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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include <sstream>
#include "ObjectiveScore.h"
#include "Alignment.h"
#include "../general/userparams.h"
#include "../general/debuglogObject.h"
namespace clustalw
{
ObjectiveScore::ObjectiveScore()
: score(0),
alignToScore(0),
scale(100000),
sagaGapEx(12),
sagaGapOp(8),
gapPos1(userParameters->getGapPos1()),
gapPos2(userParameters->getGapPos2())
{
}
long ObjectiveScore::getScore(const Alignment* alnToScore)
{
#if DEBUGFULL
if(logObject && DEBUGLOG)
{
logObject->logMsg("In getScore function");
}
#endif
alignToScore = alnToScore;
// If it doesnt point to any object return 0;
if(!alignToScore)
{
return 0;
}
int maxRes = subMatrix->getAlnScoreMatrix(matrix);
if (maxRes == 0)
{
utilityObject->error("Matrix for alignment scoring not found\n");
return 0;
}
const vector<int>* seqWeight = alignToScore->getSeqWeights();
vector<float> normalisedSeqWeights;
calcNormalisedSeqWeights(seqWeight, &normalisedSeqWeights);
int seq1, seq2;
float w1, w2 = 1.0;
float weight = 1.0;
score = 0;
float pwScoreLetters = 0, pwScoreGaps = 0, pwScore = 0;
float scoreTotal = 0.0;
int numSeqs = alignToScore->getNumSeqs();
int sizeNormalSeqWeight = normalisedSeqWeights.size();
for (seq1 = 1; seq1 <= numSeqs && seq1 <= sizeNormalSeqWeight; seq1++)
{
w1 = normalisedSeqWeights[seq1 - 1];
for (seq2 = seq1 + 1; seq2 <= numSeqs && seq2 <= sizeNormalSeqWeight; seq2++)
{
w2 = normalisedSeqWeights[seq2 - 1];
weight = w1 * w2;
pwScoreLetters = scoreLetters(seq1, seq2);
pwScoreGaps = scoreGaps(seq1, seq2);
pwScore = pwScoreLetters + pwScoreGaps;
scoreTotal += weight * pwScore;
#if DEBUGFULL
if(logObject && DEBUGLOG)
{
ostringstream outs;
outs << " weight = " << weight
<< " scoreLetters = " << pwScoreLetters << " scoreGaps = "
<< pwScoreGaps << " scorePair = "
<< pwScore << "\n"
<< "scoreTotal = " << scoreTotal << "\n";
logObject->logMsg(outs.str());
}
#endif
}
}
score = static_cast<long>(scoreTotal);
#if DEBUGFULL
if(logObject && DEBUGLOG)
{
ostringstream outs;
outs << " score = " << score;
logObject->logMsg(outs.str());
}
#endif
utilityObject->info("Alignment Score %d\n", score);
return score;
}
float ObjectiveScore::scoreLetters(int seq1, int seq2)
{
if(!alignToScore)
{
return 0;
}
const unsigned numColsSeq1 = alignToScore->getSeqLength(seq1);
const unsigned numColsSeq2 = alignToScore->getSeqLength(seq2);
if(numColsSeq1 != numColsSeq2)
{
return 0; // The sequences should be the same length after alignment.
}
float scoreLetters = 0;
unsigned colStart = 1;
bool gap1, gap2;
for(unsigned col = 1; col < numColsSeq1; col++)
{
gap1 = alignToScore->isGap(seq1, col);
gap2 = alignToScore->isGap(seq2, col);
if(!gap1 || !gap2)
{
colStart = col;
break;
}
}
unsigned colEnd = numColsSeq1;
for(unsigned col = numColsSeq1; col >= 1; --col)
{
gap1 = alignToScore->isGap(seq1, col);
gap2 = alignToScore->isGap(seq2, col);
if(!gap1 || !gap2)
{
colEnd = col;
break;
}
}
const SeqArray* seqArray = alignToScore->getSeqArray();
int scoreMatch = 0;
for(unsigned col = colStart; col <= colEnd; col++)
{
int res1 = (*seqArray)[seq1][col];
int res2 = (*seqArray)[seq2][col];
scoreMatch = matrix[res1][res2];
scoreLetters += scoreMatch;
}
return scoreLetters;
}
float ObjectiveScore::scoreGaps(int seq1, int seq2)
{
if(!alignToScore)
{
return 0;
}
const unsigned numColsSeq1 = alignToScore->getSeqLength(seq1);
const unsigned numColsSeq2 = alignToScore->getSeqLength(seq2);
if(numColsSeq1 != numColsSeq2)
{
return 0; // The sequences should be the same length after alignment.
}
unsigned colStart = 1;
bool gap1, gap2;
for(unsigned col = 1; col < numColsSeq1; col++)
{
gap1 = alignToScore->isGap(seq1, col);
gap2 = alignToScore->isGap(seq2, col);
if(!gap1 || !gap2)
{
colStart = col;
break;
}
}
unsigned colEnd = numColsSeq1;
for(unsigned col = numColsSeq1; col >= 1; --col)
{
gap1 = alignToScore->isGap(seq1, col);
gap2 = alignToScore->isGap(seq2, col);
if(!gap1 || !gap2)
{
colEnd = col;
break;
}
}
bool inGap1 = false;
bool inGap2 = false;
float gapOpen = userParameters->getGapOpen();
float gapExtend = userParameters->getGapExtend();
float scoreGaps = 0;
for(unsigned col = colStart; col <= colEnd; col++)
{
gap1 = alignToScore->isGap(seq1, col);
gap2 = alignToScore->isGap(seq2, col);
if(gap1 && gap2)
{
continue;
}
if(gap1)
{
if(!inGap1)
{
// NOTE I left out the option of having different end gaps stuff.
scoreGaps += gapOpen;
inGap1 = true; // Opening a gap in seq1
}
else
{
// Already in a gap
scoreGaps += gapExtend;
}
continue;
}
else if(gap2)
{
if(!inGap2)
{
// NOTE I left out the option of having different end gaps stuff.
scoreGaps += gapOpen;
inGap2 = true; // Opening a gap in seq2
}
else
{
// Already in a gap
scoreGaps += gapExtend;
}
continue;
}
inGap1 = inGap2 = false;
}
return scoreGaps;
}
void ObjectiveScore::calcNormalisedSeqWeights(const vector<int>* seqWeight,
vector<float>* normSeqWeight)
{
if(!seqWeight || !normSeqWeight)
{
return;
}
int sumWeights = 0;
for(int i = 0; i < (int)seqWeight->size() - 1; i++)
{
sumWeights += (*seqWeight)[i];
}
normSeqWeight->resize(seqWeight->size());
for(int i = 0; i < (int)seqWeight->size() - 1; i++)
{
(*normSeqWeight)[i] = static_cast<float>((*seqWeight)[i]) /
static_cast<float>(sumWeights);
#if DEBUGFULL
if(logObject && DEBUGLOG)
{
ostringstream outs;
outs << " normSeqWeight[i] = " << (*normSeqWeight)[i];
logObject->logMsg(outs.str());
}
#endif
}
}
}
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