/***************************************************************************** # 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 "guiAssemblyViewIncludeContigs.h" #include #include #include #include #include #include #include #include "hp_exception_kludge.h" #include "handleWindowManagerDelete2.h" #include "assemblyView.h" #include #include "bIsNumericMaybeWithWhitespace.h" #include "bIsNumericDouble.h" #include "popupErrorMessage.h" #include "consed.h" #include "rwctokenizer.h" static const int nRightPositionOfLabels = 60; static const int nLeftPositionOfInputFields = 70; #ifdef NO_POUND_POUND_MACROS #define makeLabelAndIntegerTextField( parameterNameWithoutPrefix, label ) \ Widget wid ## parameterNameWithoutPrefix ## Form = XtVaCreateManagedWidget( \ "form", \ xmFormWidgetClass, \ widRowCol, \ XmNshadowThickness, 0, \ NULL ); \ \ Widget wid ## parameterNameWithoutPrefix ## Label = XtVaCreateManagedWidget( \ label , \ xmLabelWidgetClass, \ wid ## parameterNameWithoutPrefix ## Form, \ XmNtopAttachment, XmATTACH_FORM, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNleftAttachment, XmATTACH_FORM, \ XmNrightAttachment, XmATTACH_POSITION, \ XmNrightPosition, nRightPositionOfLabels, \ XmNalignment, XmALIGNMENT_END, \ NULL ); \ \ char sz ## parameterNameWithoutPrefix[200]; \ sprintf( sz ## parameterNameWithoutPrefix, "%d", \ consedParameters::pGetConsedParameters()->n ## parameterNameWithoutPrefix ## _ ); \ \ \ wid ## parameterNameWithoutPrefix ## _ = XtVaCreateManagedWidget( \ #parameterNameWithoutPrefix , \ xmTextFieldWidgetClass, \ wid ## parameterNameWithoutPrefix ## Form, \ XmNtraversalOn, True, \ XmNtopAttachment, XmATTACH_FORM, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, nLeftPositionOfInputFields, \ XmNrightAttachment, XmATTACH_FORM, \ XmNvalue, sz ## parameterNameWithoutPrefix , \ NULL ); \ \ XtAddCallback( wid ## parameterNameWithoutPrefix ## _, \ XmNactivateCallback, \ (XtCallbackProc )XmProcessTraversal, \ (XtPointer) XmTRAVERSE_NEXT_TAB_GROUP ); #else #define makeLabelAndIntegerTextField( parameterNameWithoutPrefix, label ) \ Widget wid ## parameterNameWithoutPrefix ## Form = XtVaCreateManagedWidget( \ "form", \ xmFormWidgetClass, \ widRowCol, \ XmNshadowThickness, 0, \ NULL ); \ \ Widget wid ## parameterNameWithoutPrefix ## Label = XtVaCreateManagedWidget( \ ##label , \ xmLabelWidgetClass, \ wid ## parameterNameWithoutPrefix ## Form, \ XmNtopAttachment, XmATTACH_FORM, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNleftAttachment, XmATTACH_FORM, \ XmNrightAttachment, XmATTACH_POSITION, \ XmNrightPosition, nRightPositionOfLabels, \ XmNalignment, XmALIGNMENT_END, \ NULL ); \ \ char sz ## parameterNameWithoutPrefix ## [200]; \ sprintf( sz ## parameterNameWithoutPrefix, "%d", \ consedParameters::pGetConsedParameters()->n ## parameterNameWithoutPrefix ## _ ); \ \ \ wid ## parameterNameWithoutPrefix ## _ = XtVaCreateManagedWidget( \ #parameterNameWithoutPrefix , \ xmTextFieldWidgetClass, \ wid ## parameterNameWithoutPrefix ## Form, \ XmNtraversalOn, True, \ XmNtopAttachment, XmATTACH_FORM, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, nLeftPositionOfInputFields, \ XmNrightAttachment, XmATTACH_FORM, \ XmNvalue, sz ## parameterNameWithoutPrefix , \ NULL ); \ \ XtAddCallback( wid ## parameterNameWithoutPrefix ## _, \ XmNactivateCallback, \ (XtCallbackProc )XmProcessTraversal, \ (XtPointer) XmTRAVERSE_NEXT_TAB_GROUP ); #endif #ifdef NO_POUND_POUND_MACROS #define makeLabelAndDoubleTextField( parameterNameWithoutPrefix, label ) \ Widget wid ## parameterNameWithoutPrefix ## Form = XtVaCreateManagedWidget( \ "form", \ xmFormWidgetClass, \ widRowCol, \ XmNshadowThickness, 0, \ NULL ); \ \ Widget wid ## parameterNameWithoutPrefix ## Label = XtVaCreateManagedWidget( \ label , \ xmLabelWidgetClass, \ wid ## parameterNameWithoutPrefix ## Form, \ XmNtopAttachment, XmATTACH_FORM, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNleftAttachment, XmATTACH_FORM, \ XmNrightAttachment, XmATTACH_POSITION, \ XmNrightPosition, nRightPositionOfLabels, \ XmNalignment, XmALIGNMENT_END, \ NULL ); \ \ char sz ## parameterNameWithoutPrefix[200]; \ sprintf( sz ## parameterNameWithoutPrefix, "%.1f", \ consedParameters::pGetConsedParameters()->d ## parameterNameWithoutPrefix ## _ ); \ \ \ wid ## parameterNameWithoutPrefix ## _ = XtVaCreateManagedWidget( \ #parameterNameWithoutPrefix , \ xmTextFieldWidgetClass, \ wid ## parameterNameWithoutPrefix ## Form, \ XmNtraversalOn, True, \ XmNtopAttachment, XmATTACH_FORM, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, nLeftPositionOfInputFields, \ XmNrightAttachment, XmATTACH_FORM, \ XmNvalue, sz ## parameterNameWithoutPrefix , \ NULL ); \ \ XtAddCallback( wid ## parameterNameWithoutPrefix ## _, \ XmNactivateCallback, \ (XtCallbackProc )XmProcessTraversal, \ (XtPointer) XmTRAVERSE_NEXT_TAB_GROUP ); #else #define makeLabelAndDoubleTextField( parameterNameWithoutPrefix, label ) \ Widget wid ## parameterNameWithoutPrefix ## Form = XtVaCreateManagedWidget( \ "form", \ xmFormWidgetClass, \ widRowCol, \ XmNshadowThickness, 0, \ NULL ); \ \ Widget wid ## parameterNameWithoutPrefix ## Label = XtVaCreateManagedWidget( \ ##label , \ xmLabelWidgetClass, \ wid ## parameterNameWithoutPrefix ## Form, \ XmNtopAttachment, XmATTACH_FORM, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNleftAttachment, XmATTACH_FORM, \ XmNrightAttachment, XmATTACH_POSITION, \ XmNrightPosition, nRightPositionOfLabels, \ XmNalignment, XmALIGNMENT_END, \ NULL ); \ \ char sz ## parameterNameWithoutPrefix ## [200]; \ sprintf( sz ## parameterNameWithoutPrefix, "%.1f", \ consedParameters::pGetConsedParameters()->d ## parameterNameWithoutPrefix ## _ ); \ \ \ wid ## parameterNameWithoutPrefix ## _ = XtVaCreateManagedWidget( \ #parameterNameWithoutPrefix , \ xmTextFieldWidgetClass, \ wid ## parameterNameWithoutPrefix ## Form, \ XmNtraversalOn, True, \ XmNtopAttachment, XmATTACH_FORM, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, nLeftPositionOfInputFields, \ XmNrightAttachment, XmATTACH_FORM, \ XmNvalue, sz ## parameterNameWithoutPrefix , \ NULL ); \ \ XtAddCallback( wid ## parameterNameWithoutPrefix ## _, \ XmNactivateCallback, \ (XtCallbackProc )XmProcessTraversal, \ (XtPointer) XmTRAVERSE_NEXT_TAB_GROUP ); #endif #ifdef NO_POUND_POUND_MACROS #define makeLabelAndTextField( parameterNameWithoutPrefix, label, szValue ) \ Widget wid ## parameterNameWithoutPrefix ## Form = XtVaCreateManagedWidget( \ "form", \ xmFormWidgetClass, \ widRowCol, \ XmNshadowThickness, 0, \ NULL ); \ \ Widget wid ## parameterNameWithoutPrefix ## Label = XtVaCreateManagedWidget( \ label , \ xmLabelWidgetClass, \ wid ## parameterNameWithoutPrefix ## Form, \ XmNtopAttachment, XmATTACH_FORM, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNleftAttachment, XmATTACH_FORM, \ XmNrightAttachment, XmATTACH_POSITION, \ XmNrightPosition, nRightPositionOfLabels, \ XmNalignment, XmALIGNMENT_END, \ NULL ); \ \ \ wid ## parameterNameWithoutPrefix ## _ = XtVaCreateManagedWidget( \ #parameterNameWithoutPrefix , \ xmTextFieldWidgetClass, \ wid ## parameterNameWithoutPrefix ## Form, \ XmNtraversalOn, True, \ XmNtopAttachment, XmATTACH_FORM, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, nLeftPositionOfInputFields, \ XmNrightAttachment, XmATTACH_FORM, \ XmNvalue, szValue, \ NULL ); \ \ XtAddCallback( wid ## parameterNameWithoutPrefix ## _, \ XmNactivateCallback, \ (XtCallbackProc )XmProcessTraversal, \ (XtPointer) XmTRAVERSE_NEXT_TAB_GROUP ); #else #define makeLabelAndTextField( parameterNameWithoutPrefix, label, szValue ) \ Widget wid ## parameterNameWithoutPrefix ## Form = XtVaCreateManagedWidget( \ "form", \ xmFormWidgetClass, \ widRowCol, \ XmNshadowThickness, 0, \ NULL ); \ \ Widget wid ## parameterNameWithoutPrefix ## Label = XtVaCreateManagedWidget( \ ##label , \ xmLabelWidgetClass, \ wid ## parameterNameWithoutPrefix ## Form, \ XmNtopAttachment, XmATTACH_FORM, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNleftAttachment, XmATTACH_FORM, \ XmNrightAttachment, XmATTACH_POSITION, \ XmNrightPosition, nRightPositionOfLabels, \ XmNalignment, XmALIGNMENT_END, \ NULL ); \ \ \ wid ## parameterNameWithoutPrefix ## _ = XtVaCreateManagedWidget( \ #parameterNameWithoutPrefix , \ xmTextFieldWidgetClass, \ wid ## parameterNameWithoutPrefix ## Form, \ XmNtraversalOn, True, \ XmNtopAttachment, XmATTACH_FORM, \ XmNbottomAttachment, XmATTACH_FORM, \ XmNleftAttachment, XmATTACH_POSITION, \ XmNleftPosition, nLeftPositionOfInputFields, \ XmNrightAttachment, XmATTACH_FORM, \ XmNvalue, szValue, \ NULL ); \ \ XtAddCallback( wid ## parameterNameWithoutPrefix ## _, \ XmNactivateCallback, \ (XtCallbackProc )XmProcessTraversal, \ (XtPointer) XmTRAVERSE_NEXT_TAB_GROUP ); #endif #define checkIfNumeric( AssemblyViewParameter ) \ szValue = XmTextFieldGetString( wid ## AssemblyViewParameter ## _ );\ soValue = szValue; \ XtFree( szValue ); \ int nPerhaps ## AssemblyViewParameter; \ if ( !bIsNumericMaybeWithWhitespace( soValue, nPerhaps ## AssemblyViewParameter ) ) { \ RWCString soError = #AssemblyViewParameter " must be numeric but instead is: \""; \ soError += soValue; \ soError += "\""; \ popupErrorMessage( soError ); \ return; \ } #define checkIfNumericDouble( AssemblyViewParameter ) \ szValue = XmTextFieldGetString( wid ## AssemblyViewParameter ## _ );\ soValue = szValue; \ XtFree( szValue ); \ double dPerhaps ## AssemblyViewParameter; \ if ( !bIsNumericDouble( soValue, dPerhaps ## AssemblyViewParameter ) ) { \ RWCString soError = #AssemblyViewParameter " must be numeric