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#include "muscle.h"
#include "textfile.h"
#include "msa.h"
#include "tree.h"
#include "profile.h"
#include "objscore.h"
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_Cluster2, g_Distance2, g_Root1);
SetMuscleTree(tree);
return ProfileFromMSA(msa, g_scoreGapOpen, true);
}
// Do profile-profile alignment
void Profile()
{
if (0 == g_pstrFileName1 || 0 == g_pstrFileName2)
Quit("-profile needs -in1 and -in2");
SetSeqWeightMethod(g_SeqWeight1);
TextFile file1(g_pstrFileName1);
TextFile file2(g_pstrFileName2);
MSA msa1;
MSA msa2;
msa1.FromFile(file1);
msa2.FromFile(file2);
ALPHA Alpha = ALPHA_Undefined;
switch (g_SeqType)
{
case SEQTYPE_Auto:
Alpha = msa1.GuessAlpha();
break;
case SEQTYPE_Protein:
Alpha = ALPHA_Amino;
break;
case SEQTYPE_Nucleo:
Alpha = ALPHA_Nucleo;
break;
default:
Quit("Invalid SeqType");
}
SetAlpha(Alpha);
msa1.FixAlpha();
msa2.FixAlpha();
if (ALPHA_Nucleo == Alpha)
SetPPScore(PPSCORE_SPN);
unsigned uLength1;
unsigned uLength2;
uLength1 = msa1.GetColCount();
uLength2 = msa2.GetColCount();
const unsigned uSeqCount1 = msa1.GetSeqCount();
const unsigned uSeqCount2 = msa2.GetSeqCount();
const unsigned uMaxSeqCount = (uSeqCount1 > uSeqCount2 ? uSeqCount1 : uSeqCount2);
MSA::SetIdCount(uMaxSeqCount);
Tree tree1;
Tree tree2;
ProfPos *Prof1 = ProfileFromMSALocal(msa1, tree1);
ProfPos *Prof2 = ProfileFromMSALocal(msa2, tree2);
PWPath Path;
ProfPos *ProfOut;
unsigned uLengthOut;
AlignTwoProfs(Prof1, uLength1, 1.0, Prof2, uLength2, 1.0, Path, &ProfOut, &uLengthOut);
MSA msaOut;
AlignTwoMSAsGivenPath(Path, msa1, msa2, msaOut);
TextFile fileOut(g_pstrOutFileName, true);
msaOut.ToFile(fileOut);
}
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