void SetMSAWeightsMuscle(MSA &msa)
{
SEQWEIGHT Method = GetSeqWeightMethod();
switch (Method)
{
case SEQWEIGHT_None:
msa.SetUniformWeights();
return;
case SEQWEIGHT_Henikoff:
msa.SetHenikoffWeights();
return;
case SEQWEIGHT_HenikoffPB:
msa.SetHenikoffWeightsPB();
return;
case SEQWEIGHT_GSC:
msa.SetGSCWeights();
return;
case SEQWEIGHT_ClustalW:
SetClustalWWeightsMuscle(msa);
return;
case SEQWEIGHT_ThreeWay:
SetThreeWayWeightsMuscle(msa);
return;
}
Quit("SetMSAWeightsMuscle, Invalid method=%d", Method);
}
void SetMuscleTree(const Tree &tree)
{
g_ptrMuscleTree = &tree;
if (SEQWEIGHT_ClustalW != GetSeqWeightMethod())
return;
delete[] g_MuscleWeights;
const unsigned uLeafCount = tree.GetLeafCount();
g_uMuscleIdCount = uLeafCount;
g_MuscleWeights = new WEIGHT[uLeafCount];
CalcClustalWWeights(tree, g_MuscleWeights);
}
void SetMuscleTree(const Tree &tree)
{
MuscleContext *ctx =getMuscleContext();
WEIGHT* &g_MuscleWeights = ctx->msa2.g_MuscleWeights;
unsigned &g_uMuscleIdCount = ctx->msa2.g_uMuscleIdCount;
const Tree* &g_ptrMuscleTree = ctx->msa2.g_ptrMuscleTree;
g_ptrMuscleTree = &tree;
if (SEQWEIGHT_ClustalW != GetSeqWeightMethod())
return;
if(g_MuscleWeights!=NULL) {
delete[] g_MuscleWeights;
g_MuscleWeights = NULL;
}
const unsigned uLeafCount = tree.GetLeafCount();
g_uMuscleIdCount = uLeafCount;
g_MuscleWeights = new WEIGHT[uLeafCount];
CalcClustalWWeights(tree, g_MuscleWeights);
}
void DistPWScoreDist(const SeqVect &v, DistFunc &DF)
{
SEQWEIGHT SeqWeightSave = GetSeqWeightMethod();
SetSeqWeightMethod(SEQWEIGHT_Henikoff);
const unsigned uSeqCount = v.Length();
DF.SetCount(uSeqCount);
const unsigned uPairCount = (uSeqCount*(uSeqCount + 1))/2;
unsigned uCount = 0;
SetProgressDesc("PW ScoreDist");
for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount; ++uSeqIndex1)
{
const Seq &s1 = v.GetSeq(uSeqIndex1);
MSA msa1;
msa1.FromSeq(s1);
for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqIndex1; ++uSeqIndex2)
{
if (0 == uCount%20)
Progress(uCount, uPairCount);
++uCount;
const Seq &s2 = v.GetSeq(uSeqIndex2);
MSA msa2;
msa2.FromSeq(s2);
PWPath Path;
MSA msaOut;
AlignTwoMSAs(msa1, msa2, msaOut, Path, false, false);
float d = (float) GetScoreDist(msaOut, 0, 1);
DF.SetDist(uSeqIndex1, uSeqIndex2, d);
}
}
ProgressStepsDone();
SetSeqWeightMethod(SeqWeightSave);
}
