/*****************************************************************************
# 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 "rwcstring.h"
#include "rwctokenizer.h"
#include <fstream.h>
#include "please_wait.h"
#include "filename.h"
#include "gotoList.h"
#include "guiMultiContigNavigator.h"
#include "mbt_exception.h"
#include "filePopupAndGetFilename.h"
#include "consed.h"
#include "contig.h"
#include "locatedFragment.h"
#include "bIsNumeric.h"
#include "customNavigation.h"
#include "soLine.h"
static void parseSingleRegion(
RWCString& soConsensusOrReadRegion,
RWCString& soContig,
RWCString& soRead,
bool& bNext2AreUnpaddedReadPosInDirectionOfSequencing,
int& nUnpaddedConsPosStart,
int& nUnpaddedConsPosEnd,
RWCString& soComment );
static FileName filCustomNavigation;
static int nCurLine = 0;
static FILE *pCustomNavigationFile;
void askUserForCustomNavigationFileAndPopupWindowAndParseFile() {
filCustomNavigation = "";
filCustomNavigation = filePopupAndGetFilename( "*.nav",
"",
"Select custom navigation file:" );
// case in which user pushed 'cancel'
if ( filCustomNavigation.isNull() ) return;
gotoList* pGotoList = new gotoList();
RWCString soTitle;
PleaseWait* pPleaseWait;
try {
pPleaseWait = new PleaseWait( GuiApp::pGetGuiApp()->widGetTopLevel() );
readCustomNavigationFile( filCustomNavigation, soTitle, pGotoList );
delete pPleaseWait;
}
catch(ExceptionBase eb) {
// this is one of ours, report it if not done so
if (! eb.bUserNotified() ) {
GuiApp::popupErrorMessage(eb.szGetDesc());
}
delete pPleaseWait;
delete pGotoList;
fclose( pCustomNavigationFile );
return;
}
guiMultiContigNavigator* pGui =
new guiMultiContigNavigator( soTitle, soTitle );
ConsEd::pGetConsEd()->addGuiMultiContigNavigator( pGui );
for( int n = 0; n < pGotoList->nGetNumGotoItems(); ++n ) {
gotoItem* pGotoItem = pGotoList->pGetGotoItem( n );
pGui->appendToMultiContigNavigator( pGotoItem );
}
}
#define PARSE_ERROR( szMessage ) \
{ ostrstream ost; \
ost << "Error detected from source file " \
<< __FILE__ << " at " << __LINE__ <<endl; \
ost << "Error in file " << filCustomNavigation << " at line " << \
nCurLine << ". \nLine: " \
<< soLine << "\n" << szMessage << endl \
<< ends; \
SysRequestFailed srf(ost.str()); \
srf.includeErrnoDescription(); \
throw srf; }
#define THROW_ERROR_CN( ) \
{ SysRequestFailed srf; \
srf.setUserNotified(); \
throw srf; }
static bool bGetNextLine() {
if ( fgets( soLine.sz_, nMaxLineSize, pCustomNavigationFile ) == 0 ) {
soLine = "";
return false;
}
soLine.nCurrentLength_ = strlen( soLine.sz_ );
soLine.stripTrailingWhitespaceFast();
// bump line counter - actually read one
nCurLine++;
return true;
}
void readCustomNavigationFile( const FileName& filCustomNavigation,
RWCString& soTitle,
gotoList* pGotoList ) {
RWTPtrOrderedVector<Contig>
aContigsAlreadySetUnpaddedPositionsArray(
ConsEd::pGetAssembly()->nNumContigs(),
"aContigsAlreadySetUnpaddedPositionsArray" );
pCustomNavigationFile = 0;
pCustomNavigationFile = fopen( filCustomNavigation.data(), "r" );
// file open?
