/***************************************************************************** # 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 #include #include #include #include #include #include #include #include "guiSetGeneralPreferences.h" #include "assert.h" #include "quality.h" #include "consedParameters.h" #include "guiapp.h" #include #include #include "rwcstring.h" #include "rwcregexp.h" #include "bIsNumericMaybeWithWhitespace.h" #include "numutil.h" #include "handleWindowManagerDelete2.h" #include "consed.h" #include #include "popupErrorMessage.h" #include "hp_exception_kludge.h" static const int nRightPositionOfLabels = 70; static const int nLeftPositionOfFields = 80; #define createLineForIntegerConsedParameter( basename2, label2 ) \ createFormAndLabel( basename2, label2 ); \ \ sprintf( szTemp, "%d", \ consedParameters::pGetConsedParameters()->n ## basename2 ## _ ); \ \ createTextField( basename2, szTemp ); #define createFormAndLabel( basename, labell ) \ \ xm = XmStringCreateLtoR( labell, XmFONTLIST_DEFAULT_TAG ); \ \ Widget wid ## basename ## Form = XtVaCreateManagedWidget( "form", \ xmFormWidgetClass, \ widRowCol, \ XmNshadowThickness, 0, \ NULL ); \ \ \ Widget wid ## basename ## Label = XtVaCreateManagedWidget( labell, \ xmLabelWidgetClass, \ wid ## basename ## Form, \ XmNtopAttachment, XmATTACH_FORM, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNleftAttachment, XmATTACH_FORM, \ XmNrightAttachment, XmATTACH_POSITION, \ XmNrightPosition, nRightPositionOfLabels, \ XmNalignment, XmALIGNMENT_END, \ XmNlabelString, xm, \ NULL ); \ \ XmStringFree( xm ); // createFormAndLabel( QualityThresholdForLowConsensusQuality, // "Threshold for Low Consensus Quality (highest low)" ); // // // // Widget widQualityThresholdForLowConsensusQualityForm = XtVaCreateManagedWidget( "form", // xmFormWidgetClass, // widRowCol, // XmNshadowThickness, 0, // NULL ); // Widget widQualityThresholdForLowConsensusQualityLabel = XtVaCreateManagedWidget( // "Threshold for Low Consensus Quality (highest low)", // xmLabelWidgetClass, // widQualityThresholdForLowConsensusQualityForm, // XmNtopAttachment, XmATTACH_FORM, // XmNbottomAttachment, XmATTACH_FORM, // XmNleftAttachment, XmATTACH_FORM, // XmNrightAttachment, XmATTACH_POSITION, // XmNrightPosition, nRightPositionOfLabels, // XmNalignment, XmALIGNMENT_END, // NULL ); #define createTextField( basename, szValue ) \ wid ## basename ## _ = XtVaCreateManagedWidget( \ #basename , \ xmTextFieldWidgetClass, \ wid ## basename ## Form, \ XmNtraversalOn, True, \ XmNtopAttachment, XmATTACH_FORM, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, nLeftPositionOfFields, \ XmNrightAttachment, XmATTACH_FORM, \ XmNvalue, szValue, \ XmNcolumns, (short) 8, \ NULL ); \ \ XtAddCallback( wid ## basename ## _, \ XmNactivateCallback, \ (XtCallbackProc) XmProcessTraversal, \ (XtPointer) XmTRAVERSE_NEXT_TAB_GROUP ); // The above macro takes: // createTextField( QualityThresholdForLowConsensusQuality, // szQualityThresholdForLowConsensusQuality ); // and makes: // widQualityThresholdForLowConsensusQuality_ = XtVaCreateManagedWidget( // "low consensus quality threshold", // xmTextFieldWidgetClass, // widQualityThresholdForLowConsensusQualityForm, // XmNtraversalOn, True, // XmNtopAttachment, XmATTACH_FORM, // XmNbottomAttachment, XmATTACH_FORM, // XmNleftAttachment, XmATTACH_POSITION, // XmNleftPosition, nLeftPositionOfFields, // XmNrightAttachment, XmATTACH_FORM, // XmNvalue, szQualityThresholdForLowConsensusQuality, // XmNcolumns, (short) 