| 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 "tree.h" |
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| 5 | #include "profile.h" |
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| 6 | #include "objscore.h" |
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| 7 | |
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| 8 | bool g_bTracePPScore = false; |
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| 9 | MSA *g_ptrPPScoreMSA1 = 0; |
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| 10 | MSA *g_ptrPPScoreMSA2 = 0; |
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| 11 | |
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| 12 | static ProfPos *ProfileFromMSALocal(MSA &msa, Tree &tree) |
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| 13 | { |
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| 14 | const unsigned uSeqCount = msa.GetSeqCount(); |
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| 15 | for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) |
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| 16 | msa.SetSeqId(uSeqIndex, uSeqIndex); |
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| 17 | |
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| 18 | TreeFromMSA(msa, tree, g_Cluster2, g_Distance2, g_Root1); |
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| 19 | SetMuscleTree(tree); |
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| 20 | return ProfileFromMSA(msa); |
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| 21 | } |
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| 22 | |
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| 23 | void PPScore() |
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| 24 | { |
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| 25 | if (0 == g_pstrFileName1 || 0 == g_pstrFileName2) |
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| 26 | Quit("-ppscore needs -in1 and -in2"); |
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| 27 | |
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| 28 | SetSeqWeightMethod(g_SeqWeight1); |
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| 29 | |
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| 30 | TextFile file1(g_pstrFileName1); |
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| 31 | TextFile file2(g_pstrFileName2); |
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| 32 | |
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| 33 | MSA msa1; |
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| 34 | MSA msa2; |
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| 35 | |
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| 36 | msa1.FromFile(file1); |
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| 37 | msa2.FromFile(file2); |
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| 38 | |
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| 39 | const unsigned uLength1 = msa1.GetColCount(); |
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| 40 | const unsigned uLength2 = msa2.GetColCount(); |
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| 41 | |
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| 42 | if (uLength1 != uLength2) |
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| 43 | Quit("Profiles must have the same length"); |
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| 44 | |
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| 45 | ALPHA Alpha = ALPHA_Undefined; |
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| 46 | switch (g_SeqType) |
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| 47 | { |
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| 48 | case SEQTYPE_Auto: |
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| 49 | Alpha = msa1.GuessAlpha(); |
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| 50 | break; |
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| 51 | |
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| 52 | case SEQTYPE_Protein: |
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| 53 | Alpha = ALPHA_Amino; |
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| 54 | break; |
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| 55 | |
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| 56 | case SEQTYPE_DNA: |
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| 57 | Alpha = ALPHA_DNA; |
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| 58 | break; |
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| 59 | |
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| 60 | case SEQTYPE_RNA: |
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| 61 | Alpha = ALPHA_RNA; |
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| 62 | break; |
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| 63 | |
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| 64 | default: |
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| 65 | Quit("Invalid SeqType"); |
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| 66 | } |
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| 67 | SetAlpha(Alpha); |
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| 68 | |
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| 69 | msa1.FixAlpha(); |
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| 70 | msa2.FixAlpha(); |
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| 71 | |
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| 72 | if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha) |
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| 73 | SetPPScore(PPSCORE_SPN); |
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| 74 | |
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| 75 | const unsigned uSeqCount1 = msa1.GetSeqCount(); |
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| 76 | const unsigned uSeqCount2 = msa2.GetSeqCount(); |
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| 77 | const unsigned uMaxSeqCount = (uSeqCount1 > uSeqCount2 ? uSeqCount1 : uSeqCount2); |
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| 78 | MSA::SetIdCount(uMaxSeqCount); |
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| 79 | |
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| 80 | Tree tree1; |
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| 81 | Tree tree2; |
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| 82 | ProfPos *Prof1 = ProfileFromMSALocal(msa1, tree1); |
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| 83 | ProfPos *Prof2 = ProfileFromMSALocal(msa2, tree2); |
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| 84 | |
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| 85 | g_bTracePPScore = true; |
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| 86 | g_ptrPPScoreMSA1 = &msa1; |
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| 87 | g_ptrPPScoreMSA2 = &msa2; |
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| 88 | |
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| 89 | SCORE Score = ObjScoreDP_Profs(Prof1, Prof2, uLength1); |
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| 90 | |
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| 91 | Log("Score=%.4g\n", Score); |
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| 92 | printf("Score=%.4g\n", Score); |
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| 93 | } |
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