/*****************************************************************************
#   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.
#
#*****************************************************************************/


   postProcessing();


}  // consedParameters()



void consedParameters :: processDoNotFinishTagTypes() {
   
   aAutoFinishTagsToNotFinish_.clear();

   RWCTokenizer tokTagTypes( soAutoFinishDoNotFinishWhereTheseTagsAre_ );

   RWCString soDoNotFinishTag;
   while( !( soDoNotFinishTag = tokTagTypes() ).isNull() ) {

      if ( !tagTypes::pGetTagTypes()->bIsAValidTagType( soDoNotFinishTag ) ) {
         ostrstream ost; 
         ost << "You specified consed.autoFinishDoNotFinishWhereTheseTagsAre: " <<
            soAutoFinishDoNotFinishWhereTheseTagsAre_ << " but \"" << soDoNotFinishTag << "\" is not a recognized tag type." << ends;
         InputDataError ide(ost.str());
         throw ide;
      }
      aAutoFinishTagsToNotFinish_.insert( soDoNotFinishTag );
   }
}


void consedParameters :: processDoNotExtendTagTypes() {

    aAutoFinishTagsToNotExtend_.clear();
    
    RWCTokenizer tokTagTypes(
soAutoFinishDoNotExtendContigsWhereTheseTagsAre_ );

    RWCString soDoNotExtendTag;
    while( !( soDoNotExtendTag = tokTagTypes() ).isNull() ) {
    
        if ( !tagTypes::pGetTagTypes()->bIsAValidTagType( soDoNotExtendTag ) ) {
            RWCString soError = "You specified consed.autoFinishDoNotExtendContigsWhereTheseTagsAre: ";
            soError += soAutoFinishDoNotExtendContigsWhereTheseTagsAre_;
            soError += " but \"";
            soError += soDoNotExtendTag;
            soError += "\" is not a recognized tag type.";
            THROW_ERROR( soError );
        }
        aAutoFinishTagsToNotExtend_.insert( soDoNotExtendTag );
    }
}



// this is useful for setting parameters that depend on other parameters
void consedParameters :: postProcessing() {

//    dAutoFinishMinNumberOfErrorsFixedByAnExpToUse_ =
//       dAutoFinishMinNumberOfErrorsFixedByAnExp_ /
//       (double) dAutoFinishRedundancy_;

   dAutoFinishMinNumberOfErrorsFixedByAnExpToUse_ =
      dAutoFinishMinNumberOfErrorsFixedByAnExp_;


    RWCTokenizer tok( soUserDefinedKeys_ );
    RWCString soWord;
    while( !( soWord = tok() ).isNull() ) {
       int nKey;
       if ( !bIsNumericMaybeWithWhitespace( soWord, nKey ) ) {
          PANIC_OST( ost ) << "resource consed.userDefinedKeys should contain just integers which are the values of keysyms of keys defined in /usr/include/X11/keysymdefs.h, but instead it contains " << soUserDefinedKeys_ << ends;
          InputDataError ide( ost.str() );
          throw ide;
       }
       aUserDefinedKeys_.insert( nKey );
    }

    RWCTokenizer tok2( soProgramsForUserDefinedKeys_ );
    while( !( soWord = tok2() ).isNull() ) {
       aProgramsForUserDefinedKeys_.insert( soWord );
    }

    RWCTokenizer tok3( soArgumentsToPassToUserDefinedPrograms_ );
    while( !( soWord = tok3() ).isNull() ) {
       aArgumentsToPassToUserDefinedPrograms_.insert( soWord );
    }


    RWCTokenizer tok4( soTagsToApplyWithUserDefinedKeys_ );
    while( !( soWord = tok4() ).isNull() ) {
       aTagsToApplyWithUserDefinedKeys_.insert( soWord );
    }


    if ( ! ( 
             aUserDefinedKeys_.length() ==
             aProgramsForUserDefinedKeys_.length() &&
             
             aProgramsForUserDefinedKeys_.length() ==
             aArgumentsToPassToUserDefinedPrograms_.length() &&

             aArgumentsToPassToUserDefinedPrograms_.length() ==
             aTagsToApplyWithUserDefinedKeys_.length() 
             ) ) {

       PANIC_OST( ost ) << "resource consed.userDefinedKeys has # of keys: " 
                        << aUserDefinedKeys_.length() 
                        << " with value " 
                        << soUserDefinedKeys_ 
                        << " resource consed.programsForUserDefinedKeys has # of entries: " 
                        << aProgramsForUserDefinedKeys_.length() 
                        << " with value " << soProgramsForUserDefinedKeys_ 
                        << " resource consed.argumentsToPassToUserDefinedPrograms " 
                        << " has # of entries: " 
                        << aArgumentsToPassToUserDefinedPrograms_.length()
                        << " with value " << soArgumentsToPassToUserDefinedPrograms_
                        << " but these should all have the same number of entries" 
                        << ends;
       InputDataError ide( ost.str() );
       throw ide;
    }


    readFileToOrderReadsInAlignedReadsWindow();



    // parse:
    // pCP->soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_
    // to load 
    // pCP->aAutoReportPatternsOfReadsToIgnore_ 

