| 1 | #include "muscle.h" |
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| 2 | #include "textfile.h" |
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| 3 | #include "seqvect.h" |
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| 4 | #include "distfunc.h" |
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| 5 | #include "msa.h" |
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| 6 | #include "tree.h" |
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| 7 | #include "clust.h" |
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| 8 | #include "profile.h" |
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| 9 | #include "clustsetmsa.h" |
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| 10 | |
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| 11 | void Refine() |
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| 12 | { |
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| 13 | SetOutputFileName(g_pstrOutFileName); |
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| 14 | SetInputFileName(g_pstrInFileName); |
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| 15 | SetStartTime(); |
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| 16 | |
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| 17 | SetMaxIters(g_uMaxIters); |
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| 18 | SetSeqWeightMethod(g_SeqWeight1); |
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| 19 | |
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| 20 | TextFile fileIn(g_pstrInFileName); |
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| 21 | MSA msa; |
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| 22 | msa.FromFile(fileIn); |
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| 23 | |
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| 24 | const unsigned uSeqCount = msa.GetSeqCount(); |
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| 25 | if (0 == uSeqCount) |
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| 26 | Quit("No sequences in input file"); |
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| 27 | |
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| 28 | ALPHA Alpha = ALPHA_Undefined; |
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| 29 | switch (g_SeqType) |
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| 30 | { |
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| 31 | case SEQTYPE_Auto: |
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| 32 | Alpha = msa.GuessAlpha(); |
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| 33 | break; |
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| 34 | |
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| 35 | case SEQTYPE_Protein: |
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| 36 | Alpha = ALPHA_Amino; |
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| 37 | break; |
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| 38 | |
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| 39 | case SEQTYPE_DNA: |
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| 40 | Alpha = ALPHA_DNA; |
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| 41 | break; |
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| 42 | |
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| 43 | case SEQTYPE_RNA: |
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| 44 | Alpha = ALPHA_RNA; |
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| 45 | break; |
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| 46 | |
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| 47 | default: |
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| 48 | Quit("Invalid SeqType"); |
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| 49 | } |
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| 50 | SetAlpha(Alpha); |
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| 51 | msa.FixAlpha(); |
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| 52 | |
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| 53 | SetPPScore(); |
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| 54 | if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha) |
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| 55 | SetPPScore(PPSCORE_SPN); |
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| 56 | |
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| 57 | MSA::SetIdCount(uSeqCount); |
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| 58 | |
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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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| 64 | |
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| 65 | Tree GuideTree; |
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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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| 68 | |
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| 69 | if (g_bAnchors) |
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| 70 | RefineVert(msa, GuideTree, g_uMaxIters); |
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| 71 | else |
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| 72 | RefineHoriz(msa, GuideTree, g_uMaxIters, false, false); |
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| 73 | |
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| 74 | ValidateMuscleIds(msa); |
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| 75 | ValidateMuscleIds(GuideTree); |
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| 76 | |
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| 77 | // TextFile fileOut(g_pstrOutFileName, true); |
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| 78 | // msa.ToFile(fileOut); |
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| 79 | MuscleOutput(msa); |
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| 80 | } |
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