pFileToWrite, "consed.autoReportCompareHQSWithLQS: %s\n", ( resources_.bAutoReportCompareHQSWithLQS_ ? "true" : "false" ) ); } // consed.autoReportCountColumnsForGroupsOfSpecies if ( resources_.bAutoReportCountColumnsForGroupsOfSpecies_ != CONDEF->bAutoReportCountColumnsForGroupsOfSpecies_ ) { fprintf( pFileToWrite, "consed.autoReportCountColumnsForGroupsOfSpecies: %s\n", ( resources_.bAutoReportCountColumnsForGroupsOfSpecies_ ? "true" : "false" ) ); } // consed.autoReportSingleSignalInfo if ( resources_.bAutoReportSingleSignalInfo_ != CONDEF->bAutoReportSingleSignalInfo_ ) { fprintf( pFileToWrite, "consed.autoReportSingleSignalInfo: %s\n", ( resources_.bAutoReportSingleSignalInfo_ ? "true" : "false" ) ); } // consed.autoReportSingleSignalInfo2 if ( resources_.bAutoReportSingleSignalInfo2_ != CONDEF->bAutoReportSingleSignalInfo2_ ) { fprintf( pFileToWrite, "consed.autoReportSingleSignalInfo2: %s\n", ( resources_.bAutoReportSingleSignalInfo2_ ? "true" : "false" ) ); } // consed.autoReportCompareTopAndBottomStrands if ( resources_.bAutoReportCompareTopAndBottomStrands_ != CONDEF->bAutoReportCompareTopAndBottomStrands_ ) { fprintf( pFileToWrite, "consed.autoReportCompareTopAndBottomStrands: %s\n", ( resources_.bAutoReportCompareTopAndBottomStrands_ ? "true" : "false" ) ); } // consed.autoReportCompareTopAndBottomStrandsNoHuman if ( resources_.bAutoReportCompareTopAndBottomStrandsNoHuman_ != CONDEF->bAutoReportCompareTopAndBottomStrandsNoHuman_ ) { fprintf( pFileToWrite, "consed.autoReportCompareTopAndBottomStrandsNoHuman: %s\n", ( resources_.bAutoReportCompareTopAndBottomStrandsNoHuman_ ? "true" : "false" ) ); } // consed.autoReportCompareTopAndBottomStrands2 if ( resources_.bAutoReportCompareTopAndBottomStrands2_ != CONDEF->bAutoReportCompareTopAndBottomStrands2_ ) { fprintf( pFileToWrite, "consed.autoReportCompareTopAndBottomStrands2: %s\n", ( resources_.bAutoReportCompareTopAndBottomStrands2_ ? "true" : "false" ) ); } // consed.autoReportCompareTopAndBottomStrands3 if ( resources_.bAutoReportCompareTopAndBottomStrands3_ != CONDEF->bAutoReportCompareTopAndBottomStrands3_ ) { fprintf( pFileToWrite, "consed.autoReportCompareTopAndBottomStrands3: %s\n", ( resources_.bAutoReportCompareTopAndBottomStrands3_ ? "true" : "false" ) ); } // consed.autoReportCompareTopAndBottomStrands4 if ( resources_.bAutoReportCompareTopAndBottomStrands4_ != CONDEF->bAutoReportCompareTopAndBottomStrands4_ ) { fprintf( pFileToWrite, "consed.autoReportCompareTopAndBottomStrands4: %s\n", ( resources_.bAutoReportCompareTopAndBottomStrands4_ ? "true" : "false" ) ); } // consed.autoReportTopStrandPinnedPosition if ( resources_.nAutoReportTopStrandPinnedPosition_ != CONDEF->nAutoReportTopStrandPinnedPosition_ ) { fprintf( pFileToWrite, "consed.autoReportTopStrandPinnedPosition: %d\n", resources_.nAutoReportTopStrandPinnedPosition_ ); } // consed.autoReportBottomStrandPinnedPosition if ( resources_.nAutoReportBottomStrandPinnedPosition_ != CONDEF->nAutoReportBottomStrandPinnedPosition_ ) { fprintf( pFileToWrite, "consed.autoReportBottomStrandPinnedPosition: %d\n", resources_.nAutoReportBottomStrandPinnedPosition_ ); } // consed.autoReportCompareTopAndBottomStrandsWithHuman if ( resources_.bAutoReportCompareTopAndBottomStrandsWithHuman_ != CONDEF->bAutoReportCompareTopAndBottomStrandsWithHuman_ ) { fprintf( pFileToWrite, "consed.autoReportCompareTopAndBottomStrandsWithHuman: %s\n", ( resources_.bAutoReportCompareTopAndBottomStrandsWithHuman_ ? "true" : "false" ) ); } // consed.autoReportPrintLengthsOfAlignedSegmentsOfReads if ( resources_.bAutoReportPrintLengthsOfAlignedSegmentsOfReads_ != CONDEF->bAutoReportPrintLengthsOfAlignedSegmentsOfReads_ ) { fprintf( pFileToWrite, "consed.autoReportPrintLengthsOfAlignedSegmentsOfReads: %s\n", ( resources_.bAutoReportPrintLengthsOfAlignedSegmentsOfReads_ ? "true" : "false" ) ); } // consed.autoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads if ( resources_.bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_ != CONDEF->bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_ ) { fprintf( pFileToWrite, "consed.autoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads: %s\n", ( resources_.bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_ ? "true" : "false" ) ); } // consed.autoReportPrintIfReadsAreCorrectlyAligned if ( resources_.bAutoReportPrintIfReadsAreCorrectlyAligned_ != CONDEF->bAutoReportPrintIfReadsAreCorrectlyAligned_ ) { fprintf( pFileToWrite, "consed.autoReportPrintIfReadsAreCorrectlyAligned: %s\n", ( resources_.bAutoReportPrintIfReadsAreCorrectlyAligned_ ? "true" : "false" ) ); } // consed.autoReportCalculateErrorProbabilitiesByComparingPTroPPan if ( resources_.bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_ != CONDEF->bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_ ) { fprintf( pFileToWrite, "consed.autoReportCalculateErrorProbabilitiesByComparingPTroPPan: %s\n", ( resources_.bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_ ? "true" : "false" ) ); } // consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies if ( resources_.bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_ != CONDEF->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_ ) { fprintf( pFileToWrite, "consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies: %s\n", ( resources_.bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_ ? "true" : "false" ) ); } // consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies2 if ( resources_.bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_ != CONDEF->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_ ) { fprintf( pFileToWrite, "consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies2: %s\n", ( resources_.bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_ ? "true" : "false" ) ); } // consed.autoReportFilterSingleSignal if ( resources_.bAutoReportFilterSingleSignal_ != CONDEF->bAutoReportFilterSingleSignal_ ) { fprintf( pFileToWrite, "consed.autoReportFilterSingleSignal: %s\n", ( resources_.bAutoReportFilterSingleSignal_ ? "true" : "false" ) ); } // consed.autoReportGoodHitReads if ( resources_.filAutoReportGoodHitReads_ != CONDEF->filAutoReportGoodHitReads_ ) { fprintf( pFileToWrite, "consed.autoReportGoodHitReads: %s\n", resources_.filAutoReportGoodHitReads_.data() ); } // consed.autoReportQualityWindowLow if ( resources_.nAutoReportQualityWindowLow_ != CONDEF->nAutoReportQualityWindowLow_ ) { fprintf( pFileToWrite, "consed.autoReportQualityWindowLow: %d\n", resources_.nAutoReportQualityWindowLow_ ); } // consed.autoReportQualityWindowHigh if ( resources_.nAutoReportQualityWindowHigh_ != CONDEF->nAutoReportQualityWindowHigh_ ) { fprintf( pFileToWrite, "consed.autoReportQualityWindowHigh: %d\n", resources_.nAutoReportQualityWindowHigh_ ); } // consed.autoReportPrintNumberOfIsolatedPadsForEachSpecies if ( resources_.bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_ != CONDEF->bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_ ) { fprintf( pFileToWrite, "consed.autoReportPrintNumberOfIsolatedPadsForEachSpecies: %s\n", ( resources_.bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_ ? "true" : "false" ) ); } // consed.autoReportPrintNumberOfIsolatedPads if ( resources_.bAutoReportPrintNumberOfIsolatedPads_ != CONDEF->bAutoReportPrintNumberOfIsolatedPads_ ) { fprintf( pFileToWrite, "consed.autoReportPrintNumberOfIsolatedPads: %s\n", ( resources_.bAutoReportPrintNumberOfIsolatedPads_ ? "true" : "false" ) ); } // consed.autoReportIsolatedPadsOfReadsWithThisPattern if ( resources_.soAutoReportIsolatedPadsOfReadsWithThisPattern_ != CONDEF->soAutoReportIsolatedPadsOfReadsWithThisPattern_ ) { fprintf( pFileToWrite, "consed.autoReportIsolatedPadsOfReadsWithThisPattern: %s\n", resources_.soAutoReportIsolatedPadsOfReadsWithThisPattern_.data() ); } // consed.autoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy if ( resources_.nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_ != CONDEF->nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_ ) { fprintf( pFileToWrite, "consed.autoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy: %d\n", resources_.nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_ ); } // consed.autoReportMaxSizeOfDiscrepantRegion if ( resources_.nAutoReportMaxSizeOfDiscrepantRegion_ != CONDEF->nAutoReportMaxSizeOfDiscrepantRegion_ ) { fprintf( pFileToWrite, "consed.autoReportMaxSizeOfDiscrepantRegion: %d\n", resources_.nAutoReportMaxSizeOfDiscrepantRegion_ ); } // consed.autoReportSizeOfDiscrepantRegion if ( resources_.nAutoReportSizeOfDiscrepantRegion_ != CONDEF->nAutoReportSizeOfDiscrepantRegion_ ) { fprintf( pFileToWrite, "consed.autoReportSizeOfDiscrepantRegion: %d\n", resources_.nAutoReportSizeOfDiscrepantRegion_ ); } // consed.autoReportPrintMinimumQualityHistogram if ( resources_.bAutoReportPrintMinimumQualityHistogram_ != CONDEF->bAutoReportPrintMinimumQualityHistogram_ ) { fprintf( pFileToWrite, "consed.autoReportPrintMinimumQualityHistogram: %s\n", ( resources_.bAutoReportPrintMinimumQualityHistogram_ ? "true" : "false" ) ); } // consed.autoReportPrintDiscrepantRegions if ( resources_.bAutoReportPrintDiscrepantRegions_ != CONDEF->bAutoReportPrintDiscrepantRegions_ ) { fprintf( pFileToWrite, "consed.autoReportPrintDiscrepantRegions: %s\n", ( resources_.bAutoReportPrintDiscrepantRegions_ ? "true" : "false" ) ); } // consed.autoReportPrintBasesInDiscrepantRegions if ( resources_.bAutoReportPrintBasesInDiscrepantRegions_ != CONDEF->bAutoReportPrintBasesInDiscrepantRegions_ ) { fprintf( pFileToWrite, "consed.autoReportPrintBasesInDiscrepantRegions: %s\n", ( resources_.bAutoReportPrintBasesInDiscrepantRegions_ ? "true" : "false" ) ); } // consed.autoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis if ( resources_.soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_ != CONDEF->soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_ ) { fprintf( pFileToWrite, "consed.autoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis: %s\n", resources_.soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_.data() ); } // consed.autoReportBackboneReadHasThisStringInIt if ( resources_.soAutoReportBackboneReadHasThisStringInIt_ != CONDEF->soAutoReportBackboneReadHasThisStringInIt_ ) { fprintf( pFileToWrite, "consed.autoReportBackboneReadHasThisStringInIt: %s\n", resources_.soAutoReportBackboneReadHasThisStringInIt_.data() ); } // consed.autoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold if ( resources_.bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_ != CONDEF->bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_ ) { fprintf( pFileToWrite, "consed.autoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold: %s\n", ( resources_.bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_ ? "true" : "false" ) ); } // consed.autoReportPrintSpeciesAlignment if ( resources_.bAutoReportPrintSpeciesAlignment_ != CONDEF->bAutoReportPrintSpeciesAlignment_ ) { fprintf( pFileToWrite, "consed.autoReportPrintSpeciesAlignment: %s\n", ( resources_.bAutoReportPrintSpeciesAlignment_ ? "true" : "false" ) ); } // consed.autoReportPrintReadAlignment if ( resources_.bAutoReportPrintReadAlignment_ != CONDEF->bAutoReportPrintReadAlignment_ ) { fprintf( pFileToWrite, "consed.autoReportPrintReadAlignment: %s\n", ( resources_.bAutoReportPrintReadAlignment_ ? "true" : "false" ) ); } // consed.autoReportPrintTheseReads if ( resources_.filAutoReportPrintTheseReads_ != CONDEF->filAutoReportPrintTheseReads_ ) { fprintf( pFileToWrite, "consed.autoReportPrintTheseReads: %s\n", resources_.filAutoReportPrintTheseReads_.data() ); } // consed.autoReportPrintReadPositions if ( resources_.bAutoReportPrintReadPositions_ != CONDEF->bAutoReportPrintReadPositions_ ) { fprintf( pFileToWrite, "consed.autoReportPrintReadPositions: %s\n", ( resources_.bAutoReportPrintReadPositions_ ? "true" : "false" ) ); } // consed.autoReportPrintChosenReadName if ( resources_.bAutoReportPrintChosenReadName_ != CONDEF->bAutoReportPrintChosenReadName_ ) { fprintf( pFileToWrite, "consed.autoReportPrintChosenReadName: %s\n", ( resources_.bAutoReportPrintChosenReadName_ ? "true" : "false" ) ); } // consed.autoReportNumbersOfCharactersOfChosenReadNameToBePrinted if ( resources_.nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_ != CONDEF->nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_ ) { fprintf( pFileToWrite, "consed.autoReportNumbersOfCharactersOfChosenReadNameToBePrinted: %d\n", resources_.nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_ ); } // consed.autoReportPrefix if ( resources_.soAutoReportPrefix_ != CONDEF->soAutoReportPrefix_ ) { fprintf( pFileToWrite, "consed.autoReportPrefix: %s\n", resources_.soAutoReportPrefix_.data() ); } // consed.autoReportUseOldCriteriaForDeletingColumnsOfPads if ( resources_.bAutoReportUseOldCriteriaForDeletingColumnsOfPads_ != CONDEF->bAutoReportUseOldCriteriaForDeletingColumnsOfPads_ ) { fprintf( pFileToWrite, "consed.autoReportUseOldCriteriaForDeletingColumnsOfPads: %s\n", ( resources_.bAutoReportUseOldCriteriaForDeletingColumnsOfPads_ ? "true" : "false" ) ); } // consed.autoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues if ( resources_.bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_ != CONDEF->bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_ ) { fprintf( pFileToWrite, "consed.autoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues: %s\n", ( resources_.bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_ ? "true" : "false" ) ); } // consed.autoReportFlankingBasesMustBeSingleSignal if ( resources_.bAutoReportFlankingBasesMustBeSingleSignal_ != CONDEF->bAutoReportFlankingBasesMustBeSingleSignal_ ) { fprintf( pFileToWrite, "consed.autoReportFlankingBasesMustBeSingleSignal: %s\n", ( resources_.bAutoReportFlankingBasesMustBeSingleSignal_ ? "true" : "false" ) ); } // consed.autoReportMinimumQualityOfFlankingBases if ( resources_.nAutoReportMinimumQualityOfFlankingBases_ != CONDEF->nAutoReportMinimumQualityOfFlankingBases_ ) { fprintf( pFileToWrite, "consed.autoReportMinimumQualityOfFlankingBases: %d\n", resources_.nAutoReportMinimumQualityOfFlankingBases_ ); } // consed.autoReportFlankingBasesMustBeInHighQualitySegment if ( resources_.bAutoReportFlankingBasesMustBeInHighQualitySegment_ != CONDEF->bAutoReportFlankingBasesMustBeInHighQualitySegment_ ) { fprintf( pFileToWrite, "consed.autoReportFlankingBasesMustBeInHighQualitySegment: %s\n", ( resources_.bAutoReportFlankingBasesMustBeInHighQualitySegment_ ? "true" : "false" ) ); } // consed.autoReportSpecies if ( resources_.soAutoReportSpecies_ != CONDEF->soAutoReportSpecies_ ) { fprintf( pFileToWrite, "consed.autoReportSpecies: %s\n", resources_.soAutoReportSpecies_.data() ); } // guiEditResources.cpp.part7 fclose( pFileToWrite ); popupInfoMessage( widPopupShell_, "Note that these new parameters will take effect only after restarting Consed/Autofinish" ); } void guiEditResources :: checkEverything() { checkPrintPS(); checkDefaultTagType(); checkDefaultTagOnConsensusNotReads(); checkAutoFinishMinNumberOfErrorsFixedByAnExp(); checkAutoFinishRedundancy(); checkAutoFinishAverageInsertSize(); checkPrimersMaxInsertSizeOfASubclone(); checkPrimersMaxMeltingTemp(); checkPrimersMaxMeltingTempForPCR(); checkPrimersPickTemplatesForPrimers(); checkPrimersSubcloneFullPathnameOfFileOfSequencesForScreening(); checkPrimersCloneFullPathnameOfFileOfSequencesForScreening(); checkPrimersMinMeltingTemp(); checkPrimersMinMeltingTempForPCR(); checkSearchFunctionsUseUnalignedEndsOfReads(); checkSearchFunctionsUseLowQualityEndsOfReads(); checkInexactSearchForStringMaxPerCentMismatch(); checkOnlyAllowOneReadWriteConsedAtATime(); checkAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair(); checkPrintWindowCommand(); checkFileOfTagTypes(); checkAssemblyViewShowConsistentFwdRevPairs(); checkAssemblyViewShowConsistentFwdRevPairDepth(); checkAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds(); checkAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs(); checkAssemblyViewShowGapSpanningFwdRevPairs(); checkAssemblyViewShowWhichInconsistentFwdRevPairs(); checkAssemblyViewShowReadDepth(); checkAssemblyViewShowMultipleHighQualityDiscrepancies(); checkAssemblyViewShowRestrictionDigestCutSites(); checkAssemblyViewFilterSequenceMatchesBySize(); checkAssemblyViewSequenceMatchesMinSize(); checkAssemblyViewSequenceMatchesMaxSize(); checkAssemblyViewAutomaticallyStartWithConsed(); checkAssemblyViewDisplayTheseTagTypesOnTheseLines(); checkAssemblyViewShowTags(); checkAutoEditRecalculateHighQualitySegmentsOfReads(); checkAutoEditConvertCloneEndBasesToXs(); checkAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads(); checkAutoEditTagEditableLowConsensusQualityRegions(); checkAutoEditMakeFakeRead(); checkAutoEditMakeFakeReadFromRead1(); checkAutoEditMakeFakeReadFromRead2(); checkAutoEditMakeFakeReadName(); checkAutoEditMakeFakeReadFastaFilename(); checkAutoEditMergeAssembly(); checkAutoEditSecondaryAceFile(); checkAutoEditFixRunsInConsensus(); checkShowAllTracesJustShowGoodTraces(); checkAddAlignedSequenceQualityOfBases(); checkMakeLightBackgroundInAlignedReadsWindowAndTracesWindow(); checkPutVerticalLineAtCursor(); checkPutHorizontalLineAtCursor(); checkHighlightedReadsFile(); checkAutoReportPrintReadNamesInRegion(); checkAutoReportPrintReadNamesInRegionContig(); checkAutoReportPrintReadNamesInRegionLeftPos(); checkAutoReportPrintReadNamesInRegionRightPos(); checkAutoReportPrintHighlyDiscrepantRegions(); checkAutoReportPrintScaffolds(); checkNumberUnpaddedConsensusAtUserDefined(); checkAutoReportPrintHighQualityDiscrepancies(); checkAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags(); checkAutoReportHighQualityDiscrepanciesExcludeMostPads(); checkAutoReportPrintLowConsensusQualityRegions(); checkAutoReportPrintSingleSubcloneRegions(); checkAutoReportPrintSingleStrandedRegions(); checkAutoReportPrintLinkingForwardReversePairs(); checkAutoReportPrintFilteredInconsistentForwardReversePairs(); checkAutoReportPrintAssemblySummary