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;
}
void ProfileProfile(MSA &msa1, MSA &msa2, MSA &msaOut)
{
unsigned uLength1;
unsigned uLength2;
uLength1 = msa1.GetColCount();
uLength2 = msa2.GetColCount();
Tree tree1;
Tree tree2;
ProfPos *Prof1 = ProfileFromMSALocal(msa1, tree1);
ProfPos *Prof2 = ProfileFromMSALocal(msa2, tree2);
PWPath Path;
ProfPos *ProfOut;
unsigned uLengthOut;
Progress("Aligning profiles");
AlignTwoProfs(Prof1, uLength1, 1.0, Prof2, uLength2, 1.0, Path, &ProfOut, &uLengthOut);
Progress("Building output");
AlignTwoMSAsGivenPath(Path, msa1, msa2, msaOut);
delete[] Prof1;
delete[] Prof2;
delete[] ProfOut;
}
void SPTest()
{
SetPPScore(PPSCORE_SV);
SetListFileName("c:\\tmp\\muscle.log", false);
TextFile file1("c:\\tmp\\msa1.afa");
TextFile file2("c:\\tmp\\msa2.afa");
MSA msa1;
MSA msa2;
msa1.FromFile(file1);
msa2.FromFile(file2);
Log("msa1=\n");
msa1.LogMe();
Log("msa2=\n");
msa2.LogMe();
const unsigned uColCount = msa1.GetColCount();
if (msa2.GetColCount() != uColCount)
Quit("Different lengths");
const unsigned uSeqCount1 = msa1.GetSeqCount();
const unsigned uSeqCount2 = msa2.GetSeqCount();
const unsigned uSeqCount = uSeqCount1 + uSeqCount2;
MSA::SetIdCount(uSeqCount);
for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount1; ++uSeqIndex1)
{
msa1.SetSeqWeight(uSeqIndex1, 1.0);
msa1.SetSeqId(uSeqIndex1, uSeqIndex1);
}
for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqCount2; ++uSeqIndex2)
{
msa2.SetSeqWeight(uSeqIndex2, 1.0);
msa2.SetSeqId(uSeqIndex2, uSeqCount1 + uSeqIndex2);
}
MSA alnA;
MSA alnB;
char strPathA[1024];
char strPathB[1024];
MakePath(uColCount, INDELS, strPathA);
MakePath(uColCount, INDELS, strPathB);
PWPath PathA;
PWPath PathB;
PathA.FromStr(strPathA);
PathB.FromStr(strPathB);
Log("PathA=\n");
PathA.LogMe();
Log("PathB=\n");
PathB.LogMe();
AlignTwoMSAsGivenPath(PathA, msa1, msa2, alnA);
AlignTwoMSAsGivenPath(PathB, msa1, msa2, alnB);
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
{
alnA.SetSeqWeight(uSeqIndex, 1.0);
alnB.SetSeqWeight(uSeqIndex, 1.0);
}
unsigned Seqs1[1024];
unsigned Seqs2[1024];
for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount1; ++uSeqIndex1)
Seqs1[uSeqIndex1] = uSeqIndex1;
for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqCount2; ++uSeqIndex2)
Seqs2[uSeqIndex2] = uSeqCount1 + uSeqIndex2;
MSA msaA1;
MSA msaA2;
MSA msaB1;
MSA msaB2;
MSAFromSeqSubset(alnA, Seqs1, uSeqCount1, msaA1);
MSAFromSeqSubset(alnB, Seqs1, uSeqCount1, msaB1);
MSAFromSeqSubset(alnA, Seqs2, uSeqCount2, msaA2);
MSAFromSeqSubset(alnB, Seqs2, uSeqCount2, msaB2);
for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount1; ++uSeqIndex1)
{
msaA1.SetSeqWeight(uSeqIndex1, 1.0);
msaB1.SetSeqWeight(uSeqIndex1, 1.0);
}
for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqCount2; ++uSeqIndex2)
{
msaA2.SetSeqWeight(uSeqIndex2, 1.0);
msaB2.SetSeqWeight(uSeqIndex2, 1.0);
}
Log("msaA1=\n");
msaA1.LogMe();
Log("msaB1=\n");
msaB1.LogMe();
Log("msaA2=\n");
msaA2.LogMe();
Log("msaB2=\n");
msaB2.LogMe();
Log("alnA=\n");
alnA.LogMe();
Log("AlnB=\n");
alnB.LogMe();
Log("\nSPA\n---\n");
SCORE SPA = ObjScoreSP(alnA);
Log("\nSPB\n---\n");
SCORE SPB = ObjScoreSP(alnB);
Log("\nXPA\n---\n");
SCORE XPA = ObjScoreXP(msaA1, msaA2);
Log("\nXPB\n---\n");
SCORE XPB = ObjScoreXP(msaB1, msaB2);
Log("SPA=%.4g SPB=%.4g Diff=%.4g\n", SPA, SPB, SPA - SPB);
Log("XPA=%.4g XPB=%.4g Diff=%.4g\n", XPA, XPB, XPA - XPB);
}
