| 1 | #include "muscle.h" |
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| 2 | #include "msa.h" |
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| 3 | #include <errno.h> |
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| 4 | |
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| 5 | extern float VTML_SP[32][32]; |
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| 6 | extern float NUC_SP[32][32]; |
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| 7 | |
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| 8 | static double GetColScore(const MSA &msa, unsigned uCol) |
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| 9 | { |
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| 10 | const unsigned uSeqCount = msa.GetSeqCount(); |
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| 11 | unsigned uPairCount = 0; |
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| 12 | double dSum = 0.0; |
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| 13 | for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1) |
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| 14 | { |
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| 15 | if (msa.IsGap(uSeq1, uCol)) |
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| 16 | continue; |
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| 17 | unsigned uLetter1 = msa.GetLetterEx(uSeq1, uCol); |
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| 18 | if (uLetter1 >= g_AlphaSize) |
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| 19 | continue; |
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| 20 | for (unsigned uSeq2 = uSeq1 + 1; uSeq2 < uSeqCount; ++uSeq2) |
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| 21 | { |
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| 22 | if (msa.IsGap(uSeq2, uCol)) |
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| 23 | continue; |
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| 24 | unsigned uLetter2 = msa.GetLetterEx(uSeq2, uCol); |
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| 25 | if (uLetter2 >= g_AlphaSize) |
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| 26 | continue; |
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| 27 | double Score; |
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| 28 | switch (g_Alpha) |
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| 29 | { |
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| 30 | case ALPHA_Amino: |
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| 31 | Score = VTML_SP[uLetter1][uLetter2]; |
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| 32 | break; |
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| 33 | case ALPHA_DNA: |
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| 34 | case ALPHA_RNA: |
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| 35 | Score = NUC_SP[uLetter1][uLetter2]; |
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| 36 | break; |
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| 37 | default: |
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| 38 | Quit("GetColScore: invalid alpha=%d", g_Alpha); |
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| 39 | } |
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| 40 | dSum += Score; |
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| 41 | ++uPairCount; |
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| 42 | } |
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| 43 | } |
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| 44 | if (0 == uPairCount) |
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| 45 | return 0; |
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| 46 | return dSum / uPairCount; |
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| 47 | } |
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| 48 | |
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| 49 | void WriteScoreFile(const MSA &msa) |
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| 50 | { |
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| 51 | FILE *f = fopen(g_pstrScoreFileName, "w"); |
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| 52 | if (0 == f) |
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| 53 | Quit("Cannot open score file '%s' errno=%d", g_pstrScoreFileName, errno); |
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| 54 | |
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| 55 | const unsigned uColCount = msa.GetColCount(); |
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| 56 | const unsigned uSeqCount = msa.GetSeqCount(); |
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| 57 | for (unsigned uCol = 0; uCol < uColCount; ++uCol) |
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| 58 | { |
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| 59 | double Score = GetColScore(msa, uCol); |
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| 60 | fprintf(f, "%10.3f ", Score); |
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| 61 | for (unsigned uSeq = 0; uSeq < uSeqCount; ++uSeq) |
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| 62 | { |
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| 63 | char c = msa.GetChar(uSeq, uCol); |
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| 64 | fprintf(f, "%c", c); |
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| 65 | } |
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| 66 | fprintf(f, "\n"); |
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| 67 | } |
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| 68 | fclose(f); |
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| 69 | } |
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