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#include "muscle.h"
#include "textfile.h"
#include "msa.h"
#include "profile.h"
#include "pwpath.h"
#include "tree.h"
#define TRACE 0
static void MSAFromFileName(const char *FileName, MSA &a)
{
TextFile File(FileName);
a.FromFile(File);
}
static ProfPos *ProfileFromMSALocal(MSA &msa, Tree &tree)
{
const unsigned uSeqCount = msa.GetSeqCount();
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
msa.SetSeqId(uSeqIndex, uSeqIndex);
TreeFromMSA(msa, tree, g_Cluster1, g_Distance1, g_Root1);
SetMuscleTree(tree);
return ProfileFromMSA(msa);
}
void Local()
{
if (0 == g_pstrFileName1 || 0 == g_pstrFileName2)
Quit("Must specify both -in1 and -in2 for -sw");
SetSeqWeightMethod(g_SeqWeight1);
MSA msa1;
MSA msa2;
MSAFromFileName(g_pstrFileName1, msa1);
MSAFromFileName(g_pstrFileName2, msa2);
ALPHA Alpha = ALPHA_Undefined;
switch (g_SeqType)
{
case SEQTYPE_Auto:
Alpha = msa1.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);
msa1.FixAlpha();
msa2.FixAlpha();
if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)
SetPPScore(PPSCORE_SPN);
const unsigned uSeqCount1 = msa1.GetSeqCount();
const unsigned uSeqCount2 = msa2.GetSeqCount();
const unsigned uMaxSeqCount = (uSeqCount1 > uSeqCount2 ? uSeqCount1 : uSeqCount2);
MSA::SetIdCount(uMaxSeqCount);
unsigned uLength1 = msa1.GetColCount();
unsigned uLength2 = msa2.GetColCount();
Tree tree1;
Tree tree2;
ProfPos *Prof1 = ProfileFromMSALocal(msa1, tree1);
ProfPos *Prof2 = ProfileFromMSALocal(msa2, tree2);
PWPath Path;
SW(Prof1, uLength1, Prof2, uLength2, Path);
#if TRACE
Path.LogMe();
#endif
MSA msaOut;
AlignTwoMSAsGivenPathSW(Path, msa1, msa2, msaOut);
#if TRACE
msaOut.LogMe();
#endif
TextFile fileOut(g_pstrOutFileName, true);
msaOut.ToFile(fileOut);
}
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