/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/umuscle/src/muscle/ |
H A D | profilefrommsa.cpp | 62 for (unsigned n = 0; n < g_AlphaSize; ++n) in ListProfile() 66 for (unsigned n = 0; n < g_AlphaSize; ++n) in ListProfile() 79 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in ListProfile() 103 unsigned &g_AlphaSize = ctx->alpha.g_AlphaSize; in ListProfile() local 131 for (unsigned n = 0; n < g_AlphaSize; ++n) in ListProfile() 135 for (unsigned n = 0; n < g_AlphaSize; ++n) in ListProfile() 180 for (unsigned n = 0; n < g_AlphaSize - 1; ++n) in SortCounts() 261 unsigned g_AlphaSize = ctx->alpha.g_AlphaSize; in ProfileFromMSA() local 291 SortCounts(PP.m_fcCounts, PP.m_uSortOrder, g_AlphaSize); in ProfileFromMSA() 295 for (unsigned i = 0; i < g_AlphaSize; ++i) in ProfileFromMSA() [all …]
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H A D | diffobjscore.cpp | 18 unsigned &g_AlphaSize = ctx->alpha.g_AlphaSize; in ScoreColLetters() local 27 if (uLetter1 >= g_AlphaSize) in ScoreColLetters() 33 if (uLetter2 >= g_AlphaSize) in ScoreColLetters() 56 if (uLetter >= g_AlphaSize) in ScoreColLetters() 63 for (unsigned uLetter1 = 0; uLetter1 < g_AlphaSize; ++uLetter1) in ScoreColLetters() 67 for (unsigned uLetter2 = uLetter1 + 1; uLetter2 < g_AlphaSize; ++uLetter2) in ScoreColLetters()
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H A D | writescorefile.cpp | 12 unsigned &g_AlphaSize = d->alpha.g_AlphaSize; in GetColScore() local 23 if (uLetter1 >= g_AlphaSize) in GetColScore() 30 if (uLetter2 >= g_AlphaSize) in GetColScore()
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H A D | cons.cpp | 34 unsigned &g_AlphaSize = ctx->alpha.g_AlphaSize; in GetCons() local 37 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in GetCons()
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H A D | scorepp.cpp | 11 unsigned &g_AlphaSize = ctx->alpha.g_AlphaSize; in ConsensusChar() local 19 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in ConsensusChar()
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H A D | objscore2.cpp | 47 unsigned &g_AlphaSize = ctx->alpha.g_AlphaSize; in ScoreSeqPairLetters() local 106 if (uLetter1 >= g_AlphaSize) in ScoreSeqPairLetters() 109 if (uLetter2 >= g_AlphaSize) in ScoreSeqPairLetters()
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H A D | msa2.cpp | 30 unsigned g_AlphaSize = ctx->alpha.g_AlphaSize; in GetFractionalWeightedCounts() local 35 memset(fcCounts, 0, g_AlphaSize*sizeof(FCOUNT)); in GetFractionalWeightedCounts() 107 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in GetFractionalWeightedCounts()
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H A D | aligngivenpath.cpp | 98 unsigned &g_AlphaSize = ctx->alpha.g_AlphaSize; in ScoresFromFreqsPos() local 106 SortCounts(PP.m_fcCounts, PP.m_uSortOrder, g_AlphaSize); in ScoresFromFreqsPos() 133 for (unsigned i = 0; i < g_AlphaSize; ++i) in ScoresFromFreqsPos() 136 for (unsigned j = 0; j < g_AlphaSize; ++j) in ScoresFromFreqsPos()
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H A D | msa.cpp | 631 unsigned &g_AlphaSize = getMuscleContext()->alpha.g_AlphaSize; in UniqueResidueTypes() local 646 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in UniqueResidueTypes()
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H A D | alpha.cpp | 213 ctx->alpha.g_AlphaSize = GetAlphaSize(Alpha); in SetAlpha()
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H A D | muscle_context.h | 186 unsigned g_AlphaSize; member
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H A D | muscle.h | 264 void SortCounts(const FCOUNT fcCounts[], unsigned SortOrder[], unsigned g_AlphaSize);
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H A D | muscle_context.cpp | 224 alpha.g_AlphaSize = 0; in MuscleContext()
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/dports/biology/muscle/muscle-3.8.1551/ |
H A D | profilefrommsa.cpp | 54 for (unsigned n = 0; n < g_AlphaSize; ++n) in ListProfile() 58 for (unsigned n = 0; n < g_AlphaSize; ++n) in ListProfile() 71 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in ListProfile() 119 for (unsigned n = 0; n < g_AlphaSize; ++n) in ListProfile() 123 for (unsigned n = 0; n < g_AlphaSize; ++n) in ListProfile() 136 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in ListProfile() 162 memcpy(SortOrder, InitialSortOrder, g_AlphaSize*sizeof(unsigned)); in SortCounts() 168 for (unsigned n = 0; n < g_AlphaSize - 1; ++n) in SortCounts() 273 for (unsigned i = 0; i < g_AlphaSize; ++i) in ProfileFromMSA() 276 for (unsigned j = 0; j < g_AlphaSize; ++j) in ProfileFromMSA()
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H A D | diffobjscore.cpp | 20 if (uLetter1 >= g_AlphaSize) in ScoreColLetters() 26 if (uLetter2 >= g_AlphaSize) in ScoreColLetters() 49 if (uLetter >= g_AlphaSize) in ScoreColLetters() 56 for (unsigned uLetter1 = 0; uLetter1 < g_AlphaSize; ++uLetter1) in ScoreColLetters() 60 for (unsigned uLetter2 = uLetter1 + 1; uLetter2 < g_AlphaSize; ++uLetter2) in ScoreColLetters()
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H A D | writescorefile.cpp | 18 if (uLetter1 >= g_AlphaSize) in GetColScore() 25 if (uLetter2 >= g_AlphaSize) in GetColScore()
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H A D | alpha.cpp | 45 unsigned g_AlphaSize = 0; variable 214 g_AlphaSize = GetAlphaSize(Alpha); in SetAlpha()
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H A D | alpha.h | 98 extern unsigned g_AlphaSize;
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H A D | cons.cpp | 33 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in GetCons()
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H A D | scorepp.cpp | 10 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in ConsensusChar()
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H A D | objscore2.cpp | 103 if (uLetter1 >= g_AlphaSize) in ScoreSeqPairLetters() 106 if (uLetter2 >= g_AlphaSize) in ScoreSeqPairLetters()
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H A D | msa2.cpp | 24 memset(fcCounts, 0, g_AlphaSize*sizeof(FCOUNT)); in GetFractionalWeightedCounts() 96 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in GetFractionalWeightedCounts()
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H A D | aligngivenpath.cpp | 121 for (unsigned i = 0; i < g_AlphaSize; