/*****************************************************************************
# 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 "guiReorderContigs.h"
#include "handleWindowManagerDelete2.h"
#include <Xm/Form.h>
#include <Xm/Label.h>
#include <Xm/Xm.h>
#include <Xm/PushB.h>
#include <Xm/ToggleB.h>
#include <Xm/TextF.h>
#include "consed.h"
#include "hp_exception_kludge.h"
#include "guiapp.h"
#include <Xm/List.h>
#include <Xm/RowColumn.h>
#include "popupErrorMessage2.h"
#include "editAddConsensusTag.h"
#include "editDeleteConsensusTag.h"
#include "contigEndPair.h"
#include "bGuiGetAnswerYesNo.h"
#include "assemblyView.h"
static void cbAddContigEndPair( Widget wid,
XtPointer pClientData,
XtPointer pCallData ) {
TRY_CATCH_WRAPPER(
guiReorderContigs* pGuiReorderContigs = (guiReorderContigs*) pClientData;
pGuiReorderContigs->userPushedAdd();
);
}
static void cbDeleteContigEndPair( Widget wid,
XtPointer pClientData,
XtPointer pCallData ) {
TRY_CATCH_WRAPPER(
guiReorderContigs* pGuiReorderContigs = (guiReorderContigs*) pClientData;
pGuiReorderContigs->userPushedDelete();
)
}
static void cbUserPushedDismiss( Widget wid,
XtPointer pClientData,
XtPointer pCallData ) {
TRY_CATCH_WRAPPER(
guiReorderContigs* pGuiReorderContigs = (guiReorderContigs*) pClientData;
delete pGuiReorderContigs;
);
}
void guiReorderContigs :: createWindow() {
Assembly* pAssembly = ConsEd::pGetAssembly();
widPopupShell_ = XtVaCreatePopupShell(
"Reorder Contigs",
topLevelShellWidgetClass,
GAPP->widGetTopLevel(),
XmNtransient, False,
XmNdeleteResponse, XmDO_NOTHING,
NULL );
handleWindowManagerDelete2( widPopupShell_, cbUserPushedDismiss, this );
Widget widForm = XtVaCreateManagedWidget(
"form",
xmFormWidgetClass,
widPopupShell_,
NULL );
Widget widAddLineForm = XtVaCreateManagedWidget(
"addLineForm",
xmFormWidgetClass,
widForm,
XmNtopAttachment, XmATTACH_FORM,
XmNleftAttachment, XmATTACH_FORM,
XmNleftOffset, 10,
XmNrightAttachment, XmATTACH_FORM,
XmNrightOffset, 10,
NULL );
Widget widAbove = widAddLineForm;
Widget widLabel1 = XtVaCreateManagedWidget(
"Contig:",
xmLabelWidgetClass,
widAddLineForm,
XmNbottomAttachment, XmATTACH_FORM,
XmNleftAttachment, XmATTACH_FORM,
XmNtopAttachment, XmATTACH_FORM,
NULL );
widContig1_ = XtVaCreateManagedWidget(
"contig1",
xmTextFieldWidgetClass,
widAddLineForm,
XmNbottomAttachment, XmATTACH_FORM,
XmNtopAttachment, XmATTACH_FORM,
XmNleftAttachment, XmATTACH_WIDGET,
XmNleftWidget, widLabel1,
XmNcolumns, 7,
NULL );
Widget widEnd1RadioBox = XmCreateRadioBox( widAddLineForm,
"radio1",
NULL,
0 );
XtVaSetValues( widEnd1RadioBox,
XmNtopAttachment, XmATTACH_FORM,
XmNbottomAttachment, XmATTACH_FORM,
XmNleftAttachment, XmATTACH_WIDGET,
XmNleftWidget, widContig1_,
XmNorientation, XmHORIZONTAL,
NULL );
XtManageChild( widEnd1RadioBox );
widLeftEndContig1_ = XtVaCreateManagedWidget(
"Left End",
xmToggleButtonWidgetClass,
widEnd1RadioBox,
XmNset, True, // default
NULL );
Widget widRightEndContig1 = XtVaCreateManagedWidget(
"Right End",
xmToggleButtonWidgetClass,
widEnd1RadioBox,
XmNset, False, // default
NULL );
Widget widLabel2 = XtVaCreateManagedWidget(
"connected to Contig:",
xmLabelWidgetClass,
widAddLineForm,
XmNbottomAttachment, XmATTACH_FORM,
XmNtopAttachment, XmATTACH_FORM,
XmNleftAttachment, XmATTACH_WIDGET,
XmNleftWidget, widEnd1RadioBox,
NULL );
widContig2_ = XtVaCreateManagedWidget(
"contig2",
xmTextFieldWidgetClass,
widAddLineForm,
XmNbottomAttachment, XmATTACH_FORM,
XmNtopAttachment, XmATTACH_FORM,
