/*****************************************************************************
#   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.
#
#*****************************************************************************/
//
// colormode.cpp
//
// implementation for ColorMode objects
//
// gordon (orig)  Dec-94
//



#include <ctype.h>

#include "colormode.h"
#include "contig.h"
#include "colorDefaults.h"
#include "consedParameters.h"
#include "guiapp.h"



ColorMode :: ColorMode() {
   
   pColorEditCursor_ =
     new GuiColorText(
        ColorDefaults::pGetColorDefaults()->soColorMode_editCursorForeground_,
        ColorDefaults::pGetColorDefaults()->soColorMode_editCursorBackground_
                      );
}
   


GuiColorText* ColorMode :: pGuiColorTextCursorGet() { 
   return pColorEditCursor_; 
}





GuiColorText* ColorMeansQuality :: pGetGuiColorTextForConsensus(
    Contig* pContig,
    int nConsPos ) {


   GuiColorText* pColorText;

   int nQual = pContig->ntGetCons( nConsPos ).qualGetQuality();
   
   if (nQual < 5 ) 
      pColorText = pColorConsensus0_4_;
   else if (nQual < 10 )
      pColorText = pColorConsensus5_9_;
   else if (nQual < 15 )
      pColorText = pColorConsensus10_14_;
   else if (nQual < 20 )
      pColorText = pColorConsensus15_19_;
   else if (nQual < 25 )
      pColorText = pColorConsensus20_24_;
   else if (nQual < 30 )
      pColorText = pColorConsensus25_29_;
   else if (nQual < 35 )
      pColorText = pColorConsensus30_34_;
   else if (nQual < 40 )
      pColorText = pColorConsensus35_39_;
   else if (nQual < 98 )
      pColorText = pColorConsensus40_97_;
   else if (nQual == 98 )
      pColorText = pColorConsensus98_;
   else
      pColorText = pColorConsensus99_;


   return( pColorText );
}




GuiColorText* ColorMeansMatch::pGuiColorTextGet(LocatedFragment *pLocFrag, 
                                                 const int nConsPos )
{
   GuiColorText* pColorText;
   Contig* pContig = pLocFrag->pContig_;


   if (consedParameters::pGetConsedParameters()->bDimLowQualityEndsOfReads_
       && pLocFrag->bIsInLowQualityEndsOfRead( nConsPos ) ) {

      if (pContig->baseSegArray_.bIsInBaseSegment( nConsPos, pLocFrag) ) {
         pColorText = pColorLowQualConsensus_;
      }
      else {
         pColorText = pColorDimLowQualityEnds_;
      }
   }
   else if ( consedParameters::pGetConsedParameters()->bDimUnalignedEndsOfReads_ 
             && !pLocFrag->bIsInAlignedPartOfRead( nConsPos ) ) {
      if (pContig->baseSegArray_.bIsInBaseSegment( nConsPos, pLocFrag) ) {
         pColorText = pColorLowQualConsensus_;
      }
      else {
         pColorText = pColorDimLowQualityEnds_;
      }
   }
   else if (pContig->baseSegArray_.bIsInBaseSegment( nConsPos, pLocFrag) ) {
      pColorText = pColorConsensus_;
   }
   else if ( toupper( pLocFrag->ntGetFragFromConsPos(nConsPos) ) == 
            toupper( pContig->ntGetCons( nConsPos ) ) ) {
      pColorText = pColorSame_;
   }
   else {
      pColorText = pColorDifferent_;
   }

   return( pColorText );
}




ColorMeansMatch :: ColorMeansMatch( )
{

   pColorSame_ = 
     new GuiColorText( 
               ColorDefaults::pGetColorDefaults()->soColorMeansMatch_same_,
               "Black");

   pColorDifferent_ = 
     new GuiColorText(
           ColorDefaults::pGetColorDefaults()->soColorMeansMatch_different_,
           "Black");

   pColorDimLowQualityEnds_ = 
     new GuiColorText(
       ColorDefaults::pGetColorDefaults()->soColorMeansMatch_clippedEnds_,
                      "Black");                                         

   pColorConsensus_ = 
     new GuiColorText(
        ColorDefaults::pGetColorDefaults()->soColorMeansMatch_consensus_,
                      "Black" );

   pColorLowQualConsensus_ = 
     new GuiColorText(
       ColorDefaults::pGetColorDefaults()->soColorMeansMatch_lowQualConsensus_,
                      "Black" );

