source: branches/lib/GDE/MUSCLE/src/profdb.cpp

#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 ProfDB()
        {
        SetOutputFileName(g_pstrOutFileName);
        SetInputFileName(g_pstrFileName2);
        SetStartTime();

        TextFile file1(g_pstrFileName1);
        TextFile file2(g_pstrFileName2);

        SetMaxIters(g_uMaxIters);
        SetSeqWeightMethod(g_SeqWeight1);

        TextFile fileIn(g_pstrFileName1);
        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;
                ProfileProfile(msa1, msaTmp, msaOut);
                msa1.Copy(msaOut);
                }
        ProgressStepsDone();

        TextFile fileOut(g_pstrOutFileName, true);
        msa1.ToFile(fileOut);
        }