/*****************************************************************************
# 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.
#
#*****************************************************************************/
//
// gui_search_for_string.cpp
//
// implementation for GuiSearchForString class
//
// Used to put up a dialog box with query string, get a user response,
// and return a list of matches
//
// David Gordon, July 1995
//
#include <Xm/Form.h>
#include <Xm/Label.h>
#include <Xm/Text.h>
#include <stdio.h>
#include <Xm/PushB.h>
#include "gui_search_for_string.h"
#include "search_for_string.h"
#include "guiapp.h"
#include "gui_get_selection.h"
#include <iostream.h>
#include <Xm/ToggleB.h>
#include <Xm/RowColumn.h>
#include "searchMethods.h"
#include <Xm/MainW.h>
#include "handleWindowManagerDelete.h"
#include "hp_exception_kludge.h"
#include "bIsNumericMaybeWithWhitespace.h"
#include "popupErrorMessage.h"
#include "consedParameters.h"
#include "searchMethods.h"
#include "consed.h"
#include "rwcregexp.h"
#include "soGetErrno.h"
void cbSearch( Widget widCallback, XtPointer client_data,
XtPointer call_data ) {
XmAnyCallbackStruct* pXmAnyCallbackStruct =
(XmAnyCallbackStruct*) call_data;
GuiSearchForString* pGuiSearchForString = (GuiSearchForString *) client_data;
TRY_CATCH_WRAPPER(
pGuiSearchForString->guiDoSearch( widCallback,
pXmAnyCallbackStruct );
);
}
void cbClearQueryString( Widget widCallback, XtPointer client_data,
XtPointer call_data ) {
XmAnyCallbackStruct* pXmAnyCallbackStruct =
(XmAnyCallbackStruct*) call_data;
GuiSearchForString* pGuiSearchForString = (GuiSearchForString *) client_data;
TRY_CATCH_WRAPPER(
pGuiSearchForString->guiClearQueryString( );
);
}
void cbCancelSearch( Widget widCallback, XtPointer client_data,
XtPointer call_data ) {
GuiSearchForString* pGuiSearchForString = (GuiSearchForString *) client_data;
TRY_CATCH_WRAPPER(
delete pGuiSearchForString;
);
}
void cbChangeContigsVsReads( Widget wid, XtPointer client_data,
XtPointer call_data ) {
GuiSearchForString* pGuiSearchForString = (GuiSearchForString*) client_data;
TRY_CATCH_WRAPPER(
pGuiSearchForString->changeContigsVsReads();
);
}
void cbChangeSearchMethod( Widget wid, XtPointer client_data,
XtPointer call_data ) {
GuiSearchForString* pGuiSearchForString = (GuiSearchForString*) client_data;
TRY_CATCH_WRAPPER(
pGuiSearchForString->changeSearchMethod( wid, call_data );
);
}
void GuiSearchForString :: changeSearchMethod( const Widget wid,
const XtPointer& call_data ) {
XmToggleButtonCallbackStruct* pToggleButtonCallbackStruct =
(XmToggleButtonCallbackStruct*) call_data;
if ( pToggleButtonCallbackStruct -> set ) {
if (wid == widSearchMethodExact_ )
nSearchMethod_ = nExact;
else if (wid == widSearchMethodSmithWaterman_ )
nSearchMethod_ = nInexact;
}
}
void GuiSearchForString :: guiDoSearch( Widget widCallback,
XmAnyCallbackStruct* pXmAnyCallbackStruct ) {
char *szQueryString = XmTextGetString( widQueryString_ );
RWCString soQueryString = szQueryString;
XtFree( szQueryString );
if (soQueryString.length() == 0 ) {
GuiApp::popupErrorMessage( "You must enter a query string" );
return;
}
char* szPerCentMismatch = XmTextGetString( widPerCentMismatch_ );
int nPerCentMismatch;
if ( !bIsNumericMaybeWithWhitespace( szPerCentMismatch,
nPerCentMismatch ) ) {
popupErrorMessage( "The per cent mismatch must be between 0 and 30" );
return;
}
if ( !