}






GuiColorText* ColorMeansQuality::pGuiColorTextGet(LocatedFragment *pLocFrag, 
                                                  const int nConsPos )
{
   GuiColorText* pColorText;

   if (consedParameters::pGetConsedParameters()->bDimLowQualityEndsOfReads_
       && pLocFrag->bIsInLowQualityEndsOfRead( nConsPos ) )
      pColorText = GAPP->pColorMeansMatch_->pColorDimLowQualityEnds_;
   else if ( consedParameters::pGetConsedParameters()->bDimUnalignedEndsOfReads_ 
       && !pLocFrag->bIsInAlignedPartOfRead( nConsPos ) )
      pColorText = GAPP->pColorMeansMatch_->pColorDimLowQualityEnds_;
   else {

      Contig* pContig = pLocFrag->pGetContig();

      int nQual = pLocFrag->ntGetFragFromConsPos( nConsPos ).qualGetQuality();

      // per Pat, Feb 2000, wanted x'd bases to stay dark
      if ( pLocFrag->ntGetFragFromConsPos( nConsPos ).cGetBase() == 'x' )
         nQual = 0;

      if ( toupper( pLocFrag->ntGetFragFromConsPos(nConsPos) ) == 
           toupper( pContig->ntGetCons( nConsPos ) ) ) {

         if (nQual < 5 ) 
            pColorText = pColor0_4_;
         else if (nQual < 10 )
            pColorText = pColor5_9_;
         else if (nQual < 15 )
            pColorText = pColor10_14_;
         else if (nQual < 20 )
            pColorText = pColor15_19_;
         else if (nQual < 25 )
            pColorText = pColor20_24_;
         else if (nQual < 30 )
            pColorText = pColor25_29_;
         else if (nQual < 35 )
            pColorText = pColor30_34_;
         else if (nQual < 40 )
            pColorText = pColor35_39_;
         else if (nQual < 98 )
            pColorText = pColor40_97_;
         else if (nQual == 98 )
            pColorText = pColor98_;
         else
            pColorText = pColor99_;
      }
      else {
         if (nQual < 5 ) 
            pColorText = pColorDisagree0_4_;
         else if (nQual < 10 )
            pColorText = pColorDisagree5_9_;
         else if (nQual < 15 )
            pColorText = pColorDisagree10_14_;
         else if (nQual < 20 )
            pColorText = pColorDisagree15_19_;
         else if (nQual < 25 )
            pColorText = pColorDisagree20_24_;
         else if (nQual < 30 )
            pColorText = pColorDisagree25_29_;
         else if (nQual < 35 )
            pColorText = pColorDisagree30_34_;
         else if (nQual < 40 )
            pColorText = pColorDisagree35_39_;
         else if (nQual < 98 )
            pColorText = pColorDisagree40_97_;
         else if (nQual == 98 )
            pColorText = pColorDisagree98_;
         else 
            pColorText = pColorDisagree99_;

      }
   }

   return( pColorText );
}



GuiColorText* ColorMeansQuality :: pGuiColorTextGetBackgroundAgree( 
                               const int nQual ) {

   GuiColorText* pColorText;

   if (nQual < 5 ) 
      pColorText = pColor0_4_;
   else if (nQual < 10 )
      pColorText = pColor5_9_;
   else if (nQual < 15 )
      pColorText = pColor10_14_;
   else if (nQual < 20 )
      pColorText = pColor15_19_;
   else if (nQual < 25 )
      pColorText = pColor20_24_;
   else if (nQual < 30 )
      pColorText = pColor25_29_;
   else if (nQual < 35 )
      pColorText = pColor30_34_;
   else if (nQual < 40 )
      pColorText = pColor35_39_;
   else if (nQual < 98 )
      pColorText = pColor40_97_;
   else
      assert( false );

   return( pColorText );
 
}






// this routine gets a guicolortext that will be used just to draw
// the bases without background.  Thus it cares only about the agreement
// with the consensus--not with the quality.