8, // NULL ); // XtAddCallback( widQualityThresholdForLowConsensusQuality_, // XmNactivateCallback, // (XtCallbackProc )XmProcessTraversal, // (XtPointer) XmTRAVERSE_NEXT_TAB_GROUP ); #define createLineWithBooleanConsedParameter( basename, szLabel, szTrueButtonLabel, szFalseButtonLabel ) \ \ Widget wid ## basename ## Form = XtVaCreateManagedWidget( \ "form", \ xmFormWidgetClass, \ widRowCol, \ XmNshadowThickness, 0, \ NULL ); \ \ xm = XmStringCreateLtoR( szLabel, XmFONTLIST_DEFAULT_TAG ); \ \ Widget wid ## basename ## Label = XtVaCreateManagedWidget( \ szLabel, \ xmLabelWidgetClass, \ wid ## basename ## Form, \ XmNtopAttachment, XmATTACH_FORM, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNleftAttachment, XmATTACH_FORM, \ XmNrightAttachment, XmATTACH_POSITION, \ XmNrightPosition, 60, \ XmNalignment, XmALIGNMENT_END, \ XmNlabelString, xm, \ NULL ); \ \ XmStringFree( xm ); \ \ Widget wid ## basename ## RadioBox = XmCreateRadioBox( \ wid ## basename ## Form, \ "radio", \ NULL , \ 0 ); \ \ XtVaSetValues( \ wid ## basename ## RadioBox, \ XmNtraversalOn, True, \ XmNtopAttachment, XmATTACH_FORM, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, 70, \ XmNrightAttachment, XmATTACH_FORM, \ XmNorientation, XmHORIZONTAL, \ XmNshadowThickness, 0, \ XmNborderWidth, 0, \ XmNmarginWidth, 0, \ NULL ); \ \ bool b ## basename = \ consedParameters::pGetConsedParameters()->b ## basename ## _; \ \ wid ## basename ## True_ = XtVaCreateManagedWidget( \ szTrueButtonLabel, \ xmToggleButtonWidgetClass, \ wid ## basename ## RadioBox, \ XmNset, b ## basename, \ NULL ); \ \ Widget wid ## basename ## False = XtVaCreateManagedWidget( \ szFalseButtonLabel, \ xmToggleButtonWidgetClass, \ wid ## basename ## RadioBox, \ XmNset, !b ## basename, \ NULL ); \ \ XtManageChild( wid ## basename ## RadioBox ); // createLineWithBooleanConsedParameter( CountPads, "Count *'s", "True", "False" ); // makes: ///////////////////// // // whether to count *'s or not // Widget widCountPadsForm = XtVaCreateManagedWidget( // "form", // xmFormWidgetClass, // widRowCol, // XmNshadowThickness, 0, // NULL ); // Widget widCountPadsLabel = XtVaCreateManagedWidget( // "Count *'s", // xmLabelWidgetClass, // widCountPadsForm, // XmNtopAttachment, XmATTACH_FORM, // XmNbottomAttachment, XmATTACH_FORM, // XmNleftAttachment, XmATTACH_FORM, // XmNrightAttachment, XmATTACH_POSITION, // XmNrightPosition, 60, // XmNalignment, XmALIGNMENT_END, // NULL ); // Widget widCountPadsRadioBox = XmCreateRadioBox( // widCountPadsForm, // "radio", // NULL, // 0 ); // XtVaSetValues( // widCountPadsRadioBox, // XmNtraversalOn, True, // XmNtopAttachment, XmATTACH_FORM, // XmNbottomAttachment, XmATTACH_FORM, // XmNleftAttachment, XmATTACH_POSITION, // XmNleftPosition, 70, // XmNrightAttachment, XmATTACH_FORM, // XmNorientation, XmHORIZONTAL, // XmNshadowThickness, 0, // XmNborderWidth, 0, // XmNmarginWidth, 0, // NULL ); // bool bCountPads = consedParameters::pGetConsedParameters()->bCountPads_; // widCountPadsTrue_ = XtVaCreateManagedWidget( // "True", // xmToggleButtonWidgetClass, // widCountPadsRadioBox, // XmNset, bCountPads, // NULL ); // Widget widCountPadsFalse = XtVaCreateManagedWidget( // "False", // xmToggleButtonWidgetClass, // widCountPadsRadioBox, // XmNset, !bCountPads, // NULL ); // XtManageChild( widCountPadsRadioBox ); static void CancelButtonCb(Widget wid, XtPointer clientData, XtPointer pCallData ) { guiSetGeneralPreferences* pGuiSetGeneralPreferences = (guiSetGeneralPreferences* )clientData; TRY_CATCH_WRAPPER( delete