( 0 <= nPerCentMismatch &&
nPerCentMismatch <= 30 ) ) {
popupErrorMessage( "The per cent mismatch must be between 0 and 30" );
return;
}
// check that singlets file exists
FileName filSingletsFile;
if ( !bJustContigsNotReads_ ) {
filSingletsFile = XmTextGetString( widSingletsFile_ );
if ( !filSingletsFile.isNull() ) {
// check Consed can open this file
FILE* pSingletsFile = fopen( filSingletsFile.data(), "r" );
if ( !pSingletsFile ) {
RWCString soErrorMessage = "could not open ";
soErrorMessage += filSingletsFile;
soErrorMessage += " for read. ";
soErrorMessage += soGetErrno();
popupErrorMessage( soErrorMessage );
return;
}
fclose( pSingletsFile );
}
}
popupOutputWindowAndDoSearch( soQueryString,
nSearchMethod_,
bJustContigsNotReads_,
nPerCentMismatch,
filSingletsFile );
}
void GuiSearchForString :: popupAskForSearchString() {
Arg aArg[100];
int nArgs;
XmStringTable xmStringList;
int n;
widPopupShell_ = XtVaCreatePopupShell("Search For String",
topLevelShellWidgetClass,
GuiApp::pGetGuiApp()->widGetTopLevel(),
XmNdeleteResponse, XmDO_NOTHING,
NULL );
handleWindowManagerDelete( widPopupShell_ );
// the immediate child of the application shell is a
// main window
Widget widMainWin =
XtVaCreateManagedWidget("mainwin",
xmMainWindowWidgetClass, widPopupShell_,
XmNancestorSensitive, True,
NULL );
//
// create the form widget
//
nArgs = 0;
XtSetArg(aArg[nArgs],XmNshadowThickness,0); nArgs++;
XtSetArg(aArg[nArgs],XmNborderWidth,0); nArgs++;
Widget widForm = XmCreateForm(widMainWin,
"form",
aArg,
nArgs);
XtManageChild(widForm);
Widget widLabel = XtVaCreateManagedWidget("Query string: ",
xmLabelWidgetClass,
widForm,
XmNtopAttachment, XmATTACH_FORM,
XmNtopOffset, 20,
XmNleftAttachment, XmATTACH_FORM,
XmNleftOffset, 20,
NULL );
nArgs = 0;
XtSetArg( aArg[ nArgs ], XmNleftAttachment, XmATTACH_FORM ); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNrightAttachment, XmATTACH_FORM); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNleftOffset, 20); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNrightOffset, 20); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNtopAttachment, XmATTACH_WIDGET); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNtopWidget, widLabel ); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNeditMode, XmSINGLE_LINE_EDIT ); ++nArgs;
widQueryString_ = XtCreateManagedWidget( "QueryString", xmTextWidgetClass,
widForm,
aArg, nArgs );
XtAddCallback( widQueryString_,
XmNactivateCallback,
cbSearch,
this );
widClearButton_ = XtVaCreateManagedWidget( "Clear",
xmPushButtonWidgetClass,
widForm,
XmNtopAttachment, XmATTACH_WIDGET,
XmNtopWidget, widQueryString_,
XmNtopOffset, 20,
XmNleftAttachment, XmATTACH_FORM,
XmNleftOffset, 20,
XmNrightAttachment, XmATTACH_FORM,
XmNrightOffset, 20,
XmNtraversalOn, False,
NULL );
XtAddCallback( widClearButton_,
XmNactivateCallback,
cbClearQueryString,
this );
// search all reads vs search just contig
nArgs = 0;
XtSetArg( aArg[ nArgs ], XmNleftAttachment, XmATTACH_FORM ); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNrightAttachment, XmATTACH_FORM); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNleftOffset, 20); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNrightOffset, 20); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNtopAttachment, XmATTACH_WIDGET); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNtopWidget, widClearButton_ ); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNtopOffset, 40 ); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNbottomOffset, 40 ); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNmarginWidth, 0 ); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNtraversalOn, False ); ++nArgs;
Widget widContigsVsReadsRadioBox = XmCreateRadioBox( widForm,
"radio_box",
aArg,
nArgs );
