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_pstrInFileName);
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17 SetMaxIters(g_uMaxIters);
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18 SetSeqWeightMethod(g_SeqWeight1);
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20 TextFile fileIn(g_pstrInFileName);
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22 msa.FromFile(fileIn);
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24 const unsigned uSeqCount = msa.GetSeqCount();
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26 Quit("No sequences in input file");
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28 ALPHA Alpha = ALPHA_Undefined;
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32 Alpha = msa.GuessAlpha();
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35 case SEQTYPE_Protein:
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36 Alpha = ALPHA_Amino;
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48 Quit("Invalid SeqType");
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54 if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)
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55 SetPPScore(PPSCORE_SPN);
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57 MSA::SetIdCount(uSeqCount);
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59 // Initialize sequence ids.
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60 // From this point on, ids must somehow propogate from here.
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61 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
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62 msa.SetSeqId(uSeqIndex, uSeqIndex);
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63 SetMuscleInputMSA(msa);
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66 TreeFromMSA(msa, GuideTree, g_Cluster2, g_Distance2, g_Root2);
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67 SetMuscleTree(GuideTree);
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70 RefineVert(msa, GuideTree, g_uMaxIters);
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72 RefineHoriz(msa, GuideTree, g_uMaxIters, false, false);
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74 ValidateMuscleIds(msa);
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75 ValidateMuscleIds(GuideTree);
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77 // TextFile fileOut(g_pstrOutFileName, true);
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78 // msa.ToFile(fileOut);
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