void FindAnchorCols(const MSA &msa, unsigned AnchorCols[],
unsigned *ptruAnchorColCount)
{
MuscleContext *ctx = getMuscleContext();
const unsigned uColCount = msa.GetColCount();
if (uColCount < 16)
{
*ptruAnchorColCount = 0;
return;
}
SCORE *MatchScore = new SCORE[uColCount];
SCORE *SmoothScore = new SCORE[uColCount];
unsigned *BestCols = new unsigned[uColCount];
GetLetterScores(msa, MatchScore);
static_WindowSmooth(MatchScore, uColCount, ctx->params.g_uSmoothWindowLength, SmoothScore,
ctx->params.g_dSmoothScoreCeil);
unsigned uBestColCount;
FindBestColsCombo(msa, MatchScore, SmoothScore, ctx->params.g_dMinBestColScore, ctx->params.g_dMinSmoothScore,
BestCols, &uBestColCount);
#if TRACE
ListBestCols(msa, MatchScore, SmoothScore, BestCols, uBestColCount);
#endif
MergeBestCols(MatchScore, BestCols, uBestColCount, ctx->params.g_uAnchorSpacing, AnchorCols,
ptruAnchorColCount);
delete[] MatchScore;
delete[] SmoothScore;
delete[] BestCols;
}
void FindAnchorColsPP(const MSA &msa1, const MSA &msa2, unsigned AnchorCols[],
unsigned *ptruAnchorColCount)
{
const unsigned uColCount = msa1.GetColCount();
if( uColCount != msa2.GetColCount() )
{
*ptruAnchorColCount = 0;
return; // the profiles must have equal length to find anchor cols
}
SCORE *MatchScore = new SCORE[uColCount];
SCORE *SmoothScore = new SCORE[uColCount];
unsigned *BestCols = new unsigned[uColCount];
LetterObjScoreXP(msa1, msa2, MatchScore);
g_uSmoothWindowLength.get() = 21; // this is better for DNA
g_uAnchorSpacing.get() = 96;
WindowSmooth(MatchScore, uColCount, g_uSmoothWindowLength.get(), SmoothScore,
g_dSmoothScoreCeil.get());
unsigned uBestColCount;
// FindBestColsGrade(SmoothScore,uColCount,.85,BestCols,&uBestColCount);
FindBestColsComboPP(uColCount, MatchScore, SmoothScore, g_dMinBestColScore.get(), g_dMinSmoothScore.get(),
BestCols, &uBestColCount);
/*
std::cerr << "found " << uBestColCount << " anchor cols:\n";
for( size_t colI = 0; colI < uBestColCount; colI++ )
{
if( colI > 0 )
std::cerr << ", ";
std::cerr << BestCols[colI];
}
std::cerr << std::endl;
*/
#if TRACE
ListBestCols(msa, MatchScore, SmoothScore, BestCols, uBestColCount);
#endif
MergeBestCols(MatchScore, BestCols, uBestColCount, g_uAnchorSpacing.get(), AnchorCols,
ptruAnchorColCount);
/*
std::cerr << "\n\nafter merging, have " << *ptruAnchorColCount << " anchor cols:\n";
for( size_t colI = 0; colI < *ptruAnchorColCount; colI++ )
{
if( colI > 0 )
std::cerr << ", ";
std::cerr << AnchorCols[colI];
}
std::cerr << std::endl;
*/
delete[] MatchScore;
delete[] SmoothScore;
delete[] BestCols;
}