XtManageChild( widContigsVsReadsRadioBox );
bJustContigsNotReads_ = true;
widSearchJustContigs_ = XtVaCreateManagedWidget("Search Just Contigs",
xmToggleButtonWidgetClass,
widContigsVsReadsRadioBox,
XmNset,
True,
NULL );
XtAddCallback( widSearchJustContigs_, XmNvalueChangedCallback,
cbChangeContigsVsReads,
this );
widSearchJustReads_ = XtVaCreateManagedWidget("Search Just Reads",
xmToggleButtonWidgetClass,
widContigsVsReadsRadioBox,
NULL );
// Don't have this callback since the one above for widSearchJustContigs_
// will already call cbChangeContigsVsReads
// XtAddCallback( widSearchReadsAndContigs_, XmNvalueChangedCallback,
// cbChangeContigsVsReads,
// this );
// exact/ Smith-Waterman search
nArgs = 0;
XtSetArg( aArg[ nArgs ], XmNleftAttachment, XmATTACH_FORM ); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNrightAttachment, XmATTACH_FORM); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNleftOffset, 20); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNrightOffset, 20); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNtopAttachment, XmATTACH_WIDGET); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNtopWidget, widContigsVsReadsRadioBox); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNtopOffset, 40 ); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNbottomOffset, 40 ); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNmarginWidth, 0 ); ++nArgs;
XtSetArg( aArg[ nArgs ], XmNtraversalOn, False ); ++nArgs;
Widget widRadioBox = XmCreateRadioBox( widForm,
"radio_box",
aArg,
nArgs );
XtManageChild( widRadioBox );
nSearchMethod_ = nExact;
widSearchMethodExact_ = XtVaCreateManagedWidget("Exact",
xmToggleButtonWidgetClass,
widRadioBox,
XmNset,
True,
NULL );
XtAddCallback( widSearchMethodExact_, XmNvalueChangedCallback,
cbChangeSearchMethod,
this );
widSearchMethodSmithWaterman_ = XtVaCreateManagedWidget("Approximate",
xmToggleButtonWidgetClass,
widRadioBox,
NULL );
XtAddCallback( widSearchMethodSmithWaterman_, XmNvalueChangedCallback,
cbChangeSearchMethod,
this );
Widget widPerCentMismatchForm =
XtVaCreateManagedWidget( "Per Cent Mismatch Form",
xmFormWidgetClass,
widForm,
XmNshadowThickness, 0,
XmNleftAttachment, XmATTACH_FORM,
XmNrightAttachment, XmATTACH_FORM,
XmNtopAttachment, XmATTACH_WIDGET,
XmNtopWidget, widRadioBox,
XmNtopOffset, 20,
NULL );
Widget widPerCentMismatchLabel =
XtVaCreateManagedWidget( "Per Cent Mismatch: ",
xmLabelWidgetClass,
widPerCentMismatchForm,
XmNleftAttachment, XmATTACH_FORM,
XmNleftOffset, 20,
XmNtopAttachment, XmATTACH_FORM,
XmNbottomAttachment, XmATTACH_FORM,
NULL );
RWCString soDefaultPerCentMismatch( (long)
pCP->nInexactSearchForStringMaxPerCentMismatch_ );
widPerCentMismatch_ =
XtVaCreateManagedWidget( "Per Cent Mismatch",
xmTextWidgetClass,
widPerCentMismatchForm,
XmNleftAttachment, XmATTACH_WIDGET,
XmNleftWidget, widPerCentMismatchLabel,
XmNrightAttachment, XmATTACH_FORM,
XmNrightOffset, 20,
XmNtopAttachment, XmATTACH_FORM,
XmNbottomAttachment, XmATTACH_FORM,
XmNeditMode, XmSINGLE_LINE_EDIT,
XmNcolumns, 3,
XmNvalue, soDefaultPerCentMismatch.data(),
NULL );
XmString xmsSingletFile = XmStringCreateLtoR( "Singlets file to also search\n(leave blank to not search it):",
XmFONTLIST_DEFAULT_TAG );
widSingletsFileLabel_ =
XtVaCreateManagedWidget( "singlets_label",
xmLabelWidgetClass,
widForm,
XmNleftAttachment, XmATTACH_FORM,
XmNleftOffset, 20,
XmNrightAttachment, XmATTACH_FORM,
XmNrightOffset, 20,
XmNtopAttachment, XmATTACH_WIDGET,
XmNtopWidget, widPerCentMismatchForm,
XmNlabelString, xmsSingletFile,
XmNalignment, XmALIGNMENT_BEGINNING,
XmNsensitive, False, // starting out just contigs
NULL );
XmStringFree( xmsSingletFile );
FileName filSingletsFile = ConsEd::pGetAssembly()->soGetAceFileName();
// chop off everything starting with .fasta.screen.