but instead is: \""; \ soError += soValue; \ soError += "\""; \ popupErrorMessage( soError ); \ return; \ } static void cbApply( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiAssemblyViewIncludeContigs* pGAVIC = (guiAssemblyViewIncludeContigs*) pClientData; TRY_CATCH_WRAPPER( pGAVIC->userPushedApply() ); } static void cbDismiss( Widget wid, XtPointer pClientData, XtPointer pCallData ) { guiAssemblyViewIncludeContigs* pGAVIC = (guiAssemblyViewIncludeContigs*) pClientData; TRY_CATCH_WRAPPER( delete pGAVIC ); } static void cbGuiShowDocumentationForAssemblyView( Widget wid, XtPointer pClientData, XtPointer pCallData ) { TRY_CATCH_WRAPPER( if ( ConsEd::pGetConsEd()->pAssemblyView_ ) ConsEd::pGetConsEd()->pAssemblyView_->showDocumentationForAssemblyView() ); } void guiAssemblyViewIncludeContigs :: createWindow() { widPopupShell_ = XtVaCreatePopupShell( "Which Contigs to Show in Assembly View", topLevelShellWidgetClass, GAPP->widGetTopLevel(), // not connected to // assemblyView's shell so that assemblyView // can be deleted without deleting this (not used // currently) XmNtransient, False, XmNdeleteResponse, XmDO_NOTHING, NULL ); handleWindowManagerDelete2( widPopupShell_, cbDismiss, this ); // put on a main window so we can have a menu bar Widget widMainWin = XtVaCreateManagedWidget( "mainwin", xmMainWindowWidgetClass, widPopupShell_, XmNancestorSensitive, True, NULL ); // put menu bar on the main window int nArgs = 0; Arg aArg[30]; Widget widMenuBar = XmCreateMenuBar( widMainWin, "menubar", aArg, nArgs ); XtManageChild( widMenuBar ); // create help menu button nArgs = 0; Widget widHelpMenu = XmCreatePulldownMenu( widMenuBar, "Help", aArg, nArgs ); nArgs = 0; XtSetArg( aArg[ nArgs ], XmNsubMenuId, widHelpMenu ); ++nArgs; Widget widHelpCascade = XmCreateCascadeButton( widMenuBar, "Help", aArg, nArgs ); XtManageChild( widHelpCascade ); XtVaSetValues( widMenuBar, XmNmenuHelpWidget, widHelpCascade, NULL ); // now add help menu item Widget widShowDocumentation = XtVaCreateManagedWidget( "Show Documentation for Assembly View", xmPushButtonWidgetClass, widHelpMenu, NULL ); XtAddCallback( widShowDocumentation, XmNactivateCallback, cbGuiShowDocumentationForAssemblyView, this ); Widget widForm = XtVaCreateManagedWidget( "form", xmFormWidgetClass, widMainWin, XmNancestorSensitive, True, NULL ); widDismiss_ = XtVaCreateManagedWidget( "Dismiss", xmPushButtonWidgetClass, widForm, XmNbottomAttachment, XmATTACH_FORM, XmNbottomOffset, 10, XmNtraversalOn, False, XmNleftAttachment, XmATTACH_POSITION, XmNleftPosition, 70, XmNrightAttachment, XmATTACH_POSITION, XmNrightPosition, 90, NULL ); XtAddCallback( widDismiss_, XmNactivateCallback, cbDismiss, this ); widApply_ = XtVaCreateManagedWidget( "Apply and Restart Assembly View", xmPushButtonWidgetClass, widForm, XmNbottomAttachment, XmATTACH_FORM, XmNbottomOffset, 10, XmNtraversalOn, False, XmNleftAttachment, XmATTACH_POSITION, XmNleftPosition, 10, // XmNrightAttachment, XmATTACH_POSITION, // XmNrightPosition, 30, NULL ); XtAddCallback( widApply_, XmNactivateCallback, cbApply, this ); Widget widRowCol = XtVaCreateManagedWidget( "rowcol", xmRowColumnWidgetClass, widForm, XmNleftAttachment, XmATTACH_FORM, XmNrightAttachment, XmATTACH_FORM, XmNtopAttachment, XmATTACH_FORM, XmNbottomAttachment, XmATTACH_WIDGET, XmNbottomWidget, widDismiss_, NULL ); makeLabelAndIntegerTextField( AutoFinishExcludeContigIfOnlyThisManyReadsOrLess, "exclude contig if this many reads or less" ); makeLabelAndIntegerTextField( AutoFinishExcludeContigIfThisManyBasesOrLess, "exclude contig if this many bases or less" ); makeLabelAndDoubleTextField( AutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis, "exclude contig if depth of coverage greater than this" ); makeLabelAndTextField( OnlyIncludeTheseContigs, "Just show these contigs:", pCP->soAssemblyViewContigsToShow_.data() ); XtPopup( widPopupShell_, XtGrabNone ); } guiAssemblyViewIncludeContigs :: ~guiAssemblyViewIncludeContigs() { XtPopdown( widPopupShell_ ); XtDestroyWidget( widPopupShell_ ); } void guiAssemblyViewIncludeContigs :: userPushedApply() { char* szValue; RWCString soValue; checkIfNumeric( AutoFinishExcludeContigIfOnlyThisManyReadsOrLess ); pCP->nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_ = nPerhapsAutoFinishExcludeContigIfOnlyThisManyReadsOrLess; checkIfNumeric( AutoFinishExcludeContigIfThisManyBasesOrLess ); pCP->nAutoFinishExcludeContigIfThisManyBasesOrLess_ = nPerhapsAutoFinishExcludeContigIfThisManyBasesOrLess; checkIfNumericDouble( AutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis ); pCP->dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_ = dPerhapsAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis; // parse widOnlyIncludeTheseContigs and see if it makes sense szValue = XmTextFieldGetString( widOnlyIncludeTheseContigs_ ); RWCString soContigsToShow = szValue; XtFree( szValue ); soContigsToShow = soContigsToShow.stripWhitespace( RWCString::BOTH ); if ( !soContigsToShow.isNull() ) { RWCTokenizer tokContigs( soContigsToShow ); RWCString soOneContig; while( !( soOneContig = tokContigs(',' )).isNull() ) { // let's allow the user to enter either fancy contig names // or abbreviated names. Find it by either. Contig* pContig = ConsEd::pGetAssembly()->pGetContigByVariousNames( soOneContig ); if ( !pContig ) { popupErrorMessage( "In \"Just show these contigs\" is a name \"%s\" which cannot be found", soOneContig.data() ); return; } } } // if reached here, it was possible to parse the list of contigs, // so put the entire string into the variable pCP->soAssemblyViewContigsToShow_ = soContigsToShow; if ( ConsEd::pGetConsEd()->pAssemblyView_ ) delete ConsEd::pGetConsEd()->pAssemblyView_; // assemblyView dtor will call // guiAssemblyViewIncludeContigs dtor // Note: since ~guiAssemblyViewIncludeContigs will now have been called, // do *NOT* read or write to any member variables or else you will // be writing to freed memory, which is likely reallocated, and // I was getting segmentation faults in Xt routines! (April, 2003) // restart Assembly View ConsEd::pGetConsEd()->pAssemblyView_ = new assemblyView(); ConsEd::pGetConsEd()->pAssemblyView_->createWindow( ConsEd::pGetAssembly() ); } void guiAssemblyViewIncludeContigs :: raiseWindow() { XtMapWidget( widPopupShell_ ); XRaiseWindow( XtDisplay( widPopupShell_ ), XtWindow( widPopupShell_ ) ); }