/*****************************************************************************
# 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.
#
#*****************************************************************************/
// main.cpp_part11 ok to edit since not computer-generated
// get consed resources here
consedResources::getConsedResources( );
setErrorRateFromQuality();
// put consed resources into consedParameters here
new consedParameters( consedResources::pCurrentResources_ );
pAO = stderr;
// printMemory( "memory at startup" );
pCP->filFileOfPhdFiles_ = filFileOfPhdFiles;
pCP->bTerminateAfterStartup_ = bTerminateAfterStartup;
pCP->bReadOnly_ = bReadOnly;
pCP->soCommandLine_ = soCommandLine;
pCP->bAllowTimestampMismatch_ = bAllowTimestampMismatch;
pCP->myTime_ = time( NULL );
pCP->nWhatIsRunning_ = nWhatIsRunning;
pCP->filUserWantsToSaveToThisAceFile_ = filNewAceFile;
// put consed resources into tagTypes here
saveTagTypes( consedResources::pCurrentResources_ );
pCP->postProcessingAfterTagTypes();
// put consed resources into colorDefaults in ctor for GuiApp (below)
// (remove GuiApp completely from autoFinish )
try {
if ( bAutomatedFinishProgram ) {
autoFinish( filAceFileToOpen, nArgc, argv, bContigSpecified, soContig,
soID, bDoExperiments, bJustCheckAutoFinishReads,
soFilenamesFile );
_exit( 0 );
}
else if ( bAddNewReads ) {
addNewReadsAutomated add( filAceFileToOpen, filFileOfReadsOrPhdsToAdd,
filNewAceFile );
add.doIt();
_exit( 0 );
}
else if ( bAutoPCRAmplify ) {
autoPCRAmplify* pAutoPCRAmplify =
new autoPCRAmplify( filAceFileToOpen, filFileOfPrimerRegions );
pAutoPCRAmplify->doIt();
_exit( 0 );
}
else if ( bAutoEdit ) {
autoEdit* pAutoEdit = new autoEdit( filAceFileToOpen,
filNewAceFile );
pAutoEdit->doIt();
_exit( 0 );
}
else if ( bAddAlignedSequence ) {
assert( !filAlignmentFastaFile.isNull() );
if ( filPhdFileWithWRItem.isNull() ) {
cerr << "Error: if -addAlignedSequence is specified, -phdWithWRItem must also be specified" << endl;
_exit( -1 );
}
addAlignedSequence* pAddAlignedSequence =
new addAlignedSequence( filAceFileToOpen,
filNewAceFile,
filAlignmentFastaFile,
filPhdFileWithWRItem );
pAddAlignedSequence->doIt();
_exit( 0 );
}
else if ( bTagSNPs ) {
tagSNPs* pTagSNPs = new tagSNPs( filAceFileToOpen,
filNewAceFile,
filFileOfReadsOrPhdsToAddForTagSNPs );
pTagSNPs->doIt();
_exit( 0 );
}
else if ( bAutoReport ) {
autoReport* pAutoReport = new autoReport( filAceFileToOpen );
pAutoReport->doIt();
_exit( 0 );
}
else if ( bPrintSingleSignal ) {
printSingleSignal* pPrintSingleSignal =
new printSingleSignal( filAceFileToOpen,
soUnpaddedConsPosForSingleSignal );
pPrintSingleSignal->doIt();
_exit( 0 );
}
else if ( bAddReads ) {
addNewReadsWithExistingAlignments add( filAceFileToOpen,
filNewAceFile,
filAddNewReadsAlignmentsFOF,
soChemistry );
add.doIt();
_exit( 0 );
}
else if ( bRemoveContigs ) {
removeContigs myRemoveContigs( filAceFileToOpen,
filNewAceFile,
filContigsToBeRemoved );
myRemoveContigs.doIt();
_exit( 0 );
}
else if ( bRemoveReads ) {