XmNleftAttachment, XmATTACH_WIDGET,
XmNleftWidget, widLabel2,
XmNcolumns, 7,
NULL );
Widget widEnd2RadioBox = XmCreateRadioBox( widAddLineForm,
"radio2",
NULL,
0 );
XtVaSetValues( widEnd2RadioBox,
XmNtopAttachment, XmATTACH_FORM,
XmNbottomAttachment, XmATTACH_FORM,
XmNleftAttachment, XmATTACH_WIDGET,
XmNleftWidget, widContig2_,
XmNorientation, XmHORIZONTAL,
XmNshadowThickness, 0,
XmNborderWidth, 0,
XmNmarginWidth, 0,
NULL );
widLeftEndContig2_ = XtVaCreateManagedWidget(
"Left End",
xmToggleButtonWidgetClass,
widEnd2RadioBox,
XmNset, True, // default
NULL );
Widget widRightEndContig2 = XtVaCreateManagedWidget(
"Right End",
xmToggleButtonWidgetClass,
widEnd2RadioBox,
XmNset, False, // default
NULL );
XtManageChild( widEnd2RadioBox );
Widget widAddContigEndPair = XtVaCreateManagedWidget(
"Add and Restart Assembly View",
xmPushButtonWidgetClass,
widForm,
XmNtopAttachment, XmATTACH_WIDGET,
XmNtopWidget, widAbove,
XmNleftAttachment, XmATTACH_POSITION,
XmNleftPosition, 40,
NULL );
widAbove = widAddContigEndPair;
XtAddCallback( widAddContigEndPair,
XmNactivateCallback,
cbAddContigEndPair,
this );
// start from bottom up
widDismiss_ = XtVaCreateManagedWidget(
"Dismiss",
xmPushButtonWidgetClass,
widForm,
XmNbottomAttachment, XmATTACH_FORM,
XmNbottomOffset, 10,
XmNleftAttachment, XmATTACH_POSITION,
XmNleftPosition, 40,
NULL );
XtAddCallback( widDismiss_,
XmNactivateCallback,
cbUserPushedDismiss,
this );
Widget widBelow = widDismiss_;
Widget widDeleteContigEndPair = XtVaCreateManagedWidget(
"Delete Selected and Restart Assembly View",
xmPushButtonWidgetClass,
widForm,
XmNbottomAttachment, XmATTACH_WIDGET,
XmNbottomWidget, widBelow,
XmNbottomOffset, 20,
XmNleftAttachment, XmATTACH_POSITION,
XmNleftPosition, 40,
NULL );
XtAddCallback( widDeleteContigEndPair,
XmNactivateCallback,
cbDeleteContigEndPair,
this );
widBelow = widDeleteContigEndPair;
int nArgs = 0;
Arg aArg[500];
XtSetArg( aArg[nArgs], XmNselectionPolicy, XmSINGLE_SELECT ); ++nArgs;
XtSetArg( aArg[nArgs], XmNtopAttachment, XmATTACH_WIDGET ); ++nArgs;
XtSetArg( aArg[nArgs], XmNtopWidget, widAbove ); ++nArgs;
XtSetArg( aArg[nArgs], XmNbottomAttachment, XmATTACH_WIDGET ); ++nArgs;
XtSetArg( aArg[nArgs], XmNbottomWidget, widBelow ); ++nArgs;
XtSetArg( aArg[nArgs], XmNvisibleItemCount, 3 ); ++nArgs;
XtSetArg( aArg[nArgs], XmNleftAttachment, XmATTACH_FORM ); ++nArgs;
XtSetArg( aArg[nArgs], XmNrightAttachment, XmATTACH_FORM ); ++nArgs;
widContigEndPairList_ = XmCreateScrolledList( widForm,
"list",
aArg,
nArgs );
XtManageChild( widContigEndPairList_ );
XtPopup( widPopupShell_, XtGrabNone );
setExistingUserDefinedContigEndPairs();
}
void guiReorderContigs :: restartAssemblyView() {
// save this on the stack, in case the memory is freed up by the dtor
assemblyView* pASV = pAssemblyView_;
// not needed because assemblyView dtor will delete us
// delete this;
delete pASV;
ConsEd::pGetConsEd()->pAssemblyView_ =
new assemblyView( );
ConsEd::pGetConsEd()->pAssemblyView_->createWindow(
ConsEd::pGetAssembly() );
}
guiReorderContigs :: ~guiReorderContigs() {
XtPopdown( widPopupShell_ );
XtDestroyWidget( widPopupShell_ );
if ( pAssemblyView_ ) {
pAssemblyView_->pGuiReorderContigs_ = NULL;
}
}
void guiReorderContigs :: userPushedAdd() {
RWCString soContig0 = XmTextFieldGetString( widContig1_ );
RWCString soContig1 = XmTextFieldGetString( widContig2_ );
int nContigEnd[2];
nContigEnd[0] =
( XmToggleButtonGetState( widLeftEndContig1_ ) == True ) ?