pGuiSetGeneralPreferences; ); } static void cbLightBackgroundPushButton( Widget wid, XtPointer pClientData, XtPointer pCallData ) { TRY_CATCH_WRAPPER( GuiApp::pGetGuiApp()->changeDefaultToLightBackground(); ); } guiSetGeneralPreferences :: guiSetGeneralPreferences() { int nArgs; Arg aArg[50]; widPopupShell_ = XtVaCreatePopupShell("General Preferences", topLevelShellWidgetClass, GuiApp::pGetGuiApp()->widGetTopLevel(), XmNtitle, "General Preferences", XmNnoResize, False, XmNautoUnmanage, False, XmNtransient, False, XmNdeleteResponse, XmDO_NOTHING, NULL ); handleWindowManagerDelete2( widPopupShell_, CancelButtonCb, this ); // // create the form widget // nArgs = 0; XtSetArg(aArg[nArgs],XmNshadowThickness,0); nArgs++; XtSetArg(aArg[nArgs],XmNborderWidth,0); nArgs++; Widget widForm = XmCreateForm( widPopupShell_, "form", aArg, nArgs); XtManageChild(widForm); widOKButton_ = XtVaCreateManagedWidget( "Apply & Dismiss", xmPushButtonWidgetClass, widForm, XmNbottomAttachment, XmATTACH_FORM, XmNbottomOffset, 10, XmNtraversalOn, False, XmNleftAttachment, XmATTACH_FORM, XmNleftOffset, 10, NULL ); XtAddCallback(widOKButton_, XmNactivateCallback, (XtCallbackProc )OKButtonCb, this); widApplyButton_ = XtVaCreateManagedWidget( "Apply", xmPushButtonWidgetClass, widForm, XmNbottomAttachment, XmATTACH_FORM, XmNbottomOffset, 10, XmNtraversalOn, False, XmNleftAttachment, XmATTACH_WIDGET, XmNleftWidget, widOKButton_, XmNleftOffset, 10, NULL ); XtAddCallback(widApplyButton_, XmNactivateCallback, (XtCallbackProc )ApplyButtonCb, this); widCancelButton_ = XtVaCreateManagedWidget( "Cancel", xmPushButtonWidgetClass, widForm, XmNtopAttachment, XmATTACH_OPPOSITE_WIDGET, XmNtopWidget, widOKButton_, XmNbottomAttachment, XmATTACH_FORM, XmNbottomOffset, 10, XmNtraversalOn, False, XmNleftAttachment, XmATTACH_WIDGET, XmNleftWidget, widApplyButton_, XmNleftOffset, 10, NULL ); XtAddCallback(widCancelButton_, XmNactivateCallback, (XtCallbackProc )CancelButtonCb, this); Widget widScrolledWindow = XtVaCreateManagedWidget( "scrolled", xmScrolledWindowWidgetClass, widForm, XmNtopAttachment, XmATTACH_FORM, XmNleftAttachment, XmATTACH_FORM, XmNrightAttachment, XmATTACH_FORM, XmNbottomAttachment, XmATTACH_WIDGET, XmNbottomWidget, widOKButton_, XmNbottomOffset, 20, XmNscrollingPolicy, XmAUTOMATIC, XmNscrollBarDisplayPolicy, XmSTATIC, NULL ); Widget widRowCol = XtVaCreateManagedWidget( "rowcol", xmRowColumnWidgetClass, widScrolledWindow, XmNorientation, XmVERTICAL, XmNnumColumns, 1, XmNpacking, XmPACK_COLUMN, NULL ); XmScrolledWindowSetAreas( widScrolledWindow, (Widget) NULL, (Widget) NULL, widRowCol ); // needed by the #define macros char szTemp[200]; XmString xm; createLineForIntegerConsedParameter( QualityThresholdForLowConsensusQuality, "Threshold for Low Consensus Quality (highest low)" ); // threshold for high quality discrepancies createLineForIntegerConsedParameter( QualityThresholdForFindingHighQualityDiscrepancies, "Threshold for High Quality Discrepancy (lowest high)" ); // tag color per cent of base createLineForIntegerConsedParameter(TagColorPerCentOfBase, "Tag Color Per Cent Of Base" ); // vertical magnification createLineForIntegerConsedParameter( VerticalTraceMagnification, "Vertical Trace Magnification" ); // bAutomaticallyScaleTraces_ createLineWithBooleanConsedParameter( AutomaticallyScaleTraces, "Automatically scale traces", "Yes", "No" ); ///////////////// // maximum number of traces shown createLineForIntegerConsedParameter( MaximumNumberOfTracesShown, "Max