    RWCTokenizer tokReadsToIgnore( soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_ );

    RWCString soReadPatternToIgnore;
    while( !( soReadPatternToIgnore = tokReadsToIgnore() ).isNull() ) {
       aAutoReportPatternsOfReadsToIgnore_.insert( soReadPatternToIgnore );
    }



    if ( soSolexa64FastqOrSanger33Fastq_ != "auto" &&
         soSolexa64FastqOrSanger33Fastq_ != "solexa64" &&
         soSolexa64FastqOrSanger33Fastq_ != "sanger33" ) {

       RWCString soError = "consed.solexa64FastqOrSanger33Fastq: should be one of auto, solexa64, or sanger33 but is " +
          soSolexa64FastqOrSanger33Fastq_;

       THROW_ERROR( soError );
    }

}


void consedParameters :: postProcessingAfterTagTypes() {


    // add resource soAssemblyViewDisplayTheseTagTypesOnTheseLines_ 
    // into pCP->aAssemblyViewDisplayTheseTagTypesOnTheseLines_ and sort it so ready
    // for binary search.

#define ADD_ASSEMBLY_VIEW_LINE_TO_ERROR_MESSAGE \
          soError += " in line: \nconsed.assemblyViewDisplayTheseTagTypesOnTheseLines: "; \
          soError += soAssemblyViewDisplayTheseTagTypesOnTheseLines_;



    RWCTokenizer tokAssemblyViewDisplayTheseTagTypesOnTheseLines( 
         soAssemblyViewDisplayTheseTagTypesOnTheseLines_ );

    RWCString soTagType;
    while( !( soTagType = 
          tokAssemblyViewDisplayTheseTagTypesOnTheseLines() ).isNull() ) {
       // is this really a tag type, or did the user make a typo?

       if ( ! tagTypes::pGetTagTypes()->bIsAValidTagType( soTagType ) ) {
          RWCString soError = "Warning: ";
          soError += soTagType;
          soError += " is not a valid tag type ";
          ADD_ASSEMBLY_VIEW_LINE_TO_ERROR_MESSAGE;

          // I think I will not make this error fatal.  The users
          // can deal with it later (or not at all).

          cerr << soError << endl;
          break;
       }

       RWCString soLine = tokAssemblyViewDisplayTheseTagTypesOnTheseLines();
       if ( soLine.isNull() ) {
          RWCString soError = "Warning: There must be a pair of tagType and line number but ";
          soError += soTagType;
          soError += " does not have an associated line number ";
          ADD_ASSEMBLY_VIEW_LINE_TO_ERROR_MESSAGE;
          cerr << soError << endl;
          break;
       }
           
       int nLine;
       if ( !bIsNumericMaybeWithWhitespace( soLine, nLine ) ) {
          RWCString soError = "Warning:  ";
          soError += soLine;
          soError += " is not numeric but should be ";
          ADD_ASSEMBLY_VIEW_LINE_TO_ERROR_MESSAGE;
          cerr << soError << endl;
          break;
       }

       if ( nLine < 0 || nLine > nAssemblyViewDisplayTagMaxLineIndex ) {
          RWCString soError = "Warning: ";
          soError += soLine;
          soError += " is out of bounds.  Should be between ";
          soError += RWCString( (long) 0 );
          soError += " and ";
          soError += RWCString( (long) nAssemblyViewDisplayTagMaxLineIndex );
          ADD_ASSEMBLY_VIEW_LINE_TO_ERROR_MESSAGE;
          cerr << soError << endl;
          break;
       }
       
       aAssemblyViewDisplayTheseTagTypes_.insert( 
           new assemblyViewTagTypeAndLine( soTagType, nLine ) );

    }

    aAssemblyViewDisplayTheseTagTypes_.resort();

}



void consedParameters :: readFileToOrderReadsInAlignedReadsWindow() {


   aShowReadsInAlignedReadsWindowOrderGivenByFile_.clearAndDestroy();

   FILE* pFileToOrderReads = 
       fopen( filShowReadsInAlignedReadsWindowOrderedByThisFile_.data(),
          "r" );

   if ( !pFileToOrderReads ) {
      fprintf( stderr, "couldn't open %s--that's ok\n",
         filShowReadsInAlignedReadsWindowOrderedByThisFile_.data() );

      return;
   }

   while( fgets( soLine.sz_, nMaxLineSize, pFileToOrderReads ) != NULL ) {
      soLine.nCurrentLength_ = strlen( soLine.sz_ );

      soLine.stripTrailingWhitespaceFast();

      if ( soLine.isNull() ) 
         continue;

      // convert * to the regexp expression .*

      for( int n = (int) soLine.length() - 1; n >= 0; --n ) {
         if ( soLine[n] == '*' ) {
            soLine.insert( n, "." );
         }
      }

      // put ^ and $ around the string to make it completely
      // match the read name

      soLine.insert( 0, "^" );
      soLine.append( "$" );

      RWCRegexp* pRegExp = new RWCRegexp( soLine );
      aShowReadsInAlignedReadsWindowOrderGivenByFile_.insert( pRegExp );
   }      


   fclose( pFileToOrderReads );


}