nLeftGap : nRightGap;
nContigEnd[1] =
( XmToggleButtonGetState( widLeftEndContig2_ ) == True ) ?
nLeftGap : nRightGap;
// check that soContig0 and soContig1 are both legitimate
Contig* pContig[2];
Assembly* pAssembly = ConsEd::pGetAssembly();
int nContig;
for( nContig = 0; nContig <= 1; ++nContig ) {
RWCString& soContig = ( nContig == 0 ? soContig0 : soContig1 );
pContig[ nContig ] = pAssembly->pGetContigByVariousNames( soContig );
if ( ! pContig[ nContig ] ) {
popupErrorMessage2( widPopupShell_, "contig %s does not exist--please change this name",
soContig.data() );
return;
}
}
// let's see if it contradicts some existing contigEndPair. In
// case the user has added a number of user-defined contigEndPairs
// at once before pushing "RestartAssemblyView", we should also check that it
// doesn't conflict with some previously-added contigEndPair
bool bError = false;
RWCString soErrorMessage;
RWTPtrOrderedVector<contigEndPair> aUserDefinedContigEndPairs;
pAssembly->getUserDefinedContigEndPairs( aUserDefinedContigEndPairs );
int nContigEndPair;
for( nContigEndPair = 0;
nContigEndPair < aUserDefinedContigEndPairs.length();
++nContigEndPair ) {
contigEndPair* pCEP = aUserDefinedContigEndPairs[ nContigEndPair ];
for( int nContigEnd1 = 0; nContigEnd1 <= 1; ++nContigEnd1 ) {
for( int nContigEnd2 = 0; nContigEnd2 <= 1; ++nContigEnd2 ) {
if ( ( pCEP->pContig_[ nContigEnd1 ] == pContig[ nContigEnd2 ] &&
pCEP->nWhichEnd_[ nContigEnd1] == nContigEnd[ nContigEnd2 ] ) ) {
bError = true;
soErrorMessage += "Problem: there is already a user-defined contigEndPair making the connection: ";
soErrorMessage += pCEP->soGetDescription();
soErrorMessage += " ";
}
}
}
}
for( nContig = 0; nContig <= 1; ++nContig ) {
int nOtherEnd = ( nContig == 0 ? 1 : 0 );
Contig* pMyContig = pContig[ nContig ];
int nWhichEnd = nContigEnd[ nContig ];
// pContig, nWhichEnd is connected to
// pContig[ nOtherEnd], nContigEnd[ nOtherEnd ]
// Let's see if pContig, nWhichEnd is connected to some
// other contig or if it is connected to the same contig,
// but a different end of it.
// We find the contig-end that this contig-end is connected to
// by looking in the Contig object:
// It is connected to contig pContig->pContig_[ nWhichEnd ],
// end: pContig->nWhichEnd_[ nWhichEnd ]
// is the contig already connected to anything? If not,
// there is no inconsistency.
