/*****************************************************************************
#   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    "kimuraBranchProb.h"
#include    "transitionsTransversions.h"
#include    <cmath>
using namespace std;
#include    "mbt_exception.h"
#include    "rwcstring.h"
#include    "assert.h"


kimuraBranchProb :: kimuraBranchProb() {


   setTransitionsTransversionsTableIfNecessary();

   
   float fBranchLengthMMul_ex = 0.03736;
   float fBranchLengthPPyg_ex = 0.01183;
   float fBranchLengthPPyg_in = 0.00638;
   float fBranchLengthGGor_ex = 0.00592;
   float fBranchLengthGGor_in = 0.00132;
   float fBranchLengthHSap_ex = 0.00463;
   float fBranchLengthHSap_in = 0.00330;
   float fBranchLengthPTro_ex = 0.00130;
   float fBranchLengthPPan_ex = 0.00132;


   int n;
   for( n = 0; n <= 2; ++n ) {
      fMMul_ex_[n] = fGetKimuraProb( n, fBranchLengthMMul_ex );
      fPPyg_ex_[n] = fGetKimuraProb( n, fBranchLengthPPyg_ex );
      fPPyg_in_[n] = fGetKimuraProb( n, fBranchLengthPPyg_in );
      fGGor_ex_[n] = fGetKimuraProb( n, fBranchLengthGGor_ex );
      fGGor_in_[n] = fGetKimuraProb( n, fBranchLengthGGor_in );
      fHSap_ex_[n] = fGetKimuraProb( n, fBranchLengthHSap_ex );
      fHSap_in_[n] = fGetKimuraProb( n, fBranchLengthHSap_in );
      fPTro_ex_[n] = fGetKimuraProb( n, fBranchLengthPTro_ex );
      fPPan_ex_[n] = fGetKimuraProb( n, fBranchLengthPPan_ex );
   }

   for( n = 0; n <= 255; ++n ) {
      n012_[n] = -666;
   }

   n012_[ 'n' ] = 0;
   n012_[ 'i' ] = 1;
   n012_[ 'v' ] = 2;
   

}


float kimuraBranchProb ::  fGetKimuraProb( 
    const int n, 
     // 0 == no mutation
     // 1 == transition
     // 2 == transversion
    const float fBranchLength ) {

   if ( n == 0 ) {
      return( 1.0 - fGetKimuraTransitionProb( fBranchLength ) -
              fGetKimuraTransversionProb( fBranchLength ) );
   }
   else if ( n == 1 ) {
      return( fGetKimuraTransitionProb( fBranchLength ) );
   }
   else if ( n == 2 ) {
      return( fGetKimuraTransversionProb( fBranchLength ) );
   }
   else {
      assert( false ); // program bug
   }
}


float kimuraBranchProb :: fGetKimuraTransitionProb( 
                   const float fBranchLength ) {

   float fR = .5 * fTransitionTransversionRatio;

   float fProb = 0.25 - 0.5*exp( - ((2.0*fR+1.0)/(fR+1.0))*fBranchLength) +
      0.25*exp( -2.0*fBranchLength/(fR+1.0));

   return( fProb );
}


float kimuraBranchProb :: fGetKimuraTransversionProb(
                   const float fBranchLength ) {

   float fR = .5 * fTransitionTransversionRatio;

   float fProb = 0.5 - 0.5 * exp( -2.0*fBranchLength/(fR+1.0) );

   return( fProb );
}








float kimuraBranchProb :: fGetBranchProbability( 
          const int nIndexOfInitialBase,
          const int nIndexOfNewBase,
          const char cInitialBase, 
          const char cNewBase ) {


   // is this a transition, a transversion, or no mutation?
   // no mutation = 0
   // transition = 1
   // transversion = 2

   char cTransitionOrTransversions = 
      cTransitionsTransversions[cInitialBase][cNewBase ];

   int nTransitionOrTransversion =
      n012_[ cTransitionOrTransversions ];
   

   // which branch are we talking about?

   RWCString soBranchName;
   float fProb;

   switch ( nIndexOfInitialBase ) {
   case 0:
      // branches are MMul_ex, PPyg_ex, and PPyg_in
      switch (nIndexOfNewBase ) {
      case 9:
         soBranchName = "MMul_ex";
         fProb = fMMul_ex_[ nTransitionOrTransversion ];
         break;
      case 8:
         soBranchName = "PPyg_ex";
         fProb = fPPyg_ex_[ nTransitionOrTransversion ];
         break;
      case 1:
         soBranchName = "PPyg_in";
         fProb = fPPyg_in_[ nTransitionOrTransversion ];
         break;
      default:
         RWCString soError = "program error in fGetBranchProbability " +
            RWCString( (long) nIndexOfInitialBase ) + " " +
            RWCString( (long) nIndexOfNewBase );
         THROW_ERROR( soError );
      }
      break;
   case 1:
      switch( nIndexOfNewBase ) {
      case 7:
         soBranchName = "GGor_ex";
         fProb = fGGor_ex_[ nTransitionOrTransversion ];
         break;
      case 2:
         soBranchName = "GGor_in";
         fProb = fGGor_in_[ nTransitionOrTransversion ];
         break;
      default:
         RWCString soError = "program error in fGetBranchProbability " +
            RWCString( (long) nIndexOfInitialBase ) + " " +
            RWCString( (long) nIndexOfNewBase );
         THROW_ERROR( soError );

      }
      break;
   case 2:
      switch( nIndexOfNewBase ) {
      case 6:
         soBranchName = "HSap_ex";
         fProb = fHSap_ex_[ nTransitionOrTransversion ];
         break;
      case 3:
         soBranchName = "HSap_in";
         fProb = fHSap_in_[ nTransitionOrTransversion ];
         break;
      default:
         RWCString soError = "program error in fGetBranchProbability " +
            RWCString( (long) nIndexOfInitialBase ) + " " +
            RWCString( (long) nIndexOfNewBase );
         THROW_ERROR( soError );

      }
      break;
   case 3:
      switch( nIndexOfNewBase ) {
      case 5:
         soBranchName = "PTro_ex";
         fProb = fPTro_ex_[ nTransitionOrTransversion ];
         break;
      case 4:
         soBranchName = "PPan_ex";
         fProb = fPPan_ex_[ nTransitionOrTransversion ];
         break;
      default:
         RWCString soError = "program error in fGetBranchProbability " +
            RWCString( (long) nIndexOfInitialBase ) + " " +
            RWCString( (long) nIndexOfNewBase );
         THROW_ERROR( soError );
         
      }
      break;
   }
         
   
   return( fProb );
}