| 1 | #include "muscle.h" |
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| 2 | #include "msa.h" |
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| 3 | #include "objscore.h" |
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| 4 | #include "profile.h" |
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| 5 | #include "timing.h" |
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| 6 | |
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| 7 | #if TIMING |
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| 8 | TICKS g_ticksObjScore = 0; |
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| 9 | #endif |
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| 10 | |
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| 11 | SCORE ObjScore(const MSA &msa, const unsigned SeqIndexes1[], |
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| 12 | unsigned uSeqCount1, const unsigned SeqIndexes2[], unsigned uSeqCount2) |
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| 13 | { |
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| 14 | #if TIMING |
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| 15 | TICKS t1 = GetClockTicks(); |
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| 16 | #endif |
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| 17 | const unsigned uSeqCount = msa.GetSeqCount(); |
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| 18 | |
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| 19 | OBJSCORE OS = g_ObjScore; |
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| 20 | if (g_ObjScore == OBJSCORE_SPM) |
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| 21 | { |
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| 22 | if (uSeqCount <= 100) |
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| 23 | OS = OBJSCORE_XP; |
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| 24 | else |
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| 25 | OS = OBJSCORE_SPF; |
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| 26 | } |
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| 27 | |
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| 28 | MSA msa1; |
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| 29 | MSA msa2; |
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| 30 | |
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| 31 | switch (OS) |
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| 32 | { |
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| 33 | case OBJSCORE_DP: |
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| 34 | case OBJSCORE_XP: |
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| 35 | MSAFromSeqSubset(msa, SeqIndexes1, uSeqCount1, msa1); |
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| 36 | MSAFromSeqSubset(msa, SeqIndexes2, uSeqCount2, msa2); |
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| 37 | |
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| 38 | SetMSAWeightsMuscle(msa1); |
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| 39 | SetMSAWeightsMuscle(msa2); |
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| 40 | break; |
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| 41 | |
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| 42 | case OBJSCORE_SP: |
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| 43 | case OBJSCORE_SPF: |
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| 44 | case OBJSCORE_PS: |
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| 45 | // Yuck -- casting away const (design flaw) |
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| 46 | SetMSAWeightsMuscle((MSA &) msa); |
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| 47 | break; |
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| 48 | } |
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| 49 | |
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| 50 | SCORE Score = 0; |
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| 51 | switch (OS) |
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| 52 | { |
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| 53 | case OBJSCORE_SP: |
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| 54 | Score = ObjScoreSP(msa); |
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| 55 | break; |
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| 56 | |
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| 57 | case OBJSCORE_DP: |
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| 58 | Score = ObjScoreDP(msa1, msa2); |
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| 59 | break; |
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| 60 | |
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| 61 | case OBJSCORE_XP: |
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| 62 | Score = ObjScoreXP(msa1, msa2); |
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| 63 | break; |
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| 64 | |
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| 65 | case OBJSCORE_PS: |
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| 66 | Score = ObjScorePS(msa); |
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| 67 | break; |
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| 68 | |
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| 69 | case OBJSCORE_SPF: |
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| 70 | Score = ObjScoreSPDimer(msa); |
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| 71 | break; |
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| 72 | |
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| 73 | default: |
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| 74 | Quit("Invalid g_ObjScore=%d", g_ObjScore); |
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| 75 | } |
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| 76 | #if TIMING |
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| 77 | TICKS t2 = GetClockTicks(); |
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| 78 | g_ticksObjScore += (t2 - t1); |
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| 79 | #endif |
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| 80 | return Score; |
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| 81 | } |
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| 82 | |
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| 83 | SCORE ObjScoreIds(const MSA &msa, const unsigned Ids1[], |
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| 84 | unsigned uCount1, const unsigned Ids2[], unsigned uCount2) |
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| 85 | { |
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| 86 | #if TIMING |
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| 87 | TICKS t1 = GetClockTicks(); |
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| 88 | #endif |
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| 89 | unsigned *SeqIndexes1 = new unsigned[uCount1]; |
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| 90 | unsigned *SeqIndexes2 = new unsigned[uCount2]; |
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| 91 | |
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| 92 | for (unsigned n = 0; n < uCount1; ++n) |
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| 93 | SeqIndexes1[n] = msa.GetSeqIndex(Ids1[n]); |
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| 94 | |
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| 95 | for (unsigned n = 0; n < uCount2; ++n) |
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| 96 | SeqIndexes2[n] = msa.GetSeqIndex(Ids2[n]); |
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| 97 | |
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| 98 | #if DOUBLE_AFFINE |
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| 99 | extern SCORE ObjScoreDA(const MSA &msa, SCORE *ptrLetters, SCORE *ptrGaps); |
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| 100 | SCORE Letters, Gaps; |
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| 101 | SCORE dObjScore = ObjScoreDA(msa, &Letters, &Gaps); |
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| 102 | |
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| 103 | delete[] SeqIndexes1; |
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| 104 | delete[] SeqIndexes2; |
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| 105 | #else |
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| 106 | SCORE dObjScore = ObjScore(msa, SeqIndexes1, uCount1, SeqIndexes2, uCount2); |
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| 107 | #endif |
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| 108 | #if TIMING |
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| 109 | TICKS t2 = GetClockTicks(); |
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| 110 | g_ticksObjScore += (t2 - t1); |
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| 111 | #endif |
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| 112 | return dObjScore; |
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| 113 | } |
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