removeReads myRemoveReads( filAceFileToOpen,
filNewAceFile,
filReadsToBeRemoved );
myRemoveReads.doIt();
_exit( 0 );
}
else if ( bPrintDefaultResources ) {
printDefaultResources();
_exit( 0 );
}
else if ( bSolexa2PhdBall ) {
solexa2PhdBall mySolexa2PhdBall( filSolexaFOF, filNewPhdBallFOF );
mySolexa2PhdBall.doIt();
_exit( 0 );
}
else if ( bSelectRegions ) {
addNewReads myAddNewReads( filAceFileToOpen,
filRegionsFile,
filSelectRegionsAlignmentsFOF );
myAddNewReads.doItSelectRegions();
_exit( 0 );
}
else if ( bPhdBall2Fasta ) {
phdBall2Fasta myPhdBall2Fasta( filPhdBall,
filFasta,
filFastq );
myPhdBall2Fasta.doIt();
_exit( 0 );
}
else if ( bTestReadPhdBall ) {
testReadPhdBall testReadPhdBall( filPhdBallForTestRead );
testReadPhdBall.doIt();
_exit( 0 );
}
else if ( bSff2PhdBall ) {
sff2PhdBall mySff2PhdBall( filSffFile, filNewPhdBall, bFOF, filFOF );
mySff2PhdBall.doIt();
_exit( 0 );
}
else if ( bEditConsedrc ) {
guiEditResourcesStandalone myGuiEditResourcesStandalone;
myGuiEditResourcesStandalone.doIt();
_exit( 0 );
}
else if ( bChangeConsensus ) {
batchChangeConsensus myBatchChangeConsensus(
filAceFileToOpen,
filNewAceFile,
filChangeConsensus );
myBatchChangeConsensus.doIt();
_exit( 0 );
}
else if ( bSnpGenome ) {
snpGenome mySnpGenome( filSnps, filGenome, filValidation );
mySnpGenome.doIt();
_exit( 0 );
}
else if ( bDiffChromosomes ) {
diffChromosomes myDiffChromosome( filOtherDirectory );
myDiffChromosome.doIt();
_exit( 0 );
}
else if ( bAddFlowcells ) {
nextPhredPipeline myNextPhredPipeline( filControlFile );
myNextPhredPipeline.addFlowcells( filFlowcellsToAdd );
_exit( 0 );
}
else if ( bFixContigEnds ) {
fixContigEnds myFixContigEnds( filAceFileToOpen,
filNewAceFile,
filContigEndsFOF );
myFixContigEnds.doIt();
_exit( 0 );
}
else if ( bGeneClassifications ) {
geneClassifications myGeneClassifications(
filGenomicLocations,
filChromosomesFOF,
filKnownGene,
filPhyloFOF );
myGeneClassifications.doIt();
_exit( 0 );
}
else if ( bPhaster2PhdBall ) {
phaster2PhdBall myPhaster2PhdBall(
filPhasterFOF,
filPhasterLocations,
filNewPhdBallFOF );
myPhaster2PhdBall.doIt();
_exit( 0 );
}
else if ( bMiscProgram ) {
miscProgram();
_exit( 0 );
}
} // try
catch (ExceptionBase eb) {
cerr << "Fatal consed error: " << eb.szGetDesc() << endl;
cerr.flush();
_exit( EXIT_FAILURE );
}
assert( pCP->nWhatIsRunning_ = nGraphicalConsedIsRunning );
pFILE = stdout;
// create the GuiApp object which contains and manages
// the toplevel widget, display and resource info, etc.
// there is now a global pointer to this sole instance,
// set in the ctor, accessible as GuiApp::pGetGuiApp()
GuiApp guiAppGlobalInstance("consed", nArgc, argv);
// create the ConsEd object, which owns and manages the
// Assembly data structure(s) as well as the lists of
// currently existing ContigWin and Teditor objects.
// there is now a global pointer to this sole instance,
// set in the ctor, accessible as ConsEd::global()
ConsEd* pConsed = new ConsEd();
// I want this after the ConsEd object is created because it uses
// that object.
