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#include "muscle.h"
#include "msa.h"
#include "seqvect.h"
#include "msa.h"
#include "tree.h"
#include "profile.h"
void MUSCLE(SeqVect &v, MSA &msaOut)
{
const unsigned uSeqCount = v.Length();
if (0 == uSeqCount)
Quit("No sequences in input file");
ALPHA Alpha = ALPHA_Undefined;
switch (g_SeqType)
{
case SEQTYPE_Auto:
Alpha = v.GuessAlpha();
break;
case SEQTYPE_Protein:
Alpha = ALPHA_Amino;
break;
case SEQTYPE_RNA:
Alpha = ALPHA_RNA;
break;
case SEQTYPE_DNA:
Alpha = ALPHA_DNA;
break;
default:
Quit("Invalid seq type");
}
SetAlpha(Alpha);
v.FixAlpha();
if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)
{
SetPPScore(PPSCORE_SPN);
g_Distance1 = 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 = g_bDiags1;
SetSeqStats(uSeqCount, uMaxL, uTotL/uSeqCount);
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;
}
// First iteration
Tree GuideTree;
TreeFromSeqVect(v, GuideTree, g_Cluster1, g_Distance1, g_Root1);
SetMuscleTree(GuideTree);
ProgNode *ProgNodes = 0;
if (g_bLow)
ProgNodes = ProgressiveAlignE(v, GuideTree, msaOut);
else
ProgressiveAlign(v, GuideTree, msaOut);
SetCurrentAlignment(msaOut);
if (1 == g_uMaxIters || 2 == uSeqCount)
{
MHackEnd(msaOut);
return;
}
g_bDiags = g_bDiags2;
SetIter(2);
if (g_bLow)
{
if (0 != g_uMaxTreeRefineIters)
RefineTreeE(msaOut, v, GuideTree, ProgNodes);
}
else
RefineTree(msaOut, GuideTree);
extern void DeleteProgNode(ProgNode &Node);
const unsigned uNodeCount = GuideTree.GetNodeCount();
for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
DeleteProgNode(ProgNodes[uNodeIndex]);
delete[] ProgNodes;
ProgNodes = 0;
SetSeqWeightMethod(g_SeqWeight2);
SetMuscleTree(GuideTree);
if (g_bAnchors)
RefineVert(msaOut, GuideTree, g_uMaxIters - 2);
else
RefineHoriz(msaOut, GuideTree, g_uMaxIters - 2, false, false);
MHackEnd(msaOut);
}
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