GuiColorText* ColorMeansQuality::pGuiColorTextGetForeground(LocatedFragment *pLocFrag, 
                                                            const int nConsPos )
{
   GuiColorText* pColorText;

   if (consedParameters::pGetConsedParameters()->bDimLowQualityEndsOfReads_
       && pLocFrag->bIsInLowQualityEndsOfRead( nConsPos ) )
      return( GAPP->pColorMeansMatch_->pColorDimLowQualityEnds_ );

   else if ( consedParameters::pGetConsedParameters()->bDimUnalignedEndsOfReads_ 
       && !pLocFrag->bIsInAlignedPartOfRead( nConsPos ) )
      return( GAPP->pColorMeansMatch_->pColorDimLowQualityEnds_ );
   else {

      Contig* pContig = pLocFrag->pGetContig();


      // it doesn't matter which of pColor0_4_, pColor5_9_, etc
      // we use here since they all have the same foreground color--black

      if ( toupper( pLocFrag->ntGetFragFromConsPos(nConsPos) ) == 
           toupper( pContig->ntGetCons( nConsPos ) ) )
         return( pColor0_4_ );
      else
         return( pColorDisagree0_4_ );
   }
}





ColorMeansQuality :: ColorMeansQuality( )
{

   pColor0_4_ = new GuiColorText( 
                 ColorDefaults::pGetColorDefaults()->soColorMeansQualityAgree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality0_4_
                                 );

   pColor5_9_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityAgree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality5_9_
                                   );
 
   pColor10_14_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityAgree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality10_14_
                                   );

   pColor15_19_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityAgree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality15_19_
                                   );

   pColor20_24_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityAgree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality20_24_
                                   );

   pColor25_29_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityAgree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality25_29_
                                   );

   pColor30_34_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityAgree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality30_34_
                                   );

   pColor35_39_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityAgree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality35_39_
                                   );


   pColor40_97_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityAgree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality40_97_
                                   );

   pColor98_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityAgree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality98_
                                   );

   pColor99_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityAgree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality99_
                                   );


   // disagreement colors


   pColorDisagree0_4_ = new GuiColorText( 
                 ColorDefaults::pGetColorDefaults()->soColorMeansQualityDisagree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality0_4_
                                 );

   pColorDisagree5_9_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityDisagree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality5_9_
                                   );
 
   pColorDisagree10_14_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityDisagree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality10_14_
                                   );

   pColorDisagree15_19_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityDisagree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality15_19_
                                   );

   pColorDisagree20_24_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityDisagree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality20_24_
                                   );

   pColorDisagree25_29_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityDisagree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality25_29_
                                   );

   pColorDisagree30_34_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityDisagree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality30_34_
                                   );

   pColorDisagree35_39_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityDisagree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality35_39_
                                   );


   pColorDisagree40_97_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityDisagree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality40_97_
                                   );

   pColorDisagree98_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityDisagree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality98_
                                   );

   pColorDisagree99_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityDisagree_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality99_
                                   );


   // consensus colors


   pColorConsensus0_4_ = new GuiColorText( 
                 ColorDefaults::pGetColorDefaults()->soColorMeansQualityConsensusForeground_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality0_4_
                                 );

   pColorConsensus5_9_ = new GuiColorText( 
                 ColorDefaults::pGetColorDefaults()->soColorMeansQualityConsensusForeground_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality5_9_
                                   );
 
   pColorConsensus10_14_ = new GuiColorText( 
                 ColorDefaults::pGetColorDefaults()->soColorMeansQualityConsensusForeground_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality10_14_
                                   );

   pColorConsensus15_19_ = new GuiColorText( 
                 ColorDefaults::pGetColorDefaults()->soColorMeansQualityConsensusForeground_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality15_19_
                                   );

   pColorConsensus20_24_ = new GuiColorText( 
                 ColorDefaults::pGetColorDefaults()->soColorMeansQualityConsensusForeground_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality20_24_
                                   );

   pColorConsensus25_29_ = new GuiColorText( 
                 ColorDefaults::pGetColorDefaults()->soColorMeansQualityConsensusForeground_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality25_29_
                                   );

