4 #include "textfile.h"
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6 static void DoOutput(MSA &msa)
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8 bool AnyOutput = false;
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11 if (g_pstrFASTAOutFileName)
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13 TextFile File(g_pstrFASTAOutFileName, true);
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14 msa.ToFASTAFile(File);
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18 if (g_pstrMSFOutFileName)
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20 TextFile File(g_pstrMSFOutFileName, true);
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21 msa.ToMSFFile(File);
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25 if (g_pstrClwOutFileName)
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27 TextFile File(g_pstrClwOutFileName, true);
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28 msa.ToAlnFile(File);
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32 if (g_pstrClwStrictOutFileName)
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34 g_bClwStrict = true;
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35 TextFile File(g_pstrClwStrictOutFileName, true);
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36 msa.ToAlnFile(File);
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40 if (g_pstrHTMLOutFileName)
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42 TextFile File(g_pstrHTMLOutFileName, true);
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43 msa.ToHTMLFile(File);
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47 if (g_pstrPHYIOutFileName)
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49 TextFile File(g_pstrPHYIOutFileName, true);
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50 msa.ToPhyInterleavedFile(File);
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54 if (g_pstrPHYSOutFileName)
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56 TextFile File(g_pstrPHYSOutFileName, true);
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57 msa.ToPhySequentialFile(File);
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61 // Flag options, at most one used (because only one -out filename)
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62 TextFile fileOut(g_pstrOutFileName, true);
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65 msa.ToFASTAFile(fileOut);
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70 msa.ToMSFFile(fileOut);
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75 msa.ToAlnFile(fileOut);
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80 msa.ToHTMLFile(fileOut);
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85 msa.ToPhyInterleavedFile(fileOut);
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90 msa.ToPhySequentialFile(fileOut);
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94 // If -out option was given but no flags, output as FASTA
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96 msa.ToFASTAFile(fileOut);
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100 if (0 != g_pstrScoreFileName)
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101 WriteScoreFile(msa);
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104 void MuscleOutput(MSA &msa)
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110 Stabilize(msa, msaStable);
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111 msa.Clear(); // save memory
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112 DoOutput(msaStable);
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