if (!pCustomNavigationFile ) {
ostrstream ost;
ost << "Unable to open file " << filCustomNavigation << endl << ends;
SysRequestFailed srf(ost.str());
srf.includeErrnoDescription();
throw srf;
}
// count items in order to resize pGotoList
int nNumberOfRegions = 0;
while( bGetNextLine() ) {
if ( soLine == "BEGIN_REGION" )
++nNumberOfRegions;
}
rewind( pCustomNavigationFile );
nCurLine = 0;
pGotoList->resizeGotoList( nNumberOfRegions );
// look for TITLE:
if (! bGetNextLine() )
PARSE_ERROR( "Premature end of file" );
RWCTokenizer tokLine( soLine );
RWCString soTitleLabel = tokLine();
if ( soTitleLabel != "TITLE:" )
PARSE_ERROR( "Are you sure this is a navigation file? The first line in a navigation file must start with TITLE:" );
soTitle = "";
if ( soLine.length() >= 8 ) {
soTitle = soLine( 7, soLine.length() - 7 );
}
bool bUserDefinedPositions =
soTitle.bContains( "user-defined positions", cCaseInsensitive );
cerr << "using user-defined positions: " << szPrintBool( bUserDefinedPositions ) << endl;
// now looking for:
// BEGIN_REGION
// TYPE: CONSENSUS
// CONTIG: Contig1
// UNPADDED_CONS_POS: 1 5
// COMMENT: This is a comment
// END_REGION
// the only acceptable options are whitespace, BEGIN_REGION, or EOF
bool bFoundARegion = false;
while( true ) {
bool bWhitespace = true;
while( bWhitespace ) {
if ( !bGetNextLine() ) {
if (!bFoundARegion )
GuiApp::popupErrorMessage( "There were no regions in the custom navigation file." );
fclose( pCustomNavigationFile );
return;
}
else if (! soLine.bIsWhitespace() ) {
bWhitespace = false;
}
// otherwise it is whitespace so get another line
}
if (soLine != "BEGIN_REGION" )
PARSE_ERROR( "Are you sure this is navigation file? At this point there should be BEGIN_REGION" );
RWCString soConsensusOrReadRegion;
RWCString soContig;
RWCString soRead;
bool bNext2AreUnpaddedReadPos;
int nUnpaddedConsPosStart;
int nUnpaddedConsPosEnd;
RWCString soComment;
parseSingleRegion( soConsensusOrReadRegion,
soContig,
soRead,
bNext2AreUnpaddedReadPos,
nUnpaddedConsPosStart,
nUnpaddedConsPosEnd,
soComment );
bFoundARegion = true;
Contig* pContig =
ConsEd::pGetAssembly()->pGetContigByName( soContig );
if (!pContig && soConsensusOrReadRegion == "CONSENSUS" ) {
char szError[200];
sprintf( szError, "Could not find contig %s",
(char*) soContig.data() );
PARSE_ERROR( szError );
}
LocatedFragment* pLocFrag = 0;
if ( soConsensusOrReadRegion == "READ" ) {
pLocFrag =
ConsEd::pGetAssembly()->pGetLocatedFragmentByName( soRead );
if ( !pLocFrag ) {
RWCString soError = "Could not find read ";
soError += soRead;
soError += " in contig ";
soError += soContig;
PARSE_ERROR( soError );
}
pContig = pLocFrag->pGetContig();
}
int nUnpaddedStartContigConsPos;
int nUnpaddedEndContigConsPos;
// don't call setUnpaddedPositionsArray every time (DG, June 2009)
if ( !aContigsAlreadySetUnpaddedPositionsArray.bContains( pContig ) ) {
// needed by nUnpaddedIndex
pContig->setUnpaddedPositionsArray();
aContigsAlreadySetUnpaddedPositionsArray.insert( pContig );
}
if ( bNext2AreUnpaddedReadPos ) {
int nUnpadded1 =
pLocFrag->nUnpaddedConsPosFromOrientedUnpaddedFragPos( nUnpaddedConsPosStart );
int nUnpadded2 =
pLocFrag->nUnpaddedConsPosFromOrientedUnpaddedFragPos( nUnpaddedConsPosEnd );
nUnpaddedConsPosStart = MIN( nUnpadded1, nUnpadded2 );
nUnpaddedConsPosEnd = MAX( nUnpadded1, nUnpadded2 );
}
pContig->setStartNumberingUnpaddedConsensusAtUserDefinedIfNecessary();
if ( bUserDefinedPositions ) {
if ( soConsensusOrReadRegion == "READ" ) {
nUnpaddedStartContigConsPos =
pContig->nUnpaddedIndexStartingAtUserDefinedPosition2(
pContig->nGetFirstDisplayableContigPos()
