| 1 | #include "muscle.h" |
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| 2 | #include "textfile.h" |
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| 3 | #include "msa.h" |
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| 4 | #include "profile.h" |
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| 5 | #include "pwpath.h" |
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| 6 | #include "tree.h" |
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| 7 | |
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| 8 | #define TRACE 0 |
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| 9 | |
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| 10 | static void MSAFromFileName(const char *FileName, MSA &a) |
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| 11 | { |
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| 12 | TextFile File(FileName); |
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| 13 | a.FromFile(File); |
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| 14 | } |
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| 15 | |
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| 16 | static ProfPos *ProfileFromMSALocal(MSA &msa, Tree &tree) |
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| 17 | { |
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| 18 | const unsigned uSeqCount = msa.GetSeqCount(); |
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| 19 | for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) |
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| 20 | msa.SetSeqId(uSeqIndex, uSeqIndex); |
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| 21 | |
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| 22 | TreeFromMSA(msa, tree, g_Cluster1, g_Distance1, g_Root1); |
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| 23 | SetMuscleTree(tree); |
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| 24 | return ProfileFromMSA(msa); |
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| 25 | } |
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| 26 | |
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| 27 | void Local() |
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| 28 | { |
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| 29 | if (0 == g_pstrFileName1 || 0 == g_pstrFileName2) |
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| 30 | Quit("Must specify both -in1 and -in2 for -sw"); |
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| 31 | |
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| 32 | SetSeqWeightMethod(g_SeqWeight1); |
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| 33 | |
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| 34 | MSA msa1; |
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| 35 | MSA msa2; |
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| 36 | |
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| 37 | MSAFromFileName(g_pstrFileName1, msa1); |
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| 38 | MSAFromFileName(g_pstrFileName2, msa2); |
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| 39 | |
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| 40 | ALPHA Alpha = ALPHA_Undefined; |
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| 41 | switch (g_SeqType) |
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| 42 | { |
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| 43 | case SEQTYPE_Auto: |
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| 44 | Alpha = msa1.GuessAlpha(); |
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| 45 | break; |
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| 46 | |
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| 47 | case SEQTYPE_Protein: |
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| 48 | Alpha = ALPHA_Amino; |
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| 49 | break; |
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| 50 | |
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| 51 | case SEQTYPE_DNA: |
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| 52 | Alpha = ALPHA_DNA; |
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| 53 | break; |
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| 54 | |
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| 55 | case SEQTYPE_RNA: |
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| 56 | Alpha = ALPHA_RNA; |
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| 57 | break; |
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| 58 | |
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| 59 | default: |
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| 60 | Quit("Invalid SeqType"); |
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| 61 | } |
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| 62 | SetAlpha(Alpha); |
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| 63 | |
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| 64 | msa1.FixAlpha(); |
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| 65 | msa2.FixAlpha(); |
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| 66 | |
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| 67 | if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha) |
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| 68 | SetPPScore(PPSCORE_SPN); |
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| 69 | |
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| 70 | const unsigned uSeqCount1 = msa1.GetSeqCount(); |
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| 71 | const unsigned uSeqCount2 = msa2.GetSeqCount(); |
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| 72 | const unsigned uMaxSeqCount = (uSeqCount1 > uSeqCount2 ? uSeqCount1 : uSeqCount2); |
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| 73 | MSA::SetIdCount(uMaxSeqCount); |
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| 74 | |
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| 75 | unsigned uLength1 = msa1.GetColCount(); |
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| 76 | unsigned uLength2 = msa2.GetColCount(); |
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| 77 | |
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| 78 | Tree tree1; |
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| 79 | Tree tree2; |
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| 80 | |
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| 81 | ProfPos *Prof1 = ProfileFromMSALocal(msa1, tree1); |
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| 82 | ProfPos *Prof2 = ProfileFromMSALocal(msa2, tree2); |
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| 83 | |
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| 84 | PWPath Path; |
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| 85 | SW(Prof1, uLength1, Prof2, uLength2, Path); |
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| 86 | |
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| 87 | #if TRACE |
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| 88 | Path.LogMe(); |
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| 89 | #endif |
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| 90 | |
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| 91 | MSA msaOut; |
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| 92 | AlignTwoMSAsGivenPathSW(Path, msa1, msa2, msaOut); |
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| 93 | |
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| 94 | #if TRACE |
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| 95 | msaOut.LogMe(); |
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| 96 | #endif |
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| 97 | |
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| 98 | TextFile fileOut(g_pstrOutFileName, true); |
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| 99 | msaOut.ToFile(fileOut); |
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| 100 | } |
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