void MuscleOutput(MSA &msa)
{
MHackEnd(msa);
if (g_bStable)
{
MSA msaStable;
Stabilize(msa, msaStable);
msa.Clear(); // save memory
DoOutput(msaStable);
}
else
DoOutput(msa);
}
void prepareAlignResults(MSA& msa, const DNAAlphabet* al, MultipleSequenceAlignment& ma, bool mhack) {
if (mhack) {
MHackEnd(msa);
}
MuscleContext* ctx = getMuscleContext();
if (ctx->params.g_bStable) {
MSA msaStable;
Stabilize(msa, msaStable);
msa.Clear();
convertMSA2MAlignment(msaStable, al, ma);
} else {
convertMSA2MAlignment(msa, al, ma);
}
}
void ProgAlignSubFams()
{
MSA msaOut;
SetOutputFileName(g_pstrOutFileName.get());
SetInputFileName(g_pstrInFileName.get());
SetMaxIters(g_uMaxIters.get());
SetSeqWeightMethod(g_SeqWeight1.get());
TextFile fileIn(g_pstrInFileName.get());
SeqVect v;
v.FromFASTAFile(fileIn);
const unsigned uSeqCount = v.Length();
if (0 == uSeqCount)
Quit("No sequences in input file");
ALPHA Alpha = ALPHA_Undefined;
switch (g_SeqType.get())
{
case SEQTYPE_Auto:
Alpha = v.GuessAlpha();
break;
case SEQTYPE_Protein:
Alpha = ALPHA_Amino;
break;
case SEQTYPE_DNA:
Alpha = ALPHA_DNA;
break;
case SEQTYPE_RNA:
Alpha = ALPHA_RNA;
break;
default:
Quit("Invalid seq type");
}
SetAlpha(Alpha);
v.FixAlpha();
PTR_SCOREMATRIX UserMatrix = 0;
if (0 != g_pstrMatrixFileName.get())
{
const char *FileName = g_pstrMatrixFileName.get();
const char *Path = getenv("MUSCLE_MXPATH");
if (Path != 0)
{
size_t n = strlen(Path) + 1 + strlen(FileName) + 1;
char *NewFileName = new char[n];
sprintf(NewFileName, "%s/%s", Path, FileName);
FileName = NewFileName;
}
TextFile File(FileName);
UserMatrix = ReadMx(File);
g_Alpha = ALPHA_Amino;
g_PPScore = PPSCORE_SP;
}
SetPPScore();
if (0 != UserMatrix)
g_ptrScoreMatrix = UserMatrix;
if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)
{
SetPPScore(PPSCORE_SPN);
g_Distance1.get() = DISTANCE_Kmer4_6;
}
unsigned uMaxL = 0;
unsigned uTotL = 0;
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
{
unsigned L = v.GetSeq(uSeqIndex).Length();
uTotL += L;
if (L > uMaxL)
uMaxL = L;
}
SetIter(1);
g_bDiags.get() = g_bDiags1.get();
SetSeqStats(uSeqCount, uMaxL, uTotL/uSeqCount);
SetMuscleSeqVect(v);
MSA::SetIdCount(uSeqCount);
// Initialize sequence ids.
// From this point on, ids must somehow propogate from here.
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
v.SetSeqId(uSeqIndex, uSeqIndex);
if (uSeqCount > 1)
MHackStart(v);
if (0 == uSeqCount)
{
msaOut.Clear();
return;
}
if (1 == uSeqCount && ALPHA_Amino == Alpha)
{
const Seq &s = v.GetSeq(0);
msaOut.FromSeq(s);
return;
}
Tree GuideTree;
TreeFromSeqVect(v, GuideTree, g_Cluster1.get(), g_Distance1.get(), g_Root1.get());
SetMuscleTree(GuideTree);
MSA msa;
if (g_bLow.get())
{
ProgNode *ProgNodes = 0;
ProgNodes = ProgressiveAlignE(v, GuideTree, msa);
delete[] ProgNodes;
}
else
ProgressiveAlign(v, GuideTree, msa);
SetCurrentAlignment(msa);
TreeFromMSA(msa, GuideTree, g_Cluster2.get(), g_Distance2.get(), g_Root2.get());
SetMuscleTree(GuideTree);
unsigned *SubFams = new unsigned[uSeqCount];
unsigned uSubFamCount;
SubFam(GuideTree, g_uMaxSubFamCount.get(), SubFams, &uSubFamCount);
SetProgressDesc("Align node");
const unsigned uNodeCount = 2*uSeqCount - 1;
ProgNode *ProgNodes = new ProgNode[uNodeCount];
bool *NodeIsSubFam = new bool[uNodeCount];
bool *NodeInSubFam = new bool[uNodeCount];
for (unsigned i = 0; i < uNodeCount; ++i)
{
NodeIsSubFam[i] = false;
NodeInSubFam[i] = false;
}
for (unsigned i = 0; i < uSubFamCount; ++i)
{
unsigned uNodeIndex = SubFams[i];
assert(uNodeIndex < uNodeCount);
NodeIsSubFam[uNodeIndex] = true;
SetInFam(GuideTree, uNodeIndex, NodeInSubFam);
}
unsigned uJoin = 0;
unsigned uTreeNodeIndex = GuideTree.FirstDepthFirstNode();
do
{
if (NodeIsSubFam[uTreeNodeIndex])
{
#if TRACE
Log("Node %d: align subfam\n", uTreeNodeIndex);
#endif
ProgNode &Node = ProgNodes[uTreeNodeIndex];
AlignSubFam(v, GuideTree, uTreeNodeIndex, Node.m_MSA);
Node.m_uLength = Node.m_MSA.GetColCount();
}
else if (!NodeInSubFam[uTreeNodeIndex])
{
#if TRACE
Log("Node %d: align two subfams\n", uTreeNodeIndex);
#endif
Progress(uJoin, uSubFamCount - 1);
++uJoin;
const unsigned uMergeNodeIndex = uTreeNodeIndex;
ProgNode &Parent = ProgNodes[uMergeNodeIndex];
const unsigned uLeft = GuideTree.GetLeft(uTreeNodeIndex);
const unsigned uRight = GuideTree.GetRight(uTreeNodeIndex);
ProgNode &Node1 = ProgNodes[uLeft];
ProgNode &Node2 = ProgNodes[uRight];
PWPath Path;
AlignTwoMSAs(Node1.m_MSA, Node2.m_MSA, Parent.m_MSA, Path);
Parent.m_uLength = Parent.m_MSA.GetColCount();
Node1.m_MSA.Clear();
Node2.m_MSA.Clear();
}
else
{
#if TRACE
Log("Node %d: in subfam\n", uTreeNodeIndex);
#endif
;
}
uTreeNodeIndex = GuideTree.NextDepthFirstNode(uTreeNodeIndex);
}
while (NULL_NEIGHBOR != uTreeNodeIndex);
ProgressStepsDone();
unsigned uRootNodeIndex = GuideTree.GetRootNodeIndex();
ProgNode &RootProgNode = ProgNodes[uRootNodeIndex];
TextFile fOut(g_pstrOutFileName.get(), true);
MHackEnd(RootProgNode.m_MSA);
RootProgNode.m_MSA.ToFile(fOut);
delete[] NodeInSubFam;
delete[] NodeIsSubFam;
delete[] ProgNodes;
delete[] SubFams;
ProgNodes = 0;
NodeInSubFam = 0;
NodeIsSubFam = 0;
SubFams = 0;
}
