void SetClustalWWeightsMuscle(MSA &msa)
{
if (0 == g_MuscleWeights)
Quit("g_MuscleWeights = 0");
const unsigned uSeqCount = msa.GetSeqCount();
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
{
const unsigned uId = msa.GetSeqId(uSeqIndex);
if (uId >= g_uMuscleIdCount)
Quit("SetClustalWWeightsMuscle: id out of range");
msa.SetSeqWeight(uSeqIndex, g_MuscleWeights[uId]);
}
msa.NormalizeWeights((WEIGHT) 1.0);
}
void SetThreeWayWeightsMuscle(MSA &msa)
{
MuscleContext *ctx =getMuscleContext();
const Tree* &g_ptrMuscleTree = ctx->msa2.g_ptrMuscleTree;
unsigned &g_uTreeSplitNode1 = ctx->msa2.g_uTreeSplitNode1;
unsigned &g_uTreeSplitNode2 = ctx->msa2.g_uTreeSplitNode2;
if (NULL_NEIGHBOR == g_uTreeSplitNode1 || NULL_NEIGHBOR == g_uTreeSplitNode2)
{
msa.SetHenikoffWeightsPB();
return;
}
const unsigned uMuscleSeqCount = g_ptrMuscleTree->GetLeafCount();
WEIGHT *Weights = new WEIGHT[uMuscleSeqCount];
CalcThreeWayWeights(*g_ptrMuscleTree, g_uTreeSplitNode1, g_uTreeSplitNode2,
Weights);
const unsigned uMSASeqCount = msa.GetSeqCount();
for (unsigned uSeqIndex = 0; uSeqIndex < uMSASeqCount; ++uSeqIndex)
{
const unsigned uId = msa.GetSeqId(uSeqIndex);
if (uId >= uMuscleSeqCount)
Quit("SetThreeWayWeightsMuscle: id out of range");
msa.SetSeqWeight(uSeqIndex, Weights[uId]);
}
#if LOCAL_VERBOSE
{
Log("SetThreeWayWeightsMuscle\n");
for (unsigned n = 0; n < uMSASeqCount; ++n)
{
const unsigned uId = msa.GetSeqId(n);
Log("%20.20s %6.3f\n", msa.GetSeqName(n), Weights[uId]);
}
}
#endif
msa.NormalizeWeights((WEIGHT) 1.0);
delete[] Weights;
}
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);
}