GuiApp::pGetGuiApp()->startBlinking();
ConsEd::pGetConsEd()->bUsingPhdFiles_ = !bNoPhdFiles;
// ConsEd::pGetConsEd()->bSettingQualityValues_ = false;
// tell the toplevel widget to manage itself
GuiApp::pGetGuiApp()->makeVisible();
if ( pCP->bMakeLightBackgroundInAlignedReadsWindowAndTracesWindow_ )
GuiApp::pGetGuiApp()->changeDefaultToLightBackground();
consedParameters::pGetConsedParameters()->bCreateSocketToControlConsed_ =
bCreateSocketToControlConsed;
if ( bCreateSocketToControlConsed ) {
int nSocketToControlConsedLocalPortNumber;
if ( ! bIsNumericMaybeWithWhitespace(
soSocketToControlConsedLocalPortNumber,
nSocketToControlConsedLocalPortNumber
) ) {
cerr << "Fatal Error: -socket must be followed by a number (the local port number) but instead is followed by " << soSocketToControlConsedLocalPortNumber << endl;
_exit( -1 );
}
pCP->nCreateSocketToControlConsedOnThisLocalPort_ =
nSocketToControlConsedLocalPortNumber;
}
if (ConsEd::pGetConsEd()->bUsingPhdFiles_ )
terminateIfNoPhdDir();
// I want to read the list of libraries before reading the ace file
// to make debugging by the user easier
pCP->pListOfLibraries_ = new listOfLibraries();
pCP->pListOfLibraries_->aLibraries_.soName_ =
"pCP->pListOfLibraries_->aLibraries_ in main.cpp";
pCP->pListOfLibraries_->parseLibraryFile();
maybeTerminateIfAnotherReadWriteConsed();
// consed now takes a command line arg of file to open
if ( bAceFileOnCommandLine ) {
ConsEd::pGetConsEd()->openAssemblyFile( filAceFileToOpen );
// used to pick up basename
ConsEd::pGetConsEd()->pGetGuiTopWindow()->setAssemblyName( filAceFileToOpen.soGetBasename() );
if ( ! consedParameters::pGetConsedParameters()->bErrorMessageDisplayedAtStartup_ )
XRaiseWindow(
XtDisplay( GuiApp::pGetGuiApp()->widGetTopLevel() ),
XtWindow( GuiApp::pGetGuiApp()->widGetTopLevel() )
);
ConsEd::pGetConsEd()->setAssemblyNameOnAllContigwins(
filAceFileToOpen.soGetBasename()
);
ConsEd::pGetConsEd()->perhapsApplyEditHistoryFile( filAceFileToOpen );
perhapsCreateSocketToControlConsed();
ConsEd::pGetConsEd()->updateContigListOnMainConsedWindow();
if ( bCustomNavigation ) {
ConsEd::pGetConsEd()->startUpConsedWithCustomNavigationFile(
filCustomNavigation );
}
else if ( bMainContigPos ) {
ConsEd::pGetConsEd()->startUpConsedAtMainContigPos( soUnpaddedConsPos );
}
}
else {
// popup the file menu for the user to load an
// assembly into this first contigwin
ConsEd::pGetConsEd()->askUserForFileToOpen();
}
readAndProcessReadPrefixFile();
// comment out error handler for making core dumps
// if ( !bEstablishErrorHandler() )
// // try once more
// bEstablishErrorHandler();
if ( bTerminateAfterStartup )
_exit( 0 );
if ( pCP->bAssemblyViewAutomaticallyStartWithConsed_ &&
ConsEd::pGetAssembly() ) {
ConsEd::pGetConsEd()->pAssemblyView_ =
new assemblyView();
ConsEd::pGetConsEd()->pAssemblyView_->createWindow(
ConsEd::pGetAssembly() );
}
printTime( "time for consed to start: " );
// enter the main X application loop, intercepting
// exceptions and retrying
while (true) {
try {
GuiApp::pGetGuiApp()->mainLoop();
}
catch (RWInternalError rwErr) {
GuiApp::popupErrorMessage(
"Gordon C++ class toolkit has thrown an exception: %s",
rwErr.szGetDesc() );
}
catch (ExceptionBase eb) {
if (! eb.bUserNotified()) {
GuiApp::popupErrorMessage("Error (Consed exception): %s",
eb.szGetDesc());
}
}
catch (...) {
GuiApp::popupErrorMessage(
"Error (exception of unknown type)");
}
}
}