);
nUnpaddedEndContigConsPos =
pContig->nUnpaddedIndexStartingAtUserDefinedPosition2(
pContig->nGetLastDisplayableContigPos()
);
}
else {
nUnpaddedStartContigConsPos =
pContig->nUnpaddedIndexStartingAtUserDefinedPosition2(
pContig->nGetStartConsensusIndex()
);
nUnpaddedEndContigConsPos =
pContig->nUnpaddedIndexStartingAtUserDefinedPosition2(
pContig->nGetEndConsensusIndex()
);
}
}
else {
if ( soConsensusOrReadRegion == "READ" ) {
nUnpaddedStartContigConsPos = pContig->nUnpaddedIndex(
pContig->nGetFirstDisplayableContigPos()
);
nUnpaddedEndContigConsPos = pContig->nUnpaddedIndex(
pContig->nGetLastDisplayableContigPos()
);
}
else {
nUnpaddedStartContigConsPos =
pContig->nUnpaddedIndex(
pContig->nGetStartConsensusIndex()
);
nUnpaddedEndContigConsPos =
pContig->nUnpaddedIndex(
pContig->nGetEndConsensusIndex()
);
}
}
if (! (
(nUnpaddedStartContigConsPos <= nUnpaddedConsPosStart) &&
(nUnpaddedConsPosStart <= nUnpaddedConsPosEnd ) &&
(nUnpaddedConsPosEnd <= nUnpaddedEndContigConsPos )
)) {
RWCString soErrorMessage( (size_t) 1000 );
soErrorMessage.nCurrentLength_ =
sprintf(
soErrorMessage.data(),
"Range of region (%d to %d) must be in order and within the range of the contig (%d to %d) %s",
nUnpaddedConsPosStart,
nUnpaddedConsPosEnd,
nUnpaddedStartContigConsPos,
nUnpaddedEndContigConsPos,
pContig->soGetName().data() );
if ( bUserDefinedPositions ) {
soErrorMessage += " trying to use user-defined positions from tag ";
}
soErrorMessage += " and contig starts at ";
if ( pContig->nStartNumberingUnpaddedConsensusAtUserDefined_ != 1 ) {
soErrorMessage += "(user-defined) ";
}
soErrorMessage += RWCString( (long) pContig->nStartNumberingUnpaddedConsensusAtUserDefined_ );
if ( !bUserDefinedPositions &&
pContig->nStartNumberingUnpaddedConsensusAtUserDefined_ != 1 ) {
soErrorMessage += ". Put \"(user-defined positions)\" in the title of the .nav file if you want to use user-defined consensus positions rather than 1-based consensus positions.";
}
THROW_ERROR( soErrorMessage );
}
// now convert nUnpaddedConsPosStart and nUnpaddedConsPosEnd to
// 1-based positions
if ( bUserDefinedPositions ) {
if ( !pContig->bSetStartNumberingUnpaddedConsensusAtUserDefined_ )
pContig->setStartNumberingUnpaddedConsensusAtUserDefinedIfNecessary();
nUnpaddedConsPosStart -=
( pContig->nStartNumberingUnpaddedConsensusAtUserDefined_ - 1 );
nUnpaddedConsPosEnd -=
( pContig->nStartNumberingUnpaddedConsensusAtUserDefined_ - 1 );
}
// changed from nPaddedIndex to nPaddedIndexFast for performance
// (DG, June 2009)
int nPaddedConsPosStart = pContig->nPaddedIndexFast( nUnpaddedConsPosStart );
int nPaddedConsPosEnd = pContig->nPaddedIndexFast( nUnpaddedConsPosEnd );
if ( soConsensusOrReadRegion == "READ" ) {
if ( !(
( pLocFrag->nGetAlignStart() <= nPaddedConsPosStart ) &&
( nPaddedConsPosStart <= nPaddedConsPosEnd ) &&
( nPaddedConsPosEnd <= pLocFrag->nGetAlignEnd() )
)) {
GuiApp::popupErrorMessage(
"Range of the region (%d to %d in padded coordinates) of read %s must be in order and lie within the range of the read (%d to %d)",
nPaddedConsPosStart,
nPaddedConsPosEnd,
pLocFrag->soGetName().data(),
pLocFrag->nGetAlignStart(),
pLocFrag->nGetAlignEnd() );
THROW_ERROR_CN();
}
}
gotoItem* pGotoItem = new gotoItem( pContig,
pLocFrag,
nPaddedConsPosStart,
nPaddedConsPosEnd,
nUnpaddedConsPosStart,
nUnpaddedConsPosEnd,
soComment );
pGotoList->addToList( pGotoItem);
} // while( true ) {
fclose( pCustomNavigationFile );
}
void parseSingleRegion( RWCString& soConsensusOrReadRegion,
RWCString& soContig,
RWCString& soRead,
bool& bNext2AreUnpaddedReadPosInDirectionOfSequencing,