Number of Traces Shown" ); ///////////////// // // nTracesWindowInitialPixelWidth_ createLineForIntegerConsedParameter( TracesWindowInitialPixelWidth, "Initial Width of Trace Window in Pixels" ); ////////////////// // // nTracesWindowInitialPixelHeight_ createLineForIntegerConsedParameter( TracesWindowInitialPixelHeight, "Initial Height of Trace Area in Pixels" ); ////////////////////// // // whether to write ace format 1 (old) or format 2 (new) Widget widWriteThisAceFormatForm = XtVaCreateManagedWidget( "form", xmFormWidgetClass, widRowCol, XmNshadowThickness, 0, NULL ); Widget widWriteThisAceFormat = XtVaCreateManagedWidget( "Write This Ace Format", xmLabelWidgetClass, widWriteThisAceFormatForm, XmNtopAttachment, XmATTACH_FORM, XmNbottomAttachment, XmATTACH_FORM, XmNleftAttachment, XmATTACH_FORM, XmNrightAttachment, XmATTACH_POSITION, XmNrightPosition, 60, XmNalignment, XmALIGNMENT_END, NULL ); Widget widWriteThisAceFormatRadioBox = XmCreateRadioBox( widWriteThisAceFormatForm, "radio", NULL, 0 ); XtVaSetValues( widWriteThisAceFormatRadioBox, XmNtraversalOn, True, XmNtopAttachment, XmATTACH_FORM, XmNbottomAttachment, XmATTACH_FORM, XmNleftAttachment, XmATTACH_POSITION, XmNleftPosition, 70, XmNrightAttachment, XmATTACH_FORM, XmNorientation, XmHORIZONTAL, XmNshadowThickness, 0, XmNborderWidth, 0, XmNmarginWidth, 0, NULL ); bool bWriteAceFormat1 = ( consedParameters::pGetConsedParameters()->nWriteThisAceFormat_ == 1 ) ? true : false; widWriteAceFormat1_ = XtVaCreateManagedWidget( "old", xmToggleButtonWidgetClass, widWriteThisAceFormatRadioBox, XmNset, bWriteAceFormat1, NULL ); Widget widWriteAceFormat2 = XtVaCreateManagedWidget( "new", xmToggleButtonWidgetClass, widWriteThisAceFormatRadioBox, XmNset, !bWriteAceFormat1, NULL ); XtManageChild( widWriteThisAceFormatRadioBox ); ///////////////////// // // whether to count *'s or not createLineWithBooleanConsedParameter( CountPads, "Count *'s", "Yes", "No" ); createLineWithBooleanConsedParameter( ShowReadsAlphabetically, "Display reads sorted alphabetically\nor by strand/left read end", "alpha", "strand" ); ///////////////// // // nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_; createLineForIntegerConsedParameter( IgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion, "Ignore high quality discrepancies this\nmany bases from end of aligned region" ); ///////////////// // // nIgnoreUnalignedHighQualitySegmentsShorterThanThis_ createLineForIntegerConsedParameter( IgnoreUnalignedHighQualitySegmentsShorterThanThis, "Ignore unaligned high quality\nsegments shorter than this (counts pads)" ); ///////////////// // // nCompareContigsAlignsThisManyBasesMax_ createLineForIntegerConsedParameter( CompareContigsAlignsThisManyBasesMax, "Compare Contigs aligns this many bases max\n(2x bigger number means 4x longer alignment time)" ); //////////////////////// // // nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion_ createLineForIntegerConsedParameter( WhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion, "How many bases should joining read extend\nbefore and after the aligned region" ); ////////////////////// // // nDebugging_ createLineForIntegerConsedParameter( Debugging, "leave 0" ); createLineWithBooleanConsedParameter( ShowABIBasesInTraceWindow, "Show ABI Bases in Trace Window", "Yes", "No" ); createLineWithBooleanConsedParameter( DumpCoreIfBoundsError, "Dump Core If Bounds Error", "Yes", "No" ); createLineWithBooleanConsedParameter( CompareContigsUseBandedRatherThanFullSmithWaterman, "CompareContigs Use Banded (Not Full) S/W", "Yes", "No" ); createLineForIntegerConsedParameter( CompareContigsBandSize, "compare contigs band size" ); // change default background colors to light for making slides Widget widLightBackgroundForm = XtVaCreateManagedWidget( "form", xmFormWidgetClass, widRowCol, XmNshadowThickness, 0, NULL ); xm = XmStringCreateLtoR( "Make light background in Aligned Reads Windows and Traces Windows.