(); checkShowAllTracesDoNotShowTraceIfTheseTagsPresent(); checkNameOfFakeJoiningReadsIncludesAceFileName(); checkWhenUserScrollsOffWindowMillisecondsBetweenScrolling(); checkWhenUserScrollsOffWindowBasesToScrollEachTime(); checkCompareContigsUseBandedRatherThanFullSmithWaterman(); checkCompareContigsBandSize(); checkAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany(); checkAssemblyViewShowSequenceMatches(); checkAssemblyViewOKToShowSequenceMatchesBetweenContigs(); checkAssemblyViewOKToShowSequenceMatchesWithinContigs(); checkAssemblyViewOKToShowDirectSequenceMatches(); checkAssemblyViewOKToShowInvertedSequenceMatches(); checkAssemblyViewOnlyShowSequenceMatchesToAParticularRegion(); checkAssemblyViewOnlyShowSequenceMatchesToThisContig(); checkAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft(); checkAssemblyViewOnlyShowSequenceMatchesToThisRegionRight(); checkAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs(); checkAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar(); checkDefaultReadPrefix(); checkReadPrefixesFile(); checkMaxCharsDisplayedForReadPrefix(); checkAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates(); checkAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions(); checkAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis(); checkAutoFinishDoNotDoPCRIfEndIsExtendedByReads(); checkAutoFinishMaxAcceptableErrorsPerMegabase(); checkAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize(); checkPrimersNumberOfBasesToBackUpToStartLooking(); checkPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment(); checkPrimersOKToChoosePrimersInSingleSubcloneRegion(); checkPrimersOKToChoosePrimersWhereHighQualityDiscrepancies(); checkPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion(); checkAutoFinishCallReversesToFlankGaps(); checkAutoFinishAllowWholeCloneReads(); checkAutoFinishAllowCustomPrimerSubcloneReads(); checkAutoFinishAllowResequencingReads(); checkAutoFinishAllowResequencingReadsOnlyForRunsAndStops(); checkAutoFinishAllowDeNovoUniversalPrimerSubcloneReads(); checkAutoFinishAllowMinilibraries(); checkAutoFinishAllowPCR(); checkAutoFinishAllowUnorientedPCRReactions(); checkAutoFinishAllowResequencingAUniversalPrimerAutofinishRead(); checkAutoFinishAlwaysCloseGapsUsingMinilibraries(); checkAutoFinishMaximumFinishingReadLength(); checkAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger(); checkAutoFinishSuggestSpecialChemistryForRunsAndStops(); checkAutoFinishSuggestThisManyMinilibrariesPerGap(); checkPrimersWindowSizeInLooking(); checkPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified(); checkAlignedReadsWindowInitialCharsWide(); checkAlignedReadsWindowInitialCharsHigh(); checkAlignedReadsWindowMaxCharsForReadNames(); checkAlignedReadsWindowAutomaticallyExpandRoomForReadNames(); checkAutoFinishAllowResequencingReadsToExtendContigs(); checkAutoFinishCallHowManyReversesToFlankGaps(); checkAutoFinishCloseGaps(); checkAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense(); checkAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction(); checkAutoFinishCostOfCustomPrimerSubcloneReaction(); checkAutoFinishCostOfCustomPrimerCloneReaction(); checkAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction(); checkAutoFinishCostOfMinilibrary(); checkAutoFinishCoverSingleSubcloneRegions(); checkAutoFinishCoverLowConsensusQualityRegions(); checkAutoFinishDebugUniversalPrimerReadsFile(); checkAutoFinishDebugCustomPrimerReadsFile(); checkAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases(); checkAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases(); checkAutoFinishDoNotFinishWhereTheseTagsAre(); checkAutoFinishDoNotExtendContigsWhereTheseTagsAre(); checkAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd(); checkDumpContigOrderAndOrientationInfoToThisFile(); checkAutoFinishDumpTemplates(); checkAutoFinishExcludeContigIfOnlyThisManyReadsOrLess(); checkAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis(); checkAutoFinishExcludeContigIfThisManyBasesOrLess(); checkAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions(); checkPrimersMinNumberOfTemplatesForPrimers(); checkAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus(); checkAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead(); checkAutoFinishCDNANotGenomic(); checkAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion(); checkAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads(); checkAutoFinishPrintMinilibrariesSummaryFile(); checkAutoFinishNearGapsSuggestEachMissingReadOfReadPairs(); checkAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger(); checkCheckIfTooManyWalks(); checkNumberOfColumnsBeforeReadNameInAlignedReadsWindow(); checkCompareContigsAlignsThisManyBasesMax(); checkCompressedChromatExtension(); checkDimLowQualityEndsOfReads(); checkDimUnalignedEndsOfReads(); checkFakeReadsSpecifiedByFilenameExtension(); checkFullPathnameOfAddReads2ConsedScript(); checkFullPathnameOfFixContigEndScript(); checkFixContigEndsCleanUpTemporaryFiles(); checkFixContigEndsMinSmithWatermanScoreToMakeJoin(); checkFixContigEndsMinNumberOfReadsInContig(); checkFullPathnameOfCrossMatch(); checkFullPathnameOfPhred(); checkFullPathnameOfMiniassemblyScript(); checkGunzipFullPath(); checkFullPathnameOfFilter454ReadsScript(); checkFilter454ReadsAgainstThis(); check454LinkerSequences(); checkHideSomeTagTypesAtStartup(); checkMaximumNumberOfTracesShown(); checkNavigateAutomaticTracePopup(); checkNavigateAutomaticAllTracesPopup(); checkPrimersMinimumLengthOfAPrimer(); checkPrimersMaximumLengthOfAPrimer(); checkPrimersMinimumLengthOfAPrimerForPCR(); checkPrimersMaximumLengthOfAPrimerForPCR(); checkPrimersMaxMeltingTempDifferenceForPCR(); checkPrimersMaxPCRPrimerPairsToDisplay(); checkPrimersCheckJustSomePCRPrimerPairsRatherThanAll(); checkPrimersNumberOfTemplatesToDisplayInFront(); checkPrimersMaxLengthOfMononucleotideRepeat(); checkPrimersBadLibrariesFile(); checkPrimersLibrariesInfoFile(); checkPrimersBadTemplatesFile(); checkPrimersChooseTemplatesByPositionInsteadOfQuality(); checkPrimersWhenChoosingATemplateMinPotentialReadLength(); checkPrimersWindowSizeInLookingForPCR(); checkQualityThresholdForFindingHighQualityDiscrepancies(); checkQualityThresholdForNavigateByDepthOfCoverage(); checkNavigateByHighDepthOfCoverageNotLow(); checkMinDepthForNavigateByDepthOfCoverage(); checkDefaultVectorPathnameForRestrictionFragments(); checkFileOfAdditionalRestrictionEnzymes(); checkCommonRestrictionEnzymes(); checkDefaultSelectedRestrictionEnzymes(); checkRestrictionEnzymesActualFragmentsFile(); checkRestrictionDigestInitialWindowSizeInTextRows(); checkRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize(); checkShowReadsAlphabetically(); checkShowReadsInAlignedReadsWindowOrderedByFile(); checkShowReadsInAlignedReadsWindowOrderedByThisFile(); checkShowReadsAtCursorSortedHow(); checkShowABIBasesInTraceWindow(); checkTracesWindowInitialPixelHeight(); checkAssemblyViewWindowInitialPixelHeight(); checkAssemblyViewFileOfTemplatesToNotShow(); checkAssemblyViewCrossMatchMinmatch(); checkAssemblyViewCrossMatchMinscore(); checkAssemblyViewFindSequenceMatchesForConsedScript(); checkAssemblyViewCrossmatchMinmatch(); checkAssemblyViewCrossmatchMinscore(); checkAssemblyViewSequenceMatchesMinimumSimilarity(); checkTracesWindowInitialPixelWidth(); checkAssemblyViewWindowInitialPixelWidth(); checkAutomaticallyScaleTraces(); checkAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight(); checkAutomaticallyScaleTracesSamplePeakPercentile(); checkVerticalTraceMagnification(); checkUserDefinedKeys(); checkProgramsForUserDefinedKeys(); checkArgumentsToPassToUserDefinedPrograms(); checkTagsToApplyWithUserDefinedKeys(); checkSnpGenomeUseInsertionPolymorphisms(); checkListOfTagTypesToHide(); checkListOfOptionalWordsToSaveInListOfReadNames(); checkExtendConsensusWithHighQuality(); checkFastStartup(); checkFastStartupFile(); checkAlwaysRunProgramToGetChromats(); checkProgramToRunToGetChromats(); checkProgramToRunToGetChromatsOf454Reads(); checkCreateFakeChromatsForSolexaReads(); checkAutoFinishUseLongModelReadRatherThanShort(); checkAskAgainIfWantToQuitConsedIfThisManyReads(); checkPrintWindowInstructions(); checkAllowMultipleSearchForStringWindows(); checkAutoPCRAmplifyFalseProductsOKIfLargerThanThis(); checkAutoPCRAmplifyMakePrimerOutOfFirstRegion(); checkAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct(); checkAddNewReadsRecalculateConsensusQuality(); checkAddNewReadsPutReadIntoItsOwnContig(); checkAddNewReadsCheckThatCrossMatchRunCorrectly(); checkAssemblyViewNumberOfRowsOfTags(); checkWarnUserWhenTryingToEditAllReads(); checkMaybeXKEYSYMDBPath(); checkMaybeXKEYSYMDBPath2(); checkAmountToMoveWithBigLeftAndRightArrows(); checkNavigateByHighlyDiscrepantPositionsMinDiscrepantReads(); checkNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage(); checkNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality(); checkNavigateByHighlyDiscrepantPositionsJustListIndels(); checkNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation(); checkNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus(); checkNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus(); checkPhdBallDirectory(); checkNewAceFileFOF(); checkNavigateByHighOrLowDepthCoalesceRegionsIfThisClose(); checkRemoveReadsDeleteNotJustPutInOwnContig(); checkPaired454LeftReadExtension(); checkPaired454RightReadExtension(); checkSnpGenome1MSnps(); checkDiffChromosomesExcludeDeletions(); checkSnpGenomeFilterByWeight(); checkWantReadsUpToThisFarFromSnps(); checkPhaster2PhdBallSaveWhichMate(); checkPhaster2PhdBallSaveInPhasterFormat(); checkPhaster2PhdBallCalculateNewLocationsFile(); checkPhdBall2FastaIgnoreLowQualityReads(); checkPhdBall2FastaLowestAverageQuality(); checkNextPhredPipelineControlFile(); checkNextPhredPipelineTiffPerlScript(); checkNextPhredPipelinePhasterPerlScript(); checkNextPhredPipelineVersion(); checkNextPhredPipelineMainDirectory(); checkMaxNumberOfReadsPerPhdBall(); checkUserWantsToSaveToThisAceFile(); checkAutoFinishEmulate9_66Behavior(); checkPrimersPCRPrimersGroupedIntoWindowOfThisManyBases(); checkPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups(); checkAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs(); checkAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent(); checkAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether(); checkAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether(); checkAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean(); checkAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize(); checkAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize(); checkAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead(); checkAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp(); checkAutoFinishNumberOfBasesBetweenContigsAssumed(); checkAutoFinishPotentialHighQualityPartOfReadStart(); checkAutoFinishPotentialHighQualityPartOfReadEnd(); checkAutoFinishPrintCustomNavigationFileForChosenReads(); checkAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch(); checkAutoFinishTagOligosWhenDoExperiments(); checkCountPads(); checkDebugging(); checkDebugging2(); checkDebugging3(); checkDebuggingString(); checkIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion(); checkIgnoreUnalignedHighQualitySegmentsShorterThanThis(); checkPrimersLookThisFarForForwardVectorInsertJunction(); checkPrimersDNAConcentrationNanomolar(); checkPrimersMaxMatchElsewhereScore(); checkPrimersMaxMatchElsewhereScoreForPCR(); checkPrimersMaxSelfMatchScore(); checkPrimersMaxPrimerDimerScoreForPCR(); checkPrimersMinQuality(); checkPrimersPrintInfoOnRejectedTemplates(); checkPrimersSaltConcentrationMillimolar(); checkPrimersScreenForVector(); checkPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads(); checkPrimersTooManyVectorBasesInWalkingRead(); checkQualityThresholdForLowConsensusQuality(); checkTagColorPerCentOfBase(); checkUncompressedChromatDirectory(); check454sff2scfDirectory(); checkWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion(); checkWriteThisAceFormat(); checkDumpCoreIfBoundsError(); checkAutoFinishMinSmithWatermanScoreOfARun(); checkAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes(); checkRestrictionDigestMaximumBasesToCompareToVector(); checkRestrictionDigestZoomFactor(); checkRestrictionDigestZoomFactorForNavigate(); checkRestrictionDigestToleranceInPositionUnits(); checkAutoPCRAmplifyTooManySeriousFalseMatches(); checkAssemblyViewZoomFactor(); checkAssemblyViewFilterInconsistentFwdRevPairsIfThisClose(); checkAssemblyViewGridCellWidthInPixels(); checkAssemblyViewCursorSensitivityInPixels(); checkAssemblyViewReadDepthQuality(); checkShowAllTracesMaxNumberOfTracesToShowAtOnce(); checkAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess(); checkJustForPrimateProject(); checkSolexaFilesAreAssumedToBeHere(); checkSolexaAlignmentFilesPerInsertingPadsCycle(); checkSolexaAlignmentsPerAlignmentFile(); checkSolexaFastqFilesArePhredQualityNotSolexaQuality(); checkSolexa64FastqOrSanger33Fastq(); checkMaximumReadsInReadList(); checkMaxLengthOfReadsInapLocatedFragment2(); checkMaximumStartupErrorsToReport(); check454LinkerAlignmentMatchScore(); check454LinkerAlignmentMismatchScore(); check454LinkerAlignmentIndelScore(); checkFilter454ReadsDeleteCrossMatchOutput(); checkAutoReportAllNeededSpeciesCode(); checkAutoReportUseCommasInBigNumbers(); checkAutoReportPrintToCompareToReich(); checkAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites(); checkAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod(); checkAutoReportChooseTreesUsingBadData(); checkAutoReportChooseTreesByCountingDeaminationMutations(); checkAutoReportChooseTreesUsingKimura(); checkAutoReportPrintCrudeChimpHumanMutations(); checkAutoReportPrintPositionsForGraham(); checkAutoReportPrintAncestralCpGs(); checkAutoReportPrintCpGMutations(); checkAutoReportPrintMutationsWithContext(); checkAutoReportCountAllMutationsML(); checkAutoReportCountAllMutations(); checkAutoReportIgnoreMultipleTrees(); checkAutoReportCountAcceptableColumnsWithNoneOnLeft(); checkAutoReportPrintFlankedColumns4(); checkAutoReportUseAnnotationFormat(); checkAutoReportPrintFlankedColumns3(); checkAutoReportPrintFlankedColumns2(); checkAutoReportPrintFlankedColumns(); checkAutoReportHighQualitySegmentData(); checkAutoReportGoodReadsBug(); checkAutoReportDiscrepancyRateInFlankedRegions(); checkAutoReportDiscrepancyRateInFlankedRegions2(); checkAutoReportDiscrepancyRateInFlankedRegions4(); checkAutoReportDiscrepancyRateInFlankedRegions5(); checkAutoReportSingleSignalOrQuality(); checkAutoReportLowQualityBasesInHQS(); checkAutoReportCompareHQSWithLQS(); checkAutoReportCountColumnsForGroupsOfSpecies(); checkAutoReportSingleSignalInfo(); checkAutoReportSingleSignalInfo2(); checkAutoReportCompareTopAndBottomStrands(); checkAutoReportCompareTopAndBottomStrandsNoHuman(); checkAutoReportCompareTopAndBottomStrands2(); checkAutoReportCompareTopAndBottomStrands3(); checkAutoReportCompareTopAndBottomStrands4(); checkAutoReportTopStrandPinnedPosition(); checkAutoReportBottomStrandPinnedPosition(); checkAutoReportCompareTopAndBottomStrandsWithHuman(); checkAutoReportPrintLengthsOfAlignedSegmentsOfReads(); checkAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads(); checkAutoReportPrintIfReadsAreCorrectlyAligned(); checkAutoReportCalculateErrorProbabilitiesByComparingPTroPPan(); checkAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies(); checkAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2(); checkAutoReportFilterSingleSignal(); checkAutoReportGoodHitReads(); checkAutoReportQualityWindowLow(); checkAutoReportQualityWindowHigh(); checkAutoReportPrintNumberOfIsolatedPadsForEachSpecies(); checkAutoReportPrintNumberOfIsolatedPads(); checkAutoReportIsolatedPadsOfReadsWithThisPattern(); checkAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy(); checkAutoReportMaxSizeOfDiscrepantRegion(); checkAutoReportSizeOfDiscrepantRegion(); checkAutoReportPrintMinimumQualityHistogram(); checkAutoReportPrintDiscrepantRegions(); checkAutoReportPrintBasesInDiscrepantRegions(); checkAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis(); checkAutoReportBackboneReadHasThisStringInIt(); checkAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold(); checkAutoReportPrintSpeciesAlignment(); checkAutoReportPrintReadAlignment(); checkAutoReportPrintTheseReads(); checkAutoReportPrintReadPositions(); checkAutoReportPrintChosenReadName(); checkAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted(); checkAutoReportPrefix(); checkAutoReportUseOldCriteriaForDeletingColumnsOfPads(); checkAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues(); checkAutoReportFlankingBasesMustBeSingleSignal(); checkAutoReportMinimumQualityOfFlankingBases(); checkAutoReportFlankingBasesMustBeInHighQualitySegment(); checkAutoReportSpecies(); // guiEditResources.cpp.part9 } void guiEditResources :: userResizedWindow() { if ( !bAllTheWayUp_ ) return; Dimension dimClipWindowWidth; XtVaGetValues( widClipWindow_, XmNwidth, &dimClipWindowWidth, NULL ); // it is only necessary to set one form in the row-col widget // to get the entire row-col widget to increase in size and, apparently, // this causes all the form widgets within it to increase in size as well // This makes all the textfield widgets that are connected to the right end // to resize as well. XtVaSetValues( widPrimersSubcloneFullPathnameForm_, XmNwidth, dimClipWindowWidth, NULL ); // for some reason, Motif changes the increment when the window is resized. XtVaSetValues( widVerticalScrollBar_, XmNincrement, 20, NULL ); } void guiEditResources :: userPushedHelp( const RWCString& soResource ) { int n; bool bFound = false; int nStartIndex; for( n = 0; aszDefaultResources[n] && !bFound; ++n ) { char* pFound = strstr( aszDefaultResources[n], soResource.data() ); if ( pFound == aszDefaultResources[n] ) { bFound = true; nStartIndex = n; } } if ( !bFound ) { RWCString soError = "Internal program error finding "; soError += soResource; popupErrorMessage( soError ); return; } // now find the end int nEndIndex; bool bFoundEnd = false; for( n = nStartIndex + 1; !bFoundEnd; ++n ) { if ( !aszDefaultResources[n] ) { bFoundEnd = true; nEndIndex = n - 1; } else if ( memcmp( "consed.", aszDefaultResources[n], 7 ) == 0 ) { // found next resources bFoundEnd = true; nEndIndex = n - 1; } } if ( !bFoundEnd ) { RWCString soError = "Internal program error b finding "; soError += soResource; popupErrorMessage( soError ); return; } RWCString soToDisplay; for( n = nStartIndex; n <= nEndIndex; ++n ) { soToDisplay += RWCString( aszDefaultResources[n] ); } soToDisplay += "\n"; soToDisplay += "(YES) = freely customize to your own site\n"; soToDisplay += "(OK) = don't change unless you have a specific need and know what you\n"; soToDisplay += " are doing\n"; soToDisplay += "(NO) = don't change this!