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#include "muscle.h"
#include "textfile.h"
#include "seqvect.h"
#include "distfunc.h"
#include "msa.h"
#include "tree.h"
#include "clust.h"
#include "profile.h"
#include "clustsetmsa.h"
void Refine()
{
SetOutputFileName(g_pstrOutFileName);
SetInputFileName(g_pstrInFileName);
SetStartTime();
SetMaxIters(g_uMaxIters);
SetSeqWeightMethod(g_SeqWeight1);
TextFile fileIn(g_pstrInFileName);
MSA msa;
msa.FromFile(fileIn);
const unsigned uSeqCount = msa.GetSeqCount();
if (0 == uSeqCount)
Quit("No sequences in input file");
ALPHA Alpha = ALPHA_Undefined;
switch (g_SeqType)
{
case SEQTYPE_Auto:
Alpha = msa.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 SeqType");
}
SetAlpha(Alpha);
msa.FixAlpha();
SetPPScore();
if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)
SetPPScore(PPSCORE_SPN);
MSA::SetIdCount(uSeqCount);
// Initialize sequence ids.
// From this point on, ids must somehow propogate from here.
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
msa.SetSeqId(uSeqIndex, uSeqIndex);
SetMuscleInputMSA(msa);
Tree GuideTree;
TreeFromMSA(msa, GuideTree, g_Cluster2, g_Distance2, g_Root2);
SetMuscleTree(GuideTree);
if (g_bAnchors)
RefineVert(msa, GuideTree, g_uMaxIters);
else
RefineHoriz(msa, GuideTree, g_uMaxIters, false, false);
ValidateMuscleIds(msa);
ValidateMuscleIds(GuideTree);
// TextFile fileOut(g_pstrOutFileName, true);
// msa.ToFile(fileOut);
MuscleOutput(msa);
}
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