\n(Does not affect existing windows.)\n(You must restart consed if you want to change back.)", XmFONTLIST_DEFAULT_TAG ); Widget widLightBackgroundLabel = XtVaCreateManagedWidget( "label", xmLabelWidgetClass, widLightBackgroundForm, XmNtopAttachment, XmATTACH_FORM, XmNbottomAttachment, XmATTACH_FORM, XmNleftAttachment, XmATTACH_FORM, XmNrightAttachment, XmATTACH_POSITION, XmNrightPosition, nRightPositionOfLabels, XmNalignment, XmALIGNMENT_END, XmNlabelString, xm, NULL ); Widget widLightBackgroundPushButton = XtVaCreateManagedWidget( "Do it now", xmPushButtonWidgetClass, widLightBackgroundForm, XmNtopAttachment, XmATTACH_FORM, XmNbottomAttachment, XmATTACH_FORM, XmNleftAttachment, XmATTACH_POSITION, XmNleftPosition, nLeftPositionOfFields, XmNrightAttachment, XmATTACH_FORM, NULL ); XtAddCallback( widLightBackgroundPushButton, XmNactivateCallback, (XtCallbackProc )cbLightBackgroundPushButton, this); createLineForIntegerConsedParameter( AlignedReadsWindowMaxCharsForReadNames, "Max Chars For Read Names in Aligned Reads Window" ); // these values have been set empirically. // If you don't set them, then the scrolled window is set very tiny. int nSize1 = strlen( "Threshold for Low Consensus Quality (highest low)" ); int nSize2 = strlen( "Threshold for Navigate/High Quality Discrepancy" ); int nSizeOfLabel = MAX( nSize1, nSize2 ); int nWidthOfPopup = nSizeOfLabel * 100 / nRightPositionOfLabels; XtVaSetValues( widScrolledWindow, XmNwidth, (Dimension) (GuiApp::pGetGuiApp()->nGetFontWidth() * ( nWidthOfPopup + 10)), XmNheight, (Dimension) (GuiApp::pGetGuiApp()->nGetFontHeight()* 40 ), NULL ); XtPopup( widPopupShell_, XtGrabNone ); } void OKButtonCb(Widget wid, XtPointer clientData, XmAnyCallbackStruct* cbs) { guiSetGeneralPreferences* pGuiSetGeneralPreferences = (guiSetGeneralPreferences* )clientData; TRY_CATCH_WRAPPER( assert( wid == pGuiSetGeneralPreferences->widOKButton_ ); pGuiSetGeneralPreferences->userPushedOKButton(); ); } void ApplyButtonCb(Widget wid, XtPointer clientData, XmAnyCallbackStruct* cbs) { guiSetGeneralPreferences* pGuiSetGeneralPreferences = (guiSetGeneralPreferences* )clientData; TRY_CATCH_WRAPPER( assert( wid == pGuiSetGeneralPreferences->widApplyButton_ ); pGuiSetGeneralPreferences->userPushedApplyButton(); ); } void guiSetGeneralPreferences :: userPushedOKButton() { if ( !bApplyNewPreferences() ) return; delete this; } void guiSetGeneralPreferences :: userPushedApplyButton() { bApplyNewPreferences(); } bool guiSetGeneralPreferences :: bApplyNewPreferences() { // set quality threshold for low consensus quality char* szValue = XmTextFieldGetString( widQualityThresholdForLowConsensusQuality_ ); RWCString soValue( szValue ); XtFree( szValue ); int nPerhapsQualityThreshold; if (!bIsNumericMaybeWithWhitespace( soValue, nPerhapsQualityThreshold ) ) { GuiApp::popupErrorMessage( "quality threshold for low consensus quality must be numeric" ); return( false ); } if (! (ucQualityMin <= nPerhapsQualityThreshold && nPerhapsQualityThreshold <= ucQualityMax ) ) { char szError[200]; sprintf( szError, "quality