\n"; TextBox* pDocumentationWindow = new TextBox( soResource, 15, // rows visible soToDisplay ); pDocumentationWindow->makeVisible(); } void guiEditResources :: windowCameUp() { XtVaGetValues( widScrolledWindow_, XmNverticalScrollBar, &widVerticalScrollBar_, NULL ); XtVaSetValues( widVerticalScrollBar_, XmNincrement, 20, NULL ); } void guiEditResources :: userPushedFindButton( const bool bFindFirstNotFindNext ) { char* szValue = XmTextFieldGetString( widEnterParameter_ ); RWCString soValue = szValue; XtFree( szValue ); RWCString soOriginalCase = soValue; soValue.toLower(); int nStartIndex = ( bFindFirstNotFindNext ? 0 : nIndexOfLastFoundResource_ + 1 ); bool bFound = false; for( int nParameter = nStartIndex; nParameter < aConsedResources_.length() && ! bFound; ++nParameter ) { if ( aConsedResources_[ nParameter ].index( soValue ) != RW_NPOS ) { nIndexOfLastFoundResource_ = nParameter; bFound = true; } } if ( !bFound ) { popupErrorMessage( "could not find %s", soOriginalCase.data() ); return; } int nScrollBarMax; int nScrollBarMin; int nSliderSize; XtVaGetValues( widVerticalScrollBar_, XmNmaximum, &nScrollBarMax, XmNminimum, &nScrollBarMin, XmNsliderSize, &nSliderSize, NULL ); const int nMarginAtTop = 20; int nNewValue = nIndexOfLastFoundResource_ * (double) ( nScrollBarMax - nScrollBarMin + 1 ) / (double) aConsedResources_.length() - nMarginAtTop; if ( nNewValue < 0 ) nNewValue = 0; else if ( nNewValue > ( nScrollBarMax - nSliderSize - nScrollBarMin + 1 ) ) nNewValue = nScrollBarMax - nSliderSize - nScrollBarMin + 1; XtVaSetValues( widVerticalScrollBar_, XmNvalue, nNewValue, NULL ); XmScrollBarCallbackStruct xmMyScrollBarCallbackStruct; xmMyScrollBarCallbackStruct.reason = 0; xmMyScrollBarCallbackStruct.event = 0; xmMyScrollBarCallbackStruct.value = nNewValue; xmMyScrollBarCallbackStruct.pixel = 0; XtCallCallbacks( widVerticalScrollBar_, XmNvalueChangedCallback, &xmMyScrollBarCallbackStruct ); } void guiEditResources :: createResourceArray() { aConsedResources_.resize( (size_t) 200 ); // guiEditResources.cpp.part10 aConsedResources_.insert("consed.printPS" ); aConsedResources_.insert("consed.defaultTagType" ); aConsedResources_.insert("consed.defaultTagOnConsensusNotReads" ); aConsedResources_.insert("consed.autoFinishMinNumberOfErrorsFixedByAnExp" ); aConsedResources_.insert("consed.autoFinishRedundancy" ); aConsedResources_.insert("consed.autoFinishAverageInsertSize" ); aConsedResources_.insert("consed.primersMaxInsertSizeOfASubclone" ); aConsedResources_.insert("consed.primersMaxMeltingTemp" ); aConsedResources_.insert("consed.primersMaxMeltingTempForPCR" ); aConsedResources_.insert("consed.primersPickTemplatesForPrimers" ); aConsedResources_.insert("consed.primersSubcloneFullPathnameOfFileOfSequencesForScreening" ); aConsedResources_.insert("consed.primersCloneFullPathnameOfFileOfSequencesForScreening" ); aConsedResources_.insert("consed.primersMinMeltingTemp" ); aConsedResources_.insert("consed.primersMinMeltingTempForPCR" ); aConsedResources_.insert("consed.searchFunctionsUseUnalignedEndsOfReads" ); aConsedResources_.insert("consed.searchFunctionsUseLowQualityEndsOfReads" ); aConsedResources_.insert("consed.inexactSearchForStringMaxPerCentMismatch" ); aConsedResources_.insert("consed.onlyAllowOneReadWriteConsedAtATime" ); aConsedResources_.insert("consed.autoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair" ); aConsedResources_.insert("consed.printWindowCommand" ); aConsedResources_.insert("consed.fileOfTagTypes" ); aConsedResources_.insert("consed.assemblyViewShowConsistentFwdRevPairs" ); aConsedResources_.insert("consed.assemblyViewShowConsistentFwdRevPairDepth" ); aConsedResources_.insert("consed.assemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds" ); aConsedResources_.insert("consed.assemblyViewShowLegsOnSquaresForConsistentFwdRevPairs" ); aConsedResources_.insert("consed.assemblyViewShowGapSpanningFwdRevPairs" ); aConsedResources_.insert("consed.assemblyViewShowWhichInconsistentFwdRevPairs" ); aConsedResources_.insert("consed.assemblyViewShowReadDepth" ); aConsedResources_.insert("consed.assemblyViewShowMultipleHighQualityDiscrepancies" ); aConsedResources_.insert("consed.assemblyViewShowRestrictionDigestCutSites" ); aConsedResources_.insert("consed.assemblyViewFilterSequenceMatchesBySize" ); aConsedResources_.insert("consed.assemblyViewSequenceMatchesMinSize" ); aConsedResources_.insert("consed.assemblyViewSequenceMatchesMaxSize" ); aConsedResources_.insert("consed.assemblyViewAutomaticallyStartWithConsed" ); aConsedResources_.insert("consed.assemblyViewDisplayTheseTagTypesOnTheseLines" ); aConsedResources_.insert("consed.assemblyViewShowTags" ); aConsedResources_.insert("consed.autoEditRecalculateHighQualitySegmentsOfReads" ); aConsedResources_.insert("consed.autoEditConvertCloneEndBasesToXs" ); aConsedResources_.insert("consed.autoEditTellPhrapNotToOverlapMultiplyDiscrepantReads" ); aConsedResources_.insert("consed.autoEditTagEditableLowConsensusQualityRegions" ); aConsedResources_.insert("consed.autoEditMakeFakeRead" ); aConsedResources_.insert("consed.autoEditMakeFakeReadFromRead1" ); aConsedResources_.insert("consed.autoEditMakeFakeReadFromRead2" ); aConsedResources_.insert("consed.autoEditMakeFakeReadName" ); aConsedResources_.insert("consed.autoEditMakeFakeReadFastaFilename" ); aConsedResources_.insert("consed.autoEditMergeAssembly" ); aConsedResources_.insert("consed.autoEditSecondaryAceFile" ); aConsedResources_.insert("consed.autoEditFixRunsInConsensus" ); aConsedResources_.insert("consed.showAllTracesJustShowGoodTraces" ); aConsedResources_.insert("consed.addAlignedSequenceQualityOfBases" ); aConsedResources_.insert("consed.makeLightBackgroundInAlignedReadsWindowAndTracesWindow" ); aConsedResources_.insert("consed.putVerticalLineAtCursor" ); aConsedResources_.insert("consed.putHorizontalLineAtCursor" ); aConsedResources_.insert("consed.highlightedReadsFile" ); 