void AlignChime3SDRealign(const SeqData &QSD3, const SeqData &ASD3, const SeqData &BSD3,
ChimeHit2 &Hit)
{
SeqData QSD;
SeqData ASD;
SeqData BSD;
StripGapsAlloc(QSD3, QSD);
StripGapsAlloc(ASD3, ASD);
StripGapsAlloc(BSD3, BSD);
string PathQA;
string PathQB;
bool FoundQA = GlobalAlign(QSD, ASD, PathQA);
bool FoundQB = GlobalAlign(QSD, BSD, PathQB);
if (!FoundQA || !FoundQB)
{
Hit.Clear();
Hit.QLabel = QSD3.Label;
return;
}
AlignChime(QSD, ASD, BSD, PathQA, PathQB, Hit);
myfree((void *) QSD.Seq);
myfree((void *) ASD.Seq);
myfree((void *) BSD.Seq);
}
SCORE AlignTwoMSAs(const MSA &msa1, const MSA &msa2, MSA &msaOut, PWPath &Path,
bool bLockLeft, bool bLockRight)
{
const unsigned uLengthA = msa1.GetColCount();
const unsigned uLengthB = msa2.GetColCount();
ProfPos *PA = ProfileFromMSA(msa1);
ProfPos *PB = ProfileFromMSA(msa2);
if (bLockLeft)
{
PA[0].m_scoreGapOpen = MINUS_INFINITY;
PB[0].m_scoreGapOpen = MINUS_INFINITY;
}
if (bLockRight)
{
PA[uLengthA-1].m_scoreGapClose = MINUS_INFINITY;
PB[uLengthB-1].m_scoreGapClose = MINUS_INFINITY;
}
float r = (float) uLengthA/ (float) (uLengthB + 1); // +1 to prevent div 0
if (r < 1)
r = 1/r;
SCORE Score = GlobalAlign(PA, uLengthA, PB, uLengthB, Path);
AlignTwoMSAsGivenPath(Path, msa1, msa2, msaOut);
delete[] PA;
delete[] PB;
return Score;
}
SCORE GlobalAlignNoDiags(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
unsigned uLengthB, PWPath &Path)
{
return GlobalAlign(PA, uLengthA, PB, uLengthB, Path);
}