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 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;
}