if ( pMyContig->pContig_[ nWhichEnd ] ) {
if ( pMyContig->pContig_[ nWhichEnd ] !=
pContig[ nOtherEnd ] ) {
bError = true;
contigEndPair* pCEP = pMyContig->pCEP_[ nWhichEnd ];
if ( pCEP ) {
soErrorMessage += "Problem: ";
if ( pCEP->bUserDefined_ ) {
soErrorMessage += "there is already a user-defined contigEndPair making the connection: ";
soErrorMessage += pCEP->soGetDescription();
soErrorMessage += " ";
}
else {
soErrorMessage += "there are ";
soErrorMessage += RWCString( (long) pCEP->nNumberOfForwardReversePairs_ );
soErrorMessage += " forward/reverse pairs supporting the following connection: ";
soErrorMessage += pCEP->soGetDescription();
soErrorMessage += " ";
}
}
else {
soErrorMessage += "there is already a connection between ";
soErrorMessage += szWhichGap( nWhichEnd );
soErrorMessage += " of ";
soErrorMessage += pMyContig->soGetName();
soErrorMessage += " and ";
soErrorMessage +=
szWhichGap( pMyContig->nWhichEnd_[ nWhichEnd ] );
soErrorMessage += " of ";
soErrorMessage += pMyContig->pContig_[ nWhichEnd ]->soGetName();
soErrorMessage += " This link was probably inferred from fwd/rev pair links between other contigs and not directly via fwd/rev pairs between these 2 contig ends. ";
}
}
else if ( pMyContig->nWhichEnd_[ nWhichEnd ] !=
nContigEnd[ nOtherEnd ] ) {
bError = true;
contigEndPair* pCEP = pMyContig->pCEP_[ nWhichEnd ];
if ( pCEP ) {
soErrorMessage += "Problem: ";
if ( pCEP->bUserDefined_ ) {
soErrorMessage += "there is already a user-defined contigEndPair making the connection: ";
soErrorMessage += pCEP->soGetDescription();
soErrorMessage += " Perhaps you meant a different end.";
}
// note Sept 2004: I don't understand why there is an
// error message only in the case of a user-defined
// contigEndPair here. Why not also if there are
// fwd/rev pairs?
}
else {
soErrorMessage += "Problem: there is already a connection between ";
soErrorMessage += szWhichGap( nWhichEnd );
soErrorMessage += " of ";
soErrorMessage += pMyContig->soGetName();
soErrorMessage += " and ";
soErrorMessage +=
szWhichGap( pMyContig->nWhichEnd_[ nWhichEnd ] );
soErrorMessage += " of ";
soErrorMessage += pMyContig->pContig_[ nWhichEnd ]->soGetName();
soErrorMessage += " This link was probably inferred from fwd/rev pair links between other contigs and not directly via fwd/rev pairs between these 2 contig ends.";
}
}
} // if ( pMyContig->pContig_[ nwhichEnd ] ) {
}
if ( bError ) {
contigEndPair cep2( pContig[0],
pContig[1],
nContigEnd[0],
nContigEnd[1] );
soErrorMessage += " Are you sure you want to make contig-end pair ";
soErrorMessage += cep2.soGetDescription();
soErrorMessage += " ?";
if ( !bGuiGetAnswerYesNo( soErrorMessage ) ) {
return;
}
}
// put contigEndPair tags on these ends of these contigs
// I'm not so sure--shouldn't this be added when the user pushes
// "apply" ? It could check which already exist and add the ones
// that don't. But if they are added here, that wouldn't be
// necessary--it just adds the one the user has asked to add. So
// maybe this is the way to go. What does "apply" do then? I
// guess it would re-create the contig map. If assembly view is
// up, it would pop it down and up again.
RWCString soContigEndPairID = pAssembly->soGetNextContigEndPairID();
// must figure out where to put this tag.
int nConsPos[2];
tag* pTags[2];
for( nContig = 0; nContig <= 1; ++nContig ) {
nConsPos[ nContig ] =
pContig[ nContig ]->nGetGoodPlaceForContigEndPairTag( nContigEnd[ nContig ] );
// put the tag on the contig
tag* pTag = new tag( NULL, // LocatedFragment
pContig[ nContig ],
"contigEndPair",
nConsPos[ nContig ],
nConsPos[ nContig ],
false, // bNoTrans
"", // soComment
soConsed, // "consed"
soEmptyString, // current date/time
false ); // bNoTrans
// save to record in cep
pTags[ nContig ] = pTag;
int nUnpaddedStart =
pContig[ nContig ]->nUnpaddedIndex( nConsPos[ nContig ] );
RWCString soBases;
pContig[ nContig ]->getPartOfUnpaddedConsensus(
nUnpaddedStart,
10,
soBases,
( nContigEnd[ nContig ] == nLeftGap ? true : false ), // bComplemented
( nContigEnd[ nContig ] == nLeftGap ? false : true ) ); // bTowardsIncreasingUnpaddedPositions
pTag->soMiscData_ = soContigEndPairID;
pTag->soMiscData_ += "\n";
pTag->soMiscData_ += ( nContigEnd[ nContig ] == nLeftGap ?