RWCRegexp regFasta( "\\.fasta\\.screen\\..*$" );
filSingletsFile( regFasta ) = "";
filSingletsFile += ".fasta.screen.singlets";
widSingletsFile_ =
XtVaCreateManagedWidget( "singlets_file",
xmTextWidgetClass,
widForm,
XmNleftAttachment, XmATTACH_FORM,
XmNleftOffset, 20,
XmNrightAttachment, XmATTACH_FORM,
XmNrightOffset, 20,
XmNtopAttachment, XmATTACH_WIDGET,
XmNtopWidget, widSingletsFileLabel_,
XmNeditMode, XmSINGLE_LINE_EDIT,
XmNvalue, filSingletsFile.data(),
XmNsensitive, False, // starting out just contigs
NULL );
Widget widConnectToTopWidget = widSingletsFile_;
widOKButton_ = XtVaCreateManagedWidget( "OK",
xmPushButtonWidgetClass,
widForm,
XmNtopAttachment, XmATTACH_WIDGET,
XmNtopWidget, widConnectToTopWidget,
XmNtopOffset, 20,
XmNleftAttachment, XmATTACH_POSITION,
XmNleftPosition,10 ,
XmNrightAttachment, XmATTACH_POSITION,
XmNrightPosition,45 ,
XmNbottomAttachment, XmATTACH_FORM,
XmNbottomOffset, 20,
XmNtraversalOn, False,
NULL );
XtAddCallback( widOKButton_,
XmNactivateCallback,
cbSearch,
this );
widCancelButton_ = XtVaCreateManagedWidget( "Cancel",
xmPushButtonWidgetClass,
widForm,
XmNtopAttachment, XmATTACH_WIDGET,
XmNtopWidget, widConnectToTopWidget,
XmNtopOffset, 20,
XmNleftAttachment, XmATTACH_POSITION,
XmNleftPosition,55 ,
XmNrightAttachment, XmATTACH_POSITION,
XmNrightPosition,90 ,
XmNbottomAttachment, XmATTACH_FORM,
XmNbottomOffset, 20,
XmNtraversalOn, False,
NULL );
XtAddCallback( widCancelButton_,
XmNactivateCallback,
cbCancelSearch,
this );
// pop it all up
// Note: if you do this any earlier, the bottom of the dialog will be
// off the screen since it grows downward after being popped up.
XtPopup( widPopupShell_, XtGrabNone );
// make the query box initially have input focus
XmProcessTraversal( widQueryString_, XmTRAVERSE_CURRENT );
}
void GuiSearchForString :: guiClearQueryString( ) {
XmTextSetString( widQueryString_, "" );
}
void GuiSearchForString :: raiseWindow() {
XRaiseWindow(
XtDisplay( widPopupShell_ ),
XtWindow( widPopupShell_ )
);
}
GuiSearchForString :: ~GuiSearchForString() {
ConsEd::pGetConsEd()->pGuiSearchForString_ = NULL;
XtDestroyWidget( widPopupShell_ );
}
void GuiSearchForString :: changeContigsVsReads() {
bJustContigsNotReads_ = ! bJustContigsNotReads_;
if ( bJustContigsNotReads_ ) {
XtVaSetValues( widSingletsFile_, XmNsensitive, False, NULL );
XtVaSetValues( widSingletsFileLabel_, XmNsensitive, False, NULL );
}
else {
XtVaSetValues( widSingletsFile_, XmNsensitive, True, NULL );
XtVaSetValues( widSingletsFileLabel_, XmNsensitive, True, NULL );
}
}