/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/umuscle/src/muscle/ |
H A D | diffobjscore.cpp | 26 unsigned uLetter1 = msa.GetLetterEx(uSeqIndex1, uColIndex); in ScoreColLetters() local 27 if (uLetter1 >= g_AlphaSize) in ScoreColLetters() 36 BruteScore += w1*w2*Mx[uLetter1][uLetter2]; in ScoreColLetters() 63 for (unsigned uLetter1 = 0; uLetter1 < g_AlphaSize; ++uLetter1) in ScoreColLetters() local 65 const FCOUNT f1 = Freqs[uLetter1]; in ScoreColLetters() 66 Score += f1*f1*Mx[uLetter1][uLetter1]; in ScoreColLetters() 67 for (unsigned uLetter2 = uLetter1 + 1; uLetter2 < g_AlphaSize; ++uLetter2) in ScoreColLetters() 70 Score += 2*f1*f2*Mx[uLetter1][uLetter2]; in ScoreColLetters()
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H A D | writescorefile.cpp | 22 unsigned uLetter1 = msa.GetLetterEx(uSeq1, uCol); in GetColScore() local 23 if (uLetter1 >= g_AlphaSize) in GetColScore() 36 Score = VTML_SP[uLetter1][uLetter2]; in GetColScore() 40 Score = NUC_SP[uLetter1][uLetter2]; in GetColScore()
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H A D | fastdistjones.cpp | 54 const unsigned uLetter1 = CharToLetterEx(s[uPos]); in DistKmer20_3() local 55 if (uLetter1 >= 20) in DistKmer20_3() 64 const unsigned uWord = uLetter1 + uLetter2*20 + uLetter3*20*20; in DistKmer20_3() 88 const unsigned uLetter1 = uWord%20; in DistKmer20_3() local 91 LetterToCharAmino(uLetter1), in DistKmer20_3()
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H A D | cons.cpp | 111 const unsigned uLetter1 = GetLetter(uSeqIndex1, uColIndex); in GetPctGroupIdentityPair() local 113 const unsigned uGroup1 = ResidueGroup[uLetter1]; in GetPctGroupIdentityPair()
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H A D | objscore2.cpp | 105 unsigned uLetter1 = msa1.GetLetterEx(uSeqIndex1, uColIndex); in ScoreSeqPairLetters() local 106 if (uLetter1 >= g_AlphaSize) in ScoreSeqPairLetters() 112 SCORE scoreMatch = (*g_ptrScoreMatrix)[uLetter1][uLetter2]; in ScoreSeqPairLetters()
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H A D | objscoreda.cpp | 136 unsigned uLetter1 = msa1.GetLetter(uSeqIndex1, uColIndex); in ScoreSeqPair() local 139 SCORE scoreMatch = (*g_ptrScoreMatrix)[uLetter1][uLetter2]; in ScoreSeqPair()
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H A D | profile.h | 81 int PAM200_Letter(unsigned uLetter1, unsigned uLetter2);
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/dports/biology/muscle/muscle-3.8.1551/ |
H A D | diffobjscore.cpp | 19 unsigned uLetter1 = msa.GetLetterEx(uSeqIndex1, uColIndex); in ScoreColLetters() local 20 if (uLetter1 >= g_AlphaSize) in ScoreColLetters() 29 BruteScore += w1*w2*Mx[uLetter1][uLetter2]; in ScoreColLetters() 56 for (unsigned uLetter1 = 0; uLetter1 < g_AlphaSize; ++uLetter1) in ScoreColLetters() local 58 const FCOUNT f1 = Freqs[uLetter1]; in ScoreColLetters() 59 Score += f1*f1*Mx[uLetter1][uLetter1]; in ScoreColLetters() 60 for (unsigned uLetter2 = uLetter1 + 1; uLetter2 < g_AlphaSize; ++uLetter2) in ScoreColLetters() 63 Score += 2*f1*f2*Mx[uLetter1][uLetter2]; in ScoreColLetters()
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H A D | writescorefile.cpp | 17 unsigned uLetter1 = msa.GetLetterEx(uSeq1, uCol); in GetColScore() local 18 if (uLetter1 >= g_AlphaSize) in GetColScore() 31 Score = VTML_SP[uLetter1][uLetter2]; in GetColScore() 35 Score = NUC_SP[uLetter1][uLetter2]; in GetColScore()
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H A D | fastdistjones.cpp | 50 const unsigned uLetter1 = CharToLetterEx(s[uPos]); in DistKmer20_3() local 51 if (uLetter1 >= 20) in DistKmer20_3() 60 const unsigned uWord = uLetter1 + uLetter2*20 + uLetter3*20*20; in DistKmer20_3() 84 const unsigned uLetter1 = uWord%20; in DistKmer20_3() local 87 LetterToCharAmino(uLetter1), in DistKmer20_3()
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H A D | spfast.cpp | 66 unsigned uLetter1 = msa.GetLetterEx(uSeqIndex1, uColIndex); in SPColBrute() local 67 if (uLetter1 >= 20) in SPColBrute() 75 SCORE t = w1*w2*(*g_ptrScoreMatrix)[uLetter1][uLetter2]; in SPColBrute() 78 LetterToCharAmino(uLetter1), in SPColBrute() 82 (*g_ptrScoreMatrix)[uLetter1][uLetter2], in SPColBrute()
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H A D | cons.cpp | 107 const unsigned uLetter1 = GetLetter(uSeqIndex1, uColIndex); in GetPctGroupIdentityPair() local 109 const unsigned uGroup1 = ResidueGroup[uLetter1]; in GetPctGroupIdentityPair()
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H A D | objscore2.cpp | 102 unsigned uLetter1 = msa1.GetLetterEx(uSeqIndex1, uColIndex); in ScoreSeqPairLetters() local 103 if (uLetter1 >= g_AlphaSize) in ScoreSeqPairLetters() 109 SCORE scoreMatch = (*g_ptrScoreMatrix)[uLetter1][uLetter2]; in ScoreSeqPairLetters()
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H A D | objscoreda.cpp | 136 unsigned uLetter1 = msa1.GetLetter(uSeqIndex1, uColIndex); in ScoreSeqPair() local 139 SCORE scoreMatch = (*g_ptrScoreMatrix)[uLetter1][uLetter2]; in ScoreSeqPair()
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H A D | profile.h | 74 int PAM200_Letter(unsigned uLetter1, unsigned uLetter2);
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