/*****************************************************************************
#   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.
#
#*****************************************************************************/
#ifndef geneClassifications_included
#define geneClassifications_included


#include    "rwtvalorderedvector.h"
#include    "filename.h"
#include    <stdio.h>

class geneClassifications {

public:
   geneClassifications( const FileName& filGenomicLocations,
                        const FileName& filChromosomesFOF,
                        const FileName& filKnownGene,
                        const FileName& filPhyloFOF ) :
      filGenomicLocations_( filGenomicLocations ),
      filChromosomesFOF_( filChromosomesFOF ),  
      filKnownGene_( filKnownGene ),
      filPhyloFOF_( filPhyloFOF ) {

      soChromosomeBases_.increaseMaxLength( 250000000 );
      aKnownGene_.resize( 70000 );
      aConservationScores_.soName_ = "aConservationScores_";
   }

   void doIt();
   void readChromosomesFOF();
   void readPhyloFOF();

   void parseCurrentLine( const RWCString& soLine,
                          RWCString& soChromosome,
                          int& n1ChrPos,
                          RWCString& soAlternativeAlleles );

   void startNextChromosome( const RWCString& soChromosome );
   void readKnownGene();
   void processCurrentLine( const RWCString& soChromosome,
                            const int n1ChrPos,
                            const RWCString& soAlternativeAlleles );

   char cFindGeneTypeAllGenes( 
                              const RWCString& soChromosome,
                              const int n1ChrPos,
                              const RWCString& soAlternativeAlleles,
                              char& cNormalAA,
                              char& cSnpAA );

   int nFindBeginningOfGenesPossiblyOverlappingPos( 
         const RWCString& soChromosome,
         const int n1ChrPos );


   int nFindIndexOfMatchOrSuccessor( 
         const RWCString& soChromosome,
         const int n1ChrPosToLookFor );

   char cFindGeneType( 
         const RWCString& soChromosome, 
         const int n1ChrPos, 
         const char cAlternativeAllele,
         const RWCString& soKnownGeneLine,
         char& cNormalAA,
         char& cSnpAA );

   void putExonsIntoAnArray( const RWCString& soExonStarts,
                             const RWCString& soExonEnds,
                             const int nNumberOfExons );
   
   int nConvertCodingPositionToChrPos( const int n1CodingPos );

   char cCombineGeneTypes( char cGeneType1, 
                           char cGeneType2 );



public:
   FileName filGenomicLocations_;
   FileName filChromosomesFOF_;
   FileName filKnownGene_;
   RWCString soChromosomeBases_;
   FileName filPhyloFOF_;

   RWTValOrderedVector<RWCString> aKnownGene_;

   RWTValOrderedVector<FileName> aChromosomeFiles_;
   RWTValOrderedVector<FileName> aPhyloFiles_;

   // current gene info
   bool bTopNotBottomStrand_;
   // 1-based chromosome positions of current gene
   RWTValOrderedVector<int> aExonStarts_;
   RWTValOrderedVector<int> aExonEnds_;
   int n1ChrPosCodingRegionLeft_;
   int n1ChrPosCodingRegionRight_;

   RWTValOrderedVector<float> aConservationScores_;

   FILE* pOutputFile_;
   

};


#endif