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aConsedResources_.insert("consed.autoReportPrintAncestralCpGs" ); aConsedResources_.insert("consed.autoReportPrintCpGMutations" ); aConsedResources_.insert("consed.autoReportPrintMutationsWithContext" ); aConsedResources_.insert("consed.autoReportCountAllMutationsML" ); aConsedResources_.insert("consed.autoReportCountAllMutations" ); aConsedResources_.insert("consed.autoReportIgnoreMultipleTrees" ); aConsedResources_.insert("consed.autoReportCountAcceptableColumnsWithNoneOnLeft" ); aConsedResources_.insert("consed.autoReportPrintFlankedColumns4" ); aConsedResources_.insert("consed.autoReportUseAnnotationFormat" ); aConsedResources_.insert("consed.autoReportPrintFlankedColumns3" ); aConsedResources_.insert("consed.autoReportPrintFlankedColumns2" ); aConsedResources_.insert("consed.autoReportPrintFlankedColumns" ); aConsedResources_.insert("consed.autoReportHighQualitySegmentData" ); aConsedResources_.insert("consed.autoReportGoodReadsBug" ); aConsedResources_.insert("consed.autoReportDiscrepancyRateInFlankedRegions" ); aConsedResources_.insert("consed.autoReportDiscrepancyRateInFlankedRegions2" ); aConsedResources_.insert("consed.autoReportDiscrepancyRateInFlankedRegions4" ); aConsedResources_.insert("consed.autoReportDiscrepancyRateInFlankedRegions5" ); aConsedResources_.insert("consed.autoReportSingleSignalOrQuality" ); aConsedResources_.insert("consed.autoReportLowQualityBasesInHQS" ); aConsedResources_.insert("consed.autoReportCompareHQSWithLQS" ); aConsedResources_.insert("consed.autoReportCountColumnsForGroupsOfSpecies" ); aConsedResources_.insert("consed.autoReportSingleSignalInfo" ); aConsedResources_.insert("consed.autoReportSingleSignalInfo2" ); aConsedResources_.insert("consed.autoReportCompareTopAndBottomStrands" ); aConsedResources_.insert("consed.autoReportCompareTopAndBottomStrandsNoHuman" ); aConsedResources_.insert("consed.autoReportCompareTopAndBottomStrands2" ); aConsedResources_.insert("consed.autoReportCompareTopAndBottomStrands3" ); aConsedResources_.insert("consed.autoReportCompareTopAndBottomStrands4" ); aConsedResources_.insert("consed.autoReportTopStrandPinnedPosition" ); aConsedResources_.insert("consed.autoReportBottomStrandPinnedPosition" ); aConsedResources_.insert("consed.autoReportCompareTopAndBottomStrandsWithHuman" ); aConsedResources_.insert("consed.autoReportPrintLengthsOfAlignedSegmentsOfReads" ); aConsedResources_.insert("consed.autoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads" ); aConsedResources_.insert("consed.autoReportPrintIfReadsAreCorrectlyAligned" ); aConsedResources_.insert("consed.autoReportCalculateErrorProbabilitiesByComparingPTroPPan" ); aConsedResources_.insert("consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies" ); aConsedResources_.insert("consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies2" ); aConsedResources_.insert("consed.autoReportFilterSingleSignal" ); aConsedResources_.insert("consed.autoReportGoodHitReads" ); aConsedResources_.insert("consed.autoReportQualityWindowLow" ); aConsedResources_.insert("consed.autoReportQualityWindowHigh" ); aConsedResources_.insert("consed.autoReportPrintNumberOfIsolatedPadsForEachSpecies" ); aConsedResources_.insert("consed.autoReportPrintNumberOfIsolatedPads" ); aConsedResources_.insert("consed.autoReportIsolatedPadsOfReadsWithThisPattern" ); aConsedResources_.insert("consed.autoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy" ); aConsedResources_.insert("consed.autoReportMaxSizeOfDiscrepantRegion" ); aConsedResources_.insert("consed.autoReportSizeOfDiscrepantRegion" ); aConsedResources_.insert("consed.autoReportPrintMinimumQualityHistogram" ); aConsedResources_.insert("consed.autoReportPrintDiscrepantRegions" ); aConsedResources_.insert("consed.autoReportPrintBasesInDiscrepantRegions" ); aConsedResources_.insert("consed.autoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis" ); aConsedResources_.insert("consed.autoReportBackboneReadHasThisStringInIt" ); aConsedResources_.insert("consed.autoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold" ); aConsedResources_.insert("consed.autoReportPrintSpeciesAlignment" ); aConsedResources_.insert("consed.autoReportPrintReadAlignment" ); aConsedResources_.insert("consed.autoReportPrintTheseReads" ); aConsedResources_.insert("consed.autoReportPrintReadPositions" ); aConsedResources_.insert("consed.autoReportPrintChosenReadName" ); aConsedResources_.insert("consed.autoReportNumbersOfCharactersOfChosenReadNameToBePrinted" ); aConsedResources_.insert("consed.autoReportPrefix" ); aConsedResources_.insert("consed.autoReportUseOldCriteriaForDeletingColumnsOfPads" ); aConsedResources_.insert("consed.autoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues" ); aConsedResources_.insert("consed.autoReportFlankingBasesMustBeSingleSignal" ); aConsedResources_.insert("consed.autoReportMinimumQualityOfFlankingBases" ); aConsedResources_.insert("consed.autoReportFlankingBasesMustBeInHighQualitySegment" ); aConsedResources_.insert("consed.autoReportSpecies" ); for( int nResource = 0; nResource < aConsedResources_.length(); ++nResource ) { aConsedResources_[ nResource ].toLower(); } }