/*****************************************************************************
#   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    "consedResources.h"
#include    "rwcregexp.h"


// want string to contain \$CONSED_HOME
static RWCRegexp regConsedHome( "\\$CONSED_HOME" );



void consedResources :: translateCONSED_HOMEForOneResource( 
                                    RWCString& soOneResourceValue ) {

   while( soOneResourceValue.index( "$CONSED_HOME" ) != RW_NPOS ) {
      
      soOneResourceValue( regConsedHome ) = soConsedHome_;

   }
}



void consedResources :: translateCONSED_HOMEForAllResources() {



   translateCONSED_HOMEForOneResource( soDefaultTagType_ );
   translateCONSED_HOMEForOneResource( soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_ );
   translateCONSED_HOMEForOneResource( soPrimersCloneFullPathnameOfFileOfSequencesForScreening_ );
   translateCONSED_HOMEForOneResource( soPrintWindowCommand_ );
   translateCONSED_HOMEForOneResource( filFileOfTagTypes_ );
   translateCONSED_HOMEForOneResource( soAssemblyViewShowWhichInconsistentFwdRevPairs_ );
   translateCONSED_HOMEForOneResource( soAssemblyViewDisplayTheseTagTypesOnTheseLines_ );
   translateCONSED_HOMEForOneResource( soAutoEditMakeFakeReadFromRead1_ );
   translateCONSED_HOMEForOneResource( soAutoEditMakeFakeReadFromRead2_ );
   translateCONSED_HOMEForOneResource( soAutoEditMakeFakeReadName_ );
   translateCONSED_HOMEForOneResource( filAutoEditMakeFakeReadFastaFilename_ );
   translateCONSED_HOMEForOneResource( filAutoEditSecondaryAceFile_ );
   translateCONSED_HOMEForOneResource( filHighlightedReadsFile_ );
   translateCONSED_HOMEForOneResource( soAutoReportPrintReadNamesInRegionContig_ );
   translateCONSED_HOMEForOneResource( soShowAllTracesDoNotShowTraceIfTheseTagsPresent_ );
   translateCONSED_HOMEForOneResource( soAssemblyViewOnlyShowSequenceMatchesToThisContig_ );
   translateCONSED_HOMEForOneResource( soDefaultReadPrefix_ );
   translateCONSED_HOMEForOneResource( filReadPrefixesFile_ );
   translateCONSED_HOMEForOneResource( filAutoFinishDebugUniversalPrimerReadsFile_ );
   translateCONSED_HOMEForOneResource( filAutoFinishDebugCustomPrimerReadsFile_ );
   translateCONSED_HOMEForOneResource( soAutoFinishDoNotFinishWhereTheseTagsAre_ );
   translateCONSED_HOMEForOneResource( soAutoFinishDoNotExtendContigsWhereTheseTagsAre_ );
   translateCONSED_HOMEForOneResource( filDumpContigOrderAndOrientationInfoToThisFile_ );
   translateCONSED_HOMEForOneResource( soCompressedChromatExtension_ );
   translateCONSED_HOMEForOneResource( filFullPathnameOfAddReads2ConsedScript_ );
   translateCONSED_HOMEForOneResource( filFullPathnameOfFixContigEndScript_ );
   translateCONSED_HOMEForOneResource( filFullPathnameOfCrossMatch_ );
   translateCONSED_HOMEForOneResource( filFullPathnameOfPhred_ );
   translateCONSED_HOMEForOneResource( filFullPathnameOfMiniassemblyScript_ );
   translateCONSED_HOMEForOneResource( soGunzipFullPath_ );
   translateCONSED_HOMEForOneResource( filFullPathnameOfFilter454ReadsScript_ );
   translateCONSED_HOMEForOneResource( filFilter454ReadsAgainstThis_ );
   translateCONSED_HOMEForOneResource( fil454LinkerSequences_ );
   translateCONSED_HOMEForOneResource( filPrimersBadLibrariesFile_ );
   translateCONSED_HOMEForOneResource( filPrimersLibrariesInfoFile_ );
   translateCONSED_HOMEForOneResource( filPrimersBadTemplatesFile_ );
   translateCONSED_HOMEForOneResource( filDefaultVectorPathnameForRestrictionFragments_ );