   pColorConsensus30_34_ = new GuiColorText( 
                 ColorDefaults::pGetColorDefaults()->soColorMeansQualityConsensusForeground_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality30_34_
                                   );

   pColorConsensus35_39_ = new GuiColorText( 
                 ColorDefaults::pGetColorDefaults()->soColorMeansQualityConsensusForeground_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality35_39_
                                   );

   pColorConsensus40_97_ = new GuiColorText( 
                 ColorDefaults::pGetColorDefaults()->soColorMeansQualityConsensusForeground_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality40_97_
                                   );

   pColorConsensus98_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityConsensusForeground_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality98_
                                   );

   pColorConsensus99_ = new GuiColorText( 
                   ColorDefaults::pGetColorDefaults()->soColorMeansQualityConsensusForeground_,
                 ColorDefaults::pGetColorDefaults()->soColorMeansQuality99_
                                   );


}




GuiColorText* ColorMeansEdited::pGuiColorTextGetForeground(
                                                 LocatedFragment *pLocFrag,
                                                 const int nConsPos ) {

   return( pGuiColorTextGet( pLocFrag, nConsPos ) );
}





GuiColorText* ColorMeansEdited::pGuiColorTextGet(LocatedFragment *pLocFrag, 
                                                 const int nConsPos )
{
   GuiColorText* pColorText;

   if (consedParameters::pGetConsedParameters()->bDimLowQualityEndsOfReads_
       && pLocFrag->bIsInLowQualityEndsOfRead( nConsPos ) )
      pColorText = GAPP->pColorMeansMatch_->pColorDimLowQualityEnds_;
   else if ( consedParameters::pGetConsedParameters()->bDimUnalignedEndsOfReads_ 
       && !pLocFrag->bIsInAlignedPartOfRead( nConsPos ) )
      pColorText = GAPP->pColorMeansMatch_->pColorDimLowQualityEnds_;
   else {

      Contig* pContig = pLocFrag->pGetContig();


      int nQual = pLocFrag->ntGetFragFromConsPos( nConsPos ).qualGetQuality();

      if ( toupper( pLocFrag->ntGetFragFromConsPos(nConsPos) ) == 
           toupper( pContig->ntGetCons( nConsPos ) ) ) {
         if (nQual == 99 )
            pColorText = pColorAgree99_;
         else if (nQual == 98)
            pColorText = pColorAgree98_;
         else
            pColorText = pColorAgreeUnedited_;
      }
      else {
         if (nQual == 99)
            pColorText = pColorDisagree99_;
         else if (nQual == 98)
            pColorText = pColorDisagree98_;
         else
            pColorText = pColorDisagreeUnedited_;
      }
   }

   return( pColorText );
}




ColorMeansEdited :: ColorMeansEdited( )
{

   pColorDisagreeUnedited_ = 
     new GuiColorText( 
       ColorDefaults::pGetColorDefaults()->soColorMeansEditedDisagree_,
       ColorDefaults::pGetColorDefaults()->soColorMeansEditedUnedited_ );

   pColorDisagree98_ = 
     new GuiColorText(
           ColorDefaults::pGetColorDefaults()->soColorMeansEditedDisagree_,
           ColorDefaults::pGetColorDefaults()->soColorMeansEdited98_ );

   pColorDisagree99_ = 
     new GuiColorText(
       ColorDefaults::pGetColorDefaults()->soColorMeansEditedDisagree_,
       ColorDefaults::pGetColorDefaults()->soColorMeansEdited99_ );

   pColorAgreeUnedited_ = 
     new GuiColorText(
        ColorDefaults::pGetColorDefaults()->soColorMeansEditedAgree_,
        ColorDefaults::pGetColorDefaults()->soColorMeansEditedUnedited_ );

   pColorAgree98_ = 
     new GuiColorText(
       ColorDefaults::pGetColorDefaults()->soColorMeansEditedAgree_,
       ColorDefaults::pGetColorDefaults()->soColorMeansEdited98_ );

   pColorAgree99_ = 
     new GuiColorText(
        ColorDefaults::pGetColorDefaults()->soColorMeansEditedAgree_,
       ColorDefaults::pGetColorDefaults()->soColorMeansEdited99_ );

}