threshold for low consensus quality must be between %d and %d ", ucQualityMin, ucQualityMax ); GuiApp::popupErrorMessage( szError ); return( false ); } consedParameters::pGetConsedParameters()->nQualityThresholdForLowConsensusQuality_ = nPerhapsQualityThreshold; // set quality threshold for high quality discrepancies szValue = XmTextFieldGetString( widQualityThresholdForFindingHighQualityDiscrepancies_ ); soValue = szValue; XtFree( szValue ); if (!bIsNumericMaybeWithWhitespace( soValue, nPerhapsQualityThreshold ) ) { GuiApp::popupErrorMessage( "quality threshold must be numeric" ); return( false ); } if (! (ucQualityMin <= nPerhapsQualityThreshold && nPerhapsQualityThreshold <= ucQualityMax ) ) { char szError[200]; sprintf( szError, "quality must be between %d and %d ", ucQualityMin, ucQualityMax ); GuiApp::popupErrorMessage( szError ); return( false ); } consedParameters::pGetConsedParameters()->nQualityThresholdForFindingHighQualityDiscrepancies_ = nPerhapsQualityThreshold; // nTagColorPerCentOfBase_ szValue = XmTextFieldGetString( widTagColorPerCentOfBase_ ); soValue = szValue; XtFree( szValue ); int nTagColorPerCentOfBase; if (!bIsNumericMaybeWithWhitespace( soValue, nTagColorPerCentOfBase )) { GuiApp::popupErrorMessage( "tag color per cent of base must be numeric" ); return( false ); } if ( nTagColorPerCentOfBase < 0 || 100 < nTagColorPerCentOfBase ) { GuiApp::popupErrorMessage( "tag color per cent of base must be between 0 and 100" ); return( false ); } consedParameters::pGetConsedParameters()->nTagColorPerCentOfBase_ = nTagColorPerCentOfBase; // set vertical trace magnification szValue = XmTextFieldGetString( widVerticalTraceMagnification_ ); soValue = szValue; XtFree( szValue ); szValue = XmTextFieldGetString( widVerticalTraceMagnification_ ); soValue = szValue; XtFree( szValue ); int nVerticalTraceMagnification; if (!bIsNumericMaybeWithWhitespace( soValue, nVerticalTraceMagnification )) { GuiApp::popupErrorMessage( "vertical trace magnification must be numeric" ); return( false ); } int nOldValue = consedParameters::pGetConsedParameters()->nVerticalTraceMagnification_; if ( nOldValue != nVerticalTraceMagnification ) { consedParameters::pGetConsedParameters()->nVerticalTraceMagnification_ = nVerticalTraceMagnification; ConsEd::pGetConsEd()->refreshAllContigWinsAndAllTeditors(); } // bAutomaticallyScaleTraces_ bool bOldValue = pCP->bAutomaticallyScaleTraces_; pCP->bAutomaticallyScaleTraces_ = ( XmToggleButtonGetState(widAutomaticallyScaleTracesTrue_ ) == True ); if ( bOldValue != pCP->bAutomaticallyScaleTraces_ ) { ConsEd::pGetConsEd()->refreshAllContigWinsAndAllTeditors(); } // nMaximumNumberOfTracesShown szValue = XmTextFieldGetString( widMaximumNumberOfTracesShown_ ); soValue = szValue; XtFree( szValue ); int nMaximumNumberOfTracesShown; if (!bIsNumericMaybeWithWhitespace( soValue, nMaximumNumberOfTracesShown )) { GuiApp::popupErrorMessage( "maximum number of traces shown must be numeric" ); return( false ); } if ( nMaximumNumberOfTracesShown < 1 ) { GuiApp::popupErrorMessage( "maximum number of traces shown must be greater than 0" ); return( false ); } consedParameters::pGetConsedParameters()->nMaximumNumberOfTracesShown_ = nMaximumNumberOfTracesShown; // nTracesWindowInitialPixelWidth_ szValue = XmTextFieldGetString( widTracesWindowInitialPixelWidth_ ); soValue = szValue; XtFree( szValue ); int nTracesWindowInitialPixelWidth; if ( !bIsNumericMaybeWithWhitespace( soValue, nTracesWindowInitialPixelWidth ) ) { popupErrorMessage( "Initial