2 #include "textfile.h"
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4 #include "distfunc.h"
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9 #include "clustsetmsa.h"
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13 SetOutputFileName(g_pstrOutFileName);
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14 SetInputFileName(g_pstrFileName2);
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17 TextFile file1(g_pstrFileName1);
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18 TextFile file2(g_pstrFileName2);
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20 SetMaxIters(g_uMaxIters);
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21 SetSeqWeightMethod(g_SeqWeight1);
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23 TextFile fileIn(g_pstrFileName1);
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25 msa1.FromFile(fileIn);
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27 const unsigned uSeqCount1 = msa1.GetSeqCount();
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28 if (0 == uSeqCount1)
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29 Quit("No sequences in input alignment");
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32 v.FromFASTAFile(file2);
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33 const unsigned uSeqCount2 = v.Length();
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34 if (0 == uSeqCount2)
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35 Quit("No sequences in input alignment");
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37 MSA::SetIdCount(uSeqCount1 + uSeqCount2);
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38 SetProgressDesc("Align sequence database to profile");
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39 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount2; ++uSeqIndex)
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41 Progress(uSeqIndex, uSeqCount2);
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42 Seq &s = *(v[uSeqIndex]);
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47 ProfileProfile(msa1, msaTmp, msaOut);
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50 ProgressStepsDone();
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52 TextFile fileOut(g_pstrOutFileName, true);
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53 msa1.ToFile(fileOut);
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