int& nUnpaddedConsPosStart,
int& nUnpaddedConsPosEnd,
RWCString& soComment ) {
// BEGIN_REGION
// TYPE: CONSENSUS
// CONTIG: Contig1
// UNPADDED_CONS_POS: 1 5
// COMMENT: This is a comment
// END_REGION
// now looking for TYPE:
if ( !bGetNextLine() )
PARSE_ERROR( "premature end of file while looking for TYPE:" );
RWCTokenizer tokType( soLine );
RWCString soTypeLineToken = tokType();
if ( soTypeLineToken != "TYPE:" )
PARSE_ERROR( "Expected this line to start with TYPE:" );
soConsensusOrReadRegion = tokType();
soConsensusOrReadRegion.toUpper();
if (soConsensusOrReadRegion != "CONSENSUS" &&
soConsensusOrReadRegion != "READ" )
PARSE_ERROR( "Expected this line to be TYPE: CONSENSUS or TYPE: READ" );
if ( !bGetNextLine() )
PARSE_ERROR( "premature end of file while looking for CONTIG:" );
RWCTokenizer tokContig( soLine );
RWCString soContigLabel = tokContig();
bool bPutBackLineForReadType = false;
if ( soContigLabel != "CONTIG:" ) {
if ( soConsensusOrReadRegion == "CONSENSUS" ) {
PARSE_ERROR( "Expected this line to start with CONTIG:" );
}
else {
soContig = "(not specified)";
bPutBackLineForReadType = true;
}
}
else {
soContig = tokContig();
}
if ( soConsensusOrReadRegion == "READ" ) {
if ( !bPutBackLineForReadType ) {
if (!bGetNextLine() )
PARSE_ERROR( "premature end of file while looking for READ:" );
}
RWCTokenizer tokRead( soLine );
RWCString soReadLabel = tokRead();
if (soReadLabel != "READ:" )
PARSE_ERROR( "Expected this line to start with READ:" );
soRead = tokRead();
}
if ( !bGetNextLine() )
PARSE_ERROR( "premature end of file while looking for UNPADDED_CONS_POS:" );
RWCTokenizer tokUnpaddedConsPos( soLine );
RWCString soUnpaddedConsPosLabel = tokUnpaddedConsPos();
if (soUnpaddedConsPosLabel == "UNPADDED_CONS_POS:" ) {
bNext2AreUnpaddedReadPosInDirectionOfSequencing = false;
}
else if (soUnpaddedConsPosLabel == "UNPADDED_READ_POS:" ) {
bNext2AreUnpaddedReadPosInDirectionOfSequencing = true;
}
else {
PARSE_ERROR( "Expected this line to start with UNPADDED_CONS_POS: or UNPADDED_READ_POS:" );
}
if ( soConsensusOrReadRegion == "CONSENSUS" &&
bNext2AreUnpaddedReadPosInDirectionOfSequencing ) {
PARSE_ERROR( "TYPE: CONSENSUS cannot be used with UNPADDED_READ_POS: only with UNPADDED_CONS_POS:" );
}
RWCString soUnpaddedConsPosStart = tokUnpaddedConsPos();
RWCString soUnpaddedConsPosEnd = tokUnpaddedConsPos();
if (soUnpaddedConsPosStart.isNull() || soUnpaddedConsPosEnd.isNull() )
PARSE_ERROR( "UNPADDED_CONS_POS: must be followed by the start and end of the region" );
if ( !bIsNumeric( soUnpaddedConsPosStart ) || !bIsNumeric( soUnpaddedConsPosEnd ) )
PARSE_ERROR( "UNPADDED_CONS_POS: must be followed by two numbers--the start and end of the region" );
nUnpaddedConsPosStart = atoi( (char*) soUnpaddedConsPosStart.data() );
nUnpaddedConsPosEnd = atoi( (char*) soUnpaddedConsPosEnd.data() );
if ( !bGetNextLine() )
PARSE_ERROR( "premature end of file while looking for COMMENT:" );
RWCTokenizer tokComment( soLine );
RWCString soCommentLabel = tokComment();
if (soCommentLabel != "COMMENT:" )
PARSE_ERROR( "Expected this line to start with COMMENT:" );
if ( soLine.length() < 10 )
soComment = "";
else {
soComment = soLine( 9, soLine.length() - 9 );
soComment = soComment.strip( RWCString::LEADING );
}
// now read lines until see END_REGION
bool bFoundEndRegion = false;
while( !bFoundEndRegion ) {
if (!bGetNextLine() )
PARSE_ERROR( "premature end of file while looking for END_REGION" );
RWCTokenizer tokEndRegion( soLine );
RWCString soEndRegionLabel = tokEndRegion();
if ( soEndRegionLabel == "END_REGION" )
bFoundEndRegion = true;
}
}