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#include "libMUSCLE/muscle.h"
#include "libMUSCLE/textfile.h"
#include "libMUSCLE/seqvect.h"
#include "libMUSCLE/distfunc.h"
#include "libMUSCLE/msa.h"
#include "libMUSCLE/tree.h"
#include "libMUSCLE/clust.h"
#include "libMUSCLE/profile.h"
#include "libMUSCLE/clustsetmsa.h"
namespace muscle {
void ProfDB()
{
SetOutputFileName(g_pstrOutFileName.get());
SetInputFileName(g_pstrFileName2.get());
SetStartTime();
TextFile file1(g_pstrFileName1.get());
TextFile file2(g_pstrFileName2.get());
SetMaxIters(g_uMaxIters.get());
SetSeqWeightMethod(g_SeqWeight1.get());
TextFile fileIn(g_pstrFileName1.get());
MSA msa1;
msa1.FromFile(fileIn);
const unsigned uSeqCount1 = msa1.GetSeqCount();
if (0 == uSeqCount1)
Quit("No sequences in input alignment");
SeqVect v;
v.FromFASTAFile(file2);
const unsigned uSeqCount2 = v.Length();
if (0 == uSeqCount2)
Quit("No sequences in input alignment");
MSA::SetIdCount(uSeqCount1 + uSeqCount2);
SetProgressDesc("Align sequence database to profile");
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount2; ++uSeqIndex)
{
Progress(uSeqIndex, uSeqCount2);
Seq &s = *(v[uSeqIndex]);
s.SetId(0);
MSA msaTmp;
msaTmp.FromSeq(s);
MSA msaOut;
SetProfileProfileAlphabet(msa1, msaTmp);
ProfileProfile(msa1, msaTmp, msaOut);
msa1.Copy(msaOut);
}
ProgressStepsDone();
TextFile fileOut(g_pstrOutFileName.get(), true);
msa1.ToFile(fileOut);
}
}
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