/*****************************************************************************
#   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    "consedParameters.h"
#include    "restrictionEnzymes.h"
#include    "popupErrorMessage.h"
#include    "rwctokenizer.h"
#include    "restrictionEnzyme.h"
#include    "assert.h"

#define     SZLINE_SIZE 500
static  char    szLine[ SZLINE_SIZE ];


void consedParameters :: makeListOfRestrictionEnzymes() {

   aRestrictionEnzymes_.clearAndDestroy();
   aCommonRestrictionEnzymes_.clear();

   int nNumberOfAdditionalEnzymes = 0;

   FILE *pFil = NULL;

   if ( !pCP->filFileOfAdditionalRestrictionEnzymes_.isNull() ) {
      
      pFil = fopen( pCP->filFileOfAdditionalRestrictionEnzymes_.data(),
                          "r" );

      if ( !pFil ) {
         popupErrorMessage( "the resource consed.fileOfAdditionalRestrictionEnzymes: %s could not open %s for reading so not including these resources",
                  pCP->filFileOfAdditionalRestrictionEnzymes_.data() );

         

      }
      else {
         // count the lines

         while( fgets( szLine, SZLINE_SIZE, pFil ) )
            ++nNumberOfAdditionalEnzymes;

         rewind( pFil );
      }
   }
      

   // count the default enzymes

   int nNumberOfDefaultEnzymes = 0;
   while( aszRestrictionEnzymes[ nNumberOfDefaultEnzymes ] )
      ++nNumberOfDefaultEnzymes;

   

   aRestrictionEnzymes_.resize( 
                nNumberOfDefaultEnzymes + nNumberOfAdditionalEnzymes );



   for( int n = 0; n < nNumberOfDefaultEnzymes; ++n ) {

      RWCTokenizer soTok( aszRestrictionEnzymes[ n ] );
      
      restrictionEnzyme* pEnz = new restrictionEnzyme();
      pEnz->soName_ = soTok();
      pEnz->soBases_ = soTok();

      assert( !pEnz->soName_.isNull() );
      assert( !pEnz->soBases_.isNull() );

      aRestrictionEnzymes_.insert( pEnz );
   }


   if ( pFil ) {
      int nLine = 0;
      while( fgets( szLine, SZLINE_SIZE, pFil ) != NULL ) {
         RWCTokenizer soTok( szLine );
         restrictionEnzyme* pEnz = new restrictionEnzyme();
         pEnz->soName_ = soTok();
         pEnz->soBases_ = soTok();
         
         if ( pEnz->soName_.isNull() || 
              pEnz->soBases_.isNull()  ) {

            popupErrorMessage( 
                 "line %d in file %s contains %s but should be of the form \"EcoRI GAATTC\" with just 2 words separated by whitespace",
                 nLine,
                 pCP->filFileOfAdditionalRestrictionEnzymes_.data(),
                 szLine );
            continue;
         }

         pEnz->soBases_.toLower();

         RWCString soAllowedBases( "acgkmnrtwy" );

         if ( strspn( pEnz->soBases_.data(), soAllowedBases.data() ) !=
              pEnz->soBases_.length() ) {
            popupErrorMessage( 
                "line %d in file %s contains %s but should be of the form \"EcoRI GAATTC\" with just 2 words separated by whitespace where the second word should contist just of the characters %s",
                nLine,
                pCP->filFileOfAdditionalRestrictionEnzymes_.data(),
                szLine,
                soAllowedBases.data() );
            continue;
         }

         aRestrictionEnzymes_.insert( pEnz );
      } //  while( fgets( szLine, SZLINE_SIZE, pFil ) != NULL ) {
   } //   if ( pFil ) {
                               

   aRestrictionEnzymes_.resort();



   // now parse the list of commonly used restriction enzymes

   RWCTokenizer tokCommonEnzymes( pCP->soCommonRestrictionEnzymes_ );

   RWCString soCommonEnzyme;
   while( !(soCommonEnzyme = tokCommonEnzymes()).isNull() ) {
      restrictionEnzyme res;
      res.soName_ = soCommonEnzyme;
      int nIndex = aRestrictionEnzymes_.nFindIndexOfMatchOrSuccessor( &res );
      //      cerr << soCommonEnzyme << " " << nIndex << endl;
      if ( nIndex != RW_NPOS  &&
           aRestrictionEnzymes_[ nIndex ]->soName_ != soCommonEnzyme ) {
         popupErrorMessage( "consed.commonRestrictionEnzymes: %s but %s was not found in complete list of enzymes, neither in Consed's internal list nor in the file supplied with consed.fileOfAdditionalRestrictionEnzymes (if any)",
                            pCP->soCommonRestrictionEnzymes_.data(),
                            soCommonEnzyme.data() );
         continue;
      }
       
      aCommonRestrictionEnzymes_.insert( soCommonEnzyme );
   }

}