   translateCONSED_HOMEForOneResource( filFileOfAdditionalRestrictionEnzymes_ );
   translateCONSED_HOMEForOneResource( soCommonRestrictionEnzymes_ );
   translateCONSED_HOMEForOneResource( soDefaultSelectedRestrictionEnzymes_ );
   translateCONSED_HOMEForOneResource( filRestrictionEnzymesActualFragmentsFile_ );
   translateCONSED_HOMEForOneResource( filShowReadsInAlignedReadsWindowOrderedByThisFile_ );
   translateCONSED_HOMEForOneResource( soShowReadsAtCursorSortedHow_ );
   translateCONSED_HOMEForOneResource( filAssemblyViewFileOfTemplatesToNotShow_ );
   translateCONSED_HOMEForOneResource( filAssemblyViewFindSequenceMatchesForConsedScript_ );
   translateCONSED_HOMEForOneResource( soUserDefinedKeys_ );
   translateCONSED_HOMEForOneResource( soProgramsForUserDefinedKeys_ );
   translateCONSED_HOMEForOneResource( soArgumentsToPassToUserDefinedPrograms_ );
   translateCONSED_HOMEForOneResource( soTagsToApplyWithUserDefinedKeys_ );
   translateCONSED_HOMEForOneResource( soListOfTagTypesToHide_ );
   translateCONSED_HOMEForOneResource( soListOfOptionalWordsToSaveInListOfReadNames_ );
   translateCONSED_HOMEForOneResource( filFastStartupFile_ );
   translateCONSED_HOMEForOneResource( soAlwaysRunProgramToGetChromats_ );
   translateCONSED_HOMEForOneResource( filProgramToRunToGetChromats_ );
   translateCONSED_HOMEForOneResource( filProgramToRunToGetChromatsOf454Reads_ );
   translateCONSED_HOMEForOneResource( soPrintWindowInstructions_ );
   translateCONSED_HOMEForOneResource( soAddNewReadsPutReadIntoItsOwnContig_ );
   translateCONSED_HOMEForOneResource( filMaybeXKEYSYMDBPath_ );
   translateCONSED_HOMEForOneResource( filMaybeXKEYSYMDBPath2_ );
   translateCONSED_HOMEForOneResource( soNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus_ );
   translateCONSED_HOMEForOneResource( filPhdBallDirectory_ );
   translateCONSED_HOMEForOneResource( filNewAceFileFOF_ );
   translateCONSED_HOMEForOneResource( soPaired454LeftReadExtension_ );
   translateCONSED_HOMEForOneResource( soPaired454RightReadExtension_ );
   translateCONSED_HOMEForOneResource( filSnpGenome1MSnps_ );
   translateCONSED_HOMEForOneResource( soPhaster2PhdBallSaveWhichMate_ );
   translateCONSED_HOMEForOneResource( filNextPhredPipelineControlFile_ );
   translateCONSED_HOMEForOneResource( filNextPhredPipelineTiffPerlScript_ );
   translateCONSED_HOMEForOneResource( filNextPhredPipelinePhasterPerlScript_ );
   translateCONSED_HOMEForOneResource( soNextPhredPipelineVersion_ );
   translateCONSED_HOMEForOneResource( soNextPhredPipelineMainDirectory_ );
   translateCONSED_HOMEForOneResource( filUserWantsToSaveToThisAceFile_ );
   translateCONSED_HOMEForOneResource( soDebuggingString_ );
   translateCONSED_HOMEForOneResource( soUncompressedChromatDirectory_ );
   translateCONSED_HOMEForOneResource( fil454sff2scfDirectory_ );
   translateCONSED_HOMEForOneResource( filSolexaFilesAreAssumedToBeHere_ );
   translateCONSED_HOMEForOneResource( soSolexa64FastqOrSanger33Fastq_ );
   translateCONSED_HOMEForOneResource( filAutoReportGoodHitReads_ );
   translateCONSED_HOMEForOneResource( soAutoReportIsolatedPadsOfReadsWithThisPattern_ );
   translateCONSED_HOMEForOneResource( soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_ );
   translateCONSED_HOMEForOneResource( soAutoReportBackboneReadHasThisStringInIt_ );
   translateCONSED_HOMEForOneResource( filAutoReportPrintTheseReads_ );
   translateCONSED_HOMEForOneResource( soAutoReportPrefix_ );
   translateCONSED_HOMEForOneResource( soAutoReportSpecies_ );
}