Width of Trace Window in Pixels must be numeric" ); return( false ); } if ( nTracesWindowInitialPixelWidth <= 0 ) { popupErrorMessage( "Initial Width of Trace Window in Pixels must be positive" ); return( false ); } consedParameters::pGetConsedParameters()->nTracesWindowInitialPixelWidth_ = nTracesWindowInitialPixelWidth; // nTracesWindowInitialPixelHeight_ szValue = XmTextFieldGetString( widTracesWindowInitialPixelHeight_ ); soValue = szValue; XtFree( szValue ); int nTracesWindowInitialPixelHeight; if ( !bIsNumericMaybeWithWhitespace( soValue, nTracesWindowInitialPixelHeight ) ) { popupErrorMessage( "Initial Height of Trace Area in Pixels must be numeric" ); return( false ); } if ( nTracesWindowInitialPixelHeight <= 0 ) { popupErrorMessage( "Initial Height of Trace Area in Pixels must be positive" ); return( false ); } consedParameters::pGetConsedParameters()->nTracesWindowInitialPixelHeight_ = nTracesWindowInitialPixelHeight; // nWriteThisAceFormat_ consedParameters::pGetConsedParameters()->nWriteThisAceFormat_ = ( XmToggleButtonGetState( widWriteAceFormat1_ ) == True ) ? 1 : 2; // count pads true bOldValue = consedParameters::pGetConsedParameters()->bCountPads_; consedParameters::pGetConsedParameters()->bCountPads_ = XmToggleButtonGetState( widCountPadsTrue_ ); if ( bOldValue != consedParameters::pGetConsedParameters()->bCountPads_ ) { ConsEd::pGetConsEd()->refreshAllContigWinsAndAllTeditors(); } // bShowReadsAlphabetically_ true bOldValue = consedParameters::pGetConsedParameters()->bShowReadsAlphabetically_; consedParameters::pGetConsedParameters()->bShowReadsAlphabetically_ = XmToggleButtonGetState( widShowReadsAlphabeticallyTrue_ ); if ( bOldValue != consedParameters::pGetConsedParameters()->bShowReadsAlphabetically_ ) { // then get a new contigview that has the reads ordered by that number ConsEd::pGetConsEd()->getNewContigViewsForAllContigWins(); // the redisplay ConsEd::pGetConsEd()->refreshAllContigWinsAndAllTeditors(); } // IgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion szValue = XmTextFieldGetString( widIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_ ); soValue = szValue; XtFree( szValue ); int nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion; if ( !bIsNumericMaybeWithWhitespace( soValue, nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion )) { GuiApp::popupErrorMessage( " nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion must be numeric" ); return( false ); } if ( nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion < 0 ) { GuiApp::popupErrorMessage( "nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion cannot be negative" ); return( false ); } consedParameters::pGetConsedParameters()->nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_ = nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion ; // IgnoreUnalignedHighQualitySegmentsShorterThanThis szValue = XmTextFieldGetString( widIgnoreUnalignedHighQualitySegmentsShorterThanThis_ ); soValue = szValue; XtFree( szValue ); int nIgnoreUnalignedHighQualitySegmentsShorterThanThis; if ( !bIsNumericMaybeWithWhitespace( soValue, nIgnoreUnalignedHighQualitySegmentsShorterThanThis )) { GuiApp::popupErrorMessage( "nIgnoreUnalignedHighQualitySegmentsShorterThanThis must be numeric" ); return( false ); } consedParameters::pGetConsedParameters()->nIgnoreUnalignedHighQualitySegmentsShorterThanThis_ = nIgnoreUnalignedHighQualitySegmentsShorterThanThis; // nCompareContigsAlignsThisManyBasesMax szValue = XmTextFieldGetString( widCompareContigsAlignsThisManyBasesMax_ ); soValue = szValue; XtFree( szValue ); int nCompareContigsAlignsThisManyBasesMax; if ( !bIsNumericMaybeWithWhitespace( soValue, nCompareContigsAlignsThisManyBasesMax ) ) { GuiApp::popupErrorMessage( "nCompareContigsAlignsThisManyBasesMax must be numeric" ); return( false ); } consedParameters::pGetConsedParameters()->nCompareContigsAlignsThisManyBasesMax_ = nCompareContigsAlignsThisManyBasesMax; // nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion_ szValue = XmTextFieldGetString( widWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion_ ); soValue = szValue; XtFree( szValue ); int nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion; if ( !bIsNumericMaybeWithWhitespace( soValue, nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion ) ) { GuiApp::popupErrorMessage( "nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion must be numeric" ); return( false ); } consedParameters::pGetConsedParameters()->nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion_ = nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion; // nDebugging_ szValue = XmTextFieldGetString( widDebugging_ ); soValue = szValue; XtFree( szValue ); int nDebugging; if ( !bIsNumericMaybeWithWhitespace( soValue, nDebugging ) ) { GuiApp::popupErrorMessage( "nDebugging must be numeric" ); return( false ); } consedParameters::pGetConsedParameters()->nDebugging_ = nDebugging; // bShowABIBasesInTraceWindow_ bOldValue = consedParameters::pGetConsedParameters()->bShowABIBasesInTraceWindow_; consedParameters::pGetConsedParameters()->bShowABIBasesInTraceWindow_ = XmToggleButtonGetState( widShowABIBasesInTraceWindowTrue_ ); // bDumpCoreIfBoundsError_ pCP->bDumpCoreIfBoundsError_ = ( XmToggleButtonGetState( widDumpCoreIfBoundsErrorTrue_ ) == True ) ? true : false; // bCompareContigsUseBandedRatherThanFullSmithWaterman_ pCP->bCompareContigsUseBandedRatherThanFullSmithWaterman_ = ( XmToggleButtonGetState( widCompareContigsUseBandedRatherThanFullSmithWatermanTrue_ ) == True ) ? true : false; // nCompareContigsBandSize_ szValue = XmTextFieldGetString( widCompareContigsBandSize_ ); soValue = szValue; XtFree( szValue ); int nCompareContigsBandSize; if ( !bIsNumericMaybeWithWhitespace( soValue, nCompareContigsBandSize ) ) { popupErrorMessage( "consed.compareContigsBandSize must be numeric" ); return( false ); } if ( nCompareContigsBandSize < 0 ) { popupErrorMessage( "consed.compareContigsBandSize must be positive" ); return( false ); } pCP->nCompareContigsBandSize_ = nCompareContigsBandSize; // nAlignedReadsWindowMaxCharsForReadNames_ nOldValue = pCP->nAlignedReadsWindowMaxCharsForReadNames_; szValue = XmTextFieldGetString( widAlignedReadsWindowMaxCharsForReadNames_ ); soValue = szValue; XtFree( szValue ); int nPerhapsAlignedReadsWindowMaxCharsForReadNames; if ( !bIsNumericMaybeWithWhitespace( soValue, nPerhapsAlignedReadsWindowMaxCharsForReadNames ) ) { popupErrorMessage("AlignedReadsWindowMaxCharsForReadNames must be numeric" ); return( false ); } if ( nPerhapsAlignedReadsWindowMaxCharsForReadNames <= 0 ) { popupErrorMessage( "AlignedReadsWindowMaxCharsForReadNames must be positive" ); return( false ); } pCP->nAlignedReadsWindowMaxCharsForReadNames_ = nPerhapsAlignedReadsWindowMaxCharsForReadNames; if ( pCP->nAlignedReadsWindowMaxCharsForReadNames_ != nOldValue ) { // actually don't need to refresh trace windows, just // aligned reads windows ConsEd::pGetConsEd()->refreshAllContigWinsAndAllTeditors(); } return( true ); }