"<-gap" : "gap->" );
pTag->soMiscData_ += "\n";
pTag->soMiscData_ += soBases;
EditAction* pEditAction = new editAddConsensusTag( pTag );
ConsEd::pGetConsEd()->doEditAction( pEditAction,
true ); // bWriteToEditHistoryFile
}
// check that the new tag will be correctly interpreted as a contigEndPair
aUserDefinedContigEndPairs.clearAndDestroy();
pAssembly->getUserDefinedContigEndPairs(
aUserDefinedContigEndPairs );
// here is the contigEndPair we are looking for
contigEndPair cep( pContig[0],
pContig[1],
nContigEnd[0],
nContigEnd[1] );
cep.recordTags( pTags[0], pTags[1] );
cep.bUserDefined_ = true;
// look for it
bool bFound = false;
for( nContigEndPair = 0;
nContigEndPair < aUserDefinedContigEndPairs.length();
++nContigEndPair ) {
if ( cep == *aUserDefinedContigEndPairs[ nContigEndPair ] ) {
bFound = true;
break;
}
}
if ( !bFound ) {
// what shall we do? Cry? Warn the user, at least.
RWCString soError = "Sorry--for some reason, I can't find the contigEndPair you just made. This may be a bug.";
popupErrorMessage2( widPopupShell_, soError.data() );
return;
}
RWCString soDescription = cep.soGetDescription();
XmString xms = XmStringCreateLocalized( soDescription.data() );
XmListAddItem( widContigEndPairList_, xms, 0 );
XmStringFree( xms );
aContigEndPairs_.insert( cep );
restartAssemblyView();
}
void guiReorderContigs :: setExistingUserDefinedContigEndPairs() {
RWTPtrOrderedVector<contigEndPair> aUserDefinedContigEndPairs;
ConsEd::pGetAssembly()->getUserDefinedContigEndPairs(
aUserDefinedContigEndPairs );
// in case there is any item left and the list is going to
// length zero, in which case it will not be reset
XmListDeleteAllItems( widContigEndPairList_ );
if ( aUserDefinedContigEndPairs.length() == 0 )
return;
XmStringTable ppXtString =
(XmStringTable) XtMalloc( aUserDefinedContigEndPairs.length() *
sizeof( XmString ) );
aContigEndPairs_.clear();
aContigEndPairs_.resize( aUserDefinedContigEndPairs.length() );
int nContigEndPair;
for( nContigEndPair = 0;
nContigEndPair < aUserDefinedContigEndPairs.length();
++nContigEndPair ) {
contigEndPair* pContigEndPair =
aUserDefinedContigEndPairs[ nContigEndPair ];
RWCString soDescription = pContigEndPair->soGetDescription();
ppXtString[ nContigEndPair ] =
XmStringCreateLocalized( soDescription.data() );
aContigEndPairs_.insert( *pContigEndPair );
}
XtVaSetValues( widContigEndPairList_,
XmNitems, ppXtString,
XmNitemCount, aUserDefinedContigEndPairs.length(),
NULL );
// free all the memory used for the array of XmString
for( nContigEndPair = 0;
nContigEndPair < aUserDefinedContigEndPairs.length();
++nContigEndPair ) {
XmStringFree( ppXtString[ nContigEndPair ] );
}
XtFree( (char*) ppXtString );
aUserDefinedContigEndPairs.clearAndDestroy();
}
void guiReorderContigs :: userPushedDelete() {
int* pPositionList;
int nNumberOfSelectedItems = 0;
if ( !XmListGetSelectedPos( widContigEndPairList_,
&pPositionList,
&nNumberOfSelectedItems ) ||
nNumberOfSelectedItems == 0 ) {
popupErrorMessage2( widPopupShell_, "First select the contig end pair and then click \"Delete Selected\"" );
return;
}
assert( nNumberOfSelectedItems == 1 );
int nZeroBasedIndex = pPositionList[0] - 1;
contigEndPair& cep = aContigEndPairs_[ nZeroBasedIndex ];
for( int nTag = 0; nTag <= 1; ++nTag ) {
tag* pTag = cep.pTag_[ nTag ];
EditAction* pEditAction = new editDeleteConsensusTag( pTag );
ConsEd::pGetConsEd()->doEditAction( pEditAction,
true ); // write to edit history file
}
restartAssemblyView();
}
void guiReorderContigs :: raiseWindow() {
XtMapWidget( widPopupShell_ );
XRaiseWindow(
XtDisplay( widPopupShell_ ),
XtWindow( widPopupShell_ )
);
}