/*****************************************************************************
#   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    <stdio.h>
#include    "consedParameters.h"
#include    "rwcstring.h"
#include    "rwcregexp.h"
#include    "mbt_exception.h"
#include    "fileDefines.h"
#include    "filGetUniqueFilename.h"


void openAutoFinishOutputFiles( const RWCString& soAceFileToOpen,
                                const FileName& soFilenamesFile ) {
   
   pCP->filAutoFinishFilenamesFile_ = soFilenamesFile;
   if ( pCP->filAutoFinishFilenamesFile_.isNull() ) {
      pCP->filAutoFinishFilenamesFile_ = "autofinish.fof";
   }

   // find project name
   RWCString soProjectName = soAceFileToOpen;
   RWCRegexp regFasta("\\.fasta\\.screen\\..*$");
   soProjectName( regFasta ) = "";


   RWCString soUniquePrefix = filGetUniqueFilename( soProjectName );

   pCP->filAutoFinishReversesSummary_ 
      = soUniquePrefix + 
      ".univReverses";

   pCP->filAutoFinishForwardsSummary_ 
      = soUniquePrefix +
      ".univForwards";

   pCP->filAutoFinishCustomPrimersSummary_
      = soUniquePrefix +
      ".customPrimers";

   pCP->filAutoFinishSortedSummary_
      = soUniquePrefix +
      ".sorted";

   pCP->filAutoFinishFullOutput_
      = soUniquePrefix +
      ".out";

   pCP->filAutoFinishCustomNavigation_
      = soUniquePrefix +
      ".nav";

   pCP->filAutoFinishMinilibrariesSummary_
      = soUniquePrefix +
      ".minilibraries";

   
   pFORWARDS = 
      fopen( (const char*) pCP->filAutoFinishForwardsSummary_,
             "w" );

   if ( ! pFORWARDS ) {
      PANIC_OST( ost ) << "cannot open file: " <<
      pCP->filAutoFinishForwardsSummary_
                       << ends;
      throw SysRequestFailed( ost.str() );
   }

   pREVERSES = 
      fopen( (const char*) pCP->filAutoFinishReversesSummary_,
             "w" );

   if ( ! pREVERSES ) {
      PANIC_OST( ost ) << "cannot open file: " << 
         pCP->filAutoFinishReversesSummary_
                       << ends;
      throw SysRequestFailed( ost.str() );
   }


   pCUSTOM_PRIMERS = 
      fopen( (const char*) pCP->filAutoFinishCustomPrimersSummary_,
                            "w" );

   if ( ! pCUSTOM_PRIMERS ) {
      PANIC_OST( ost ) << "cannot open file: " <<
         pCP->filAutoFinishCustomPrimersSummary_ 
                       << ends;
      throw SysRequestFailed( ost.str() );

   }

   
   pSORTED_SUMMARY =
      fopen( (const char*) pCP->filAutoFinishSortedSummary_,
             "w" );

   if ( !pSORTED_SUMMARY ) {
      PANIC_OST( ost ) << "cannot open file: " <<
         pCP->filAutoFinishSortedSummary_ << ends;
      throw SysRequestFailed( ost.str() );
   }


   pAO = 
      fopen( (const char*) pCP->filAutoFinishFullOutput_, "w" );

   if ( ! pAO ) {
      PANIC_OST( ost ) << "cannot open file: " <<
         pCP->filAutoFinishFullOutput_ << ends;
      throw SysRequestFailed( ost.str() );
   }

   pCUSTOM_NAVIGATION =
      fopen( (const char*) pCP->filAutoFinishCustomNavigation_,
             "w" );

   if ( !pCUSTOM_NAVIGATION ) {
      PANIC_OST( ost ) << "cannot open file: " <<
         pCP->filAutoFinishCustomNavigation_ << ends;
      throw SysRequestFailed( ost.str() );
   }


   if ( pCP->bAutoFinishPrintMinilibrariesSummaryFile_ ) {
      pMINILIBRARIES =
         fopen( (const char*) pCP->filAutoFinishMinilibrariesSummary_,
             "w" );

      if ( !pMINILIBRARIES ) {
         PANIC_OST( ost ) << "cannot open file: " <<
            pCP->filAutoFinishMinilibrariesSummary_ << ends;
         throw SysRequestFailed( ost.str() );
      }
   }


   pFILE = pAO;

   pCP->pAutoFinishFilenamesFile_ = 
      fopen( (const char*) pCP->filAutoFinishFilenamesFile_, "w" );
   
   if ( ! pCP->pAutoFinishFilenamesFile_ ) {
      PANIC_OST( ost ) << "cannot open file: " <<
         pCP->filAutoFinishFilenamesFile_ << ends;
      throw SysRequestFailed( ost.str() );
   }


   fprintf( pCP->pAutoFinishFilenamesFile_, "%s\n",
            (const char*) pCP->filAutoFinishFullOutput_ );

   fprintf( pCP->pAutoFinishFilenamesFile_, "%s\n",
            (const char*) pCP->filAutoFinishForwardsSummary_ );

   fprintf( pCP->pAutoFinishFilenamesFile_, "%s\n",
            (const char*) pCP->filAutoFinishReversesSummary_ );

   fprintf( pCP->pAutoFinishFilenamesFile_, "%s\n",
            (const char*) pCP->filAutoFinishCustomPrimersSummary_ );

   fprintf( pCP->pAutoFinishFilenamesFile_, "%s\n",
            (const char*) pCP->filAutoFinishSortedSummary_ );

   if ( pCP->bAutoFinishPrintMinilibrariesSummaryFile_ ) {
      fprintf( pCP->pAutoFinishFilenamesFile_, "%s\n",
            (const char*) pCP->filAutoFinishMinilibrariesSummary_ );
   }


   fclose( pCP->pAutoFinishFilenamesFile_ );
}