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Searched refs:uLetter1 (Results 1 – 15 of 15) sorted by relevance

/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/umuscle/src/muscle/
H A Ddiffobjscore.cpp26 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()
H A Dwritescorefile.cpp22 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()
H A Dfastdistjones.cpp54 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()
H A Dcons.cpp111 const unsigned uLetter1 = GetLetter(uSeqIndex1, uColIndex); in GetPctGroupIdentityPair() local
113 const unsigned uGroup1 = ResidueGroup[uLetter1]; in GetPctGroupIdentityPair()
H A Dobjscore2.cpp105 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()
H A Dobjscoreda.cpp136 unsigned uLetter1 = msa1.GetLetter(uSeqIndex1, uColIndex); in ScoreSeqPair() local
139 SCORE scoreMatch = (*g_ptrScoreMatrix)[uLetter1][uLetter2]; in ScoreSeqPair()
H A Dprofile.h81 int PAM200_Letter(unsigned uLetter1, unsigned uLetter2);
/dports/biology/muscle/muscle-3.8.1551/
H A Ddiffobjscore.cpp19 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()
H A Dwritescorefile.cpp17 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()
H A Dfastdistjones.cpp50 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()
H A Dspfast.cpp66 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()
H A Dcons.cpp107 const unsigned uLetter1 = GetLetter(uSeqIndex1, uColIndex); in GetPctGroupIdentityPair() local
109 const unsigned uGroup1 = ResidueGroup[uLetter1]; in GetPctGroupIdentityPair()
H A Dobjscore2.cpp102 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()
H A Dobjscoreda.cpp136 unsigned uLetter1 = msa1.GetLetter(uSeqIndex1, uColIndex); in ScoreSeqPair() local
139 SCORE scoreMatch = (*g_ptrScoreMatrix)[uLetter1][uLetter2]; in ScoreSeqPair()
H A Dprofile.h74 int PAM200_Letter(unsigned uLetter1, unsigned uLetter2);