/*****************************************************************************
#   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    <stdlib.h>
#include    <iostream.h>
#include    "consedParameters.h"
#include    "consedResources.h"
#include    <stdio.h>
#include    "nPrimerFalseMatchScoreArray.h"
#include    "rwctokenizer.h"
#include    "tagTypes.h"
#include    "mbt_exception.h"
#include    "bIsNumericMaybeWithWhitespace.h"
#include    "guiFindRestrictionEnzymeSites.h"

#define DEFINE_SOLINE
#include    "soLine.h"

#include    "rwcregexp.h"


//
// static class members
//
consedParameters* consedParameters::pGlobalConsedParameters_ = 0;  // pointer to sole instance
bool consedParameters::bConsedParametersCreated_ = false;  // flag indicates instance exists



RWCString consedParameters :: soGetDocumentation() {
   if ( soDocumentation_.isNull() )
      setDocumentation();

   return( soDocumentation_ );
}




void consedParameters :: setParametersForSequencingPrimersNotPCRPrimers( 
                            const bool bSequencingNotPCR ) {
   
   if ( bSequencingNotPCR ) {
      nPrimersMinimumLengthOfAPrimerToUse_ = nPrimersMinimumLengthOfAPrimer_;
      nPrimersMaximumLengthOfAPrimerToUse_ = nPrimersMaximumLengthOfAPrimer_;
      nPrimersMinMeltingTempToUse_ = nPrimersMinMeltingTemp_;
      nPrimersMaxMeltingTempToUse_ = nPrimersMaxMeltingTemp_;
      nPrimersWindowSizeInLookingToUse_ = nPrimersWindowSizeInLooking_;
      nPrimersMaxMatchElsewhereScoreToUse_ = nPrimersMaxMatchElsewhereScore_;
   }
   else {
      nPrimersMinimumLengthOfAPrimerToUse_ = nPrimersMinimumLengthOfAPrimerForPCR_;
      nPrimersMaximumLengthOfAPrimerToUse_ = nPrimersMaximumLengthOfAPrimerForPCR_;
      nPrimersMinMeltingTempToUse_ = nPrimersMinMeltingTempForPCR_;
      nPrimersMaxMeltingTempToUse_ = nPrimersMaxMeltingTempForPCR_;
      nPrimersWindowSizeInLookingToUse_ = nPrimersWindowSizeInLookingForPCR_;
      nPrimersMaxMatchElsewhereScoreToUse_ = nPrimersMaxMatchElsewhereScoreForPCR_;
   }
}


consedParameters :: consedParameters() {
    // just zero-out the entire space

    memset( this, 0, sizeof( consedParameters ) );
}



void consedParameters :: copyPrimerPickingParametersToSelf(
    consedParameters* pCPSource ) {

   // I wouldn't be surprised if I missed some...

   nPrimersMinimumLengthOfAPrimerToUse_ =
      pCPSource->nPrimersMinimumLengthOfAPrimerToUse_;

   nPrimersMaximumLengthOfAPrimerToUse_ =
      pCPSource->nPrimersMaximumLengthOfAPrimerToUse_;

   nPrimersMinMeltingTempToUse_ =
      pCPSource->nPrimersMinMeltingTempToUse_;

   nPrimersMaxMeltingTempToUse_ =
      pCPSource->nPrimersMaxMeltingTempToUse_;

   nPrimersWindowSizeInLookingToUse_ =
      pCPSource->nPrimersWindowSizeInLookingToUse_;

   nPrimersMaxMatchElsewhereScoreToUse_ =
      pCPSource->nPrimersMaxMatchElsewhereScoreToUse_;

   nPrimersMinMeltingTempForPCR_ =
      pCPSource->nPrimersMinMeltingTempForPCR_;

   nPrimersMaxMeltingTempForPCR_ =
      pCPSource->nPrimersMaxMeltingTempForPCR_;

   nPrimersMinMeltingTemp_ =
      pCPSource->nPrimersMinMeltingTemp_;

   nPrimersMaxMeltingTemp_ =
      pCPSource->nPrimersMaxMeltingTemp_;

   nPrimersWindowSizeInLooking_ =
      pCPSource->nPrimersWindowSizeInLooking_;

   nPrimersALittleLessThanAverageInsertSizeOfASubcloneToUse_ =
      pCPSource->nPrimersALittleLessThanAverageInsertSizeOfASubcloneToUse_;

   nPrimersTooManyVectorBasesInWalkingRead_ =
      pCPSource->nPrimersTooManyVectorBasesInWalkingRead_;

   nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_ =
      pCPSource->nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_;

   bPrimersScreenForVector_ =
      pCPSource->bPrimersScreenForVector_;

   dPrimersSaltConcentrationMillimolar_ =
      pCPSource->dPrimersSaltConcentrationMillimolar_;

   bPrimersPrintInfoOnRejectedTemplates_ =
      pCPSource->bPrimersPrintInfoOnRejectedTemplates_;

   nPrimersMinQuality_ =
      pCPSource->nPrimersMinQuality_;

   nPrimersMaxPrimerDimerScoreForPCR_ =
      pCPSource->nPrimersMaxPrimerDimerScoreForPCR_;

   nPrimersMaxSelfMatchScore_ =
      pCPSource->nPrimersMaxSelfMatchScore_;

   nPrimersMaxMatchElsewhereScoreForPCR_ =
      pCPSource->nPrimersMaxMatchElsewhereScoreForPCR_;

   nPrimersMaxMatchElsewhereScore_ =
      pCPSource->nPrimersMaxMatchElsewhereScore_;

   dPrimersDNAConcentrationNanomolar_ =
      pCPSource->dPrimersDNAConcentrationNanomolar_;

   nPrimersLookThisFarForForwardVectorInsertJunction_ =
      pCPSource->nPrimersLookThisFarForForwardVectorInsertJunction_;

   nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_ =
      pCPSource->nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_;

   nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_ =
      pCPSource->nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_;

   nPrimersWindowSizeInLookingForPCR_ =
      pCPSource->nPrimersWindowSizeInLookingForPCR_;

   nPrimersWhenChoosingATemplateMinPotentialReadLength_ =
      pCPSource->nPrimersWhenChoosingATemplateMinPotentialReadLength_;

   bPrimersChooseTemplatesByPositionInsteadOfQuality_ =
      pCPSource->bPrimersChooseTemplatesByPositionInsteadOfQuality_;

   filPrimersBadTemplatesFile_ =
      pCPSource->filPrimersBadTemplatesFile_;

   filPrimersLibrariesInfoFile_ =
      pCPSource->filPrimersLibrariesInfoFile_;

   filPrimersBadLibrariesFile_ =
      pCPSource->filPrimersBadLibrariesFile_;

   nPrimersMaxLengthOfMononucleotideRepeat_ =
      pCPSource->nPrimersMaxLengthOfMononucleotideRepeat_;

   nPrimersNumberOfTemplatesToDisplayInFront_ =
      pCPSource->nPrimersNumberOfTemplatesToDisplayInFront_;

   bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_ =
      pCPSource->bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_;

   nPrimersMaxPCRPrimerPairsToDisplay_ =
      pCPSource->nPrimersMaxPCRPrimerPairsToDisplay_;

   dPrimersMaxMeltingTempDifferenceForPCR_ =
      pCPSource->dPrimersMaxMeltingTempDifferenceForPCR_;

   nPrimersMaximumLengthOfAPrimerForPCR_ =
      pCPSource->nPrimersMaximumLengthOfAPrimerForPCR_;

   nPrimersMinimumLengthOfAPrimerForPCR_ =
      pCPSource->nPrimersMinimumLengthOfAPrimerForPCR_;

   nPrimersMaximumLengthOfAPrimer_ =
      pCPSource->nPrimersMaximumLengthOfAPrimer_;

   nPrimersMinimumLengthOfAPrimer_ =
      pCPSource->nPrimersMinimumLengthOfAPrimer_;

   nPrimersMinNumberOfTemplatesForPrimers_ =
      pCPSource->nPrimersMinNumberOfTemplatesForPrimers_;

   bPrimersOKToChoosePrimersInSingleSubcloneRegion_ =
      pCPSource->bPrimersOKToChoosePrimersInSingleSubcloneRegion_;

   bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_ =
      pCPSource->bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_;
   
   bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_ =
      pCPSource->bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_;

}




consedParameters::consedParameters( consedResources* pRes ) :
   bWarnUserAboutOverstrikingWithUppercase_( true ),
   bErrorMessageDisplayedAtStartup_( false ),
   nAutoFinishLastUsedPrimerNumber_( 0 ),
   bOKToUseGui_( true ),
   nAutoFinishNumberOfCloningSitesFound_( 0 ),
   nLastUsedExpID_( 0 ),
   nWhatIsRunning_( 0 ),
   bReadyToPickSecondPCRPrimer_( false ),
   pDefaultLibrary_( NULL ),
   bReadOnly_( false ),
   pAutoFinishFullOutput_( stdout ),
   bNeedToSetContigTemplateArrays_( true ),
   cFindRestrictionEnzymeSitesLastUsedWholeCloneOrPartOfCloneOrWholeContig_( guiFindRestrictionEnzymeSites::cWHOLE_CLONE ),
   soFindRestrictionEnzymeSitesLastUsedUserEnteredContigMap_( soEmptyString ),
   nFindRestrictionEnzymeSitesLastUsedStartUnpaddedConsPos_( -666 ),
   nFindRestrictionEnzymeSitesLastUsedEndUnpaddedConsPos_( -666 ),
   soFindRestrictionEnzymeSitesLastUsedContigAbbreviatedName_( soEmptyString ),
   bWarnUserAboutAmbiguityCodes_( true ),
   bAllowTimestampMismatch_( false ),
   bPrintInFigureOutContigOrderAndOrientation_( true ),
   bLimitNumberOfErrorsReported_( false ),
   nNumberOfStartupErrors_( 0 )
{
   //
   // fail crudely if one already exists - we may not have
   // a gui at all yet
   //
   if (bConsedParametersCreated_) {
      cerr << "Fatal program error:  consedParameters ctor called twice." << endl;
      cerr.flush();
      exit(-1);
   }

   // save pointer to yourself
   pGlobalConsedParameters_ = this;

   // remember you have been created (allow no others)
   bConsedParametersCreated_ = true;


#ifdef NO_POUND_POUND_MACROS

#define saveAConsedParameter( nameWithoutFinalUnderscore ) \
consedParameters::pGetConsedParameters()->nameWithoutFinalUnderscore ## _ \
= pRes->nameWithoutFinalUnderscore ## _

#else

#define saveAConsedParameter( nameWithoutFinalUnderscore ) \
consedParameters::pGetConsedParameters()-> ## nameWithoutFinalUnderscore ## _ \
= pRes-> ## nameWithoutFinalUnderscore ## _

#endif


// This macro expands saveAConsedParameter( nPrimersMaxSelfMatchScore )
//   into
// consedParameters::pGetConsedParameters()->nPrimersMaxSelfMatchScore_
// = pRes->nPrimersMaxSelfMatchScore_

  if ( pRes->bShowProteinTranslation_ == true ) {
     consedParameters::pGetConsedParameters()->nShowProteinTranslation_ =
        nShowProteinTranslationTopStrand;
  }
  else {
     consedParameters::pGetConsedParameters()->nShowProteinTranslation_ =
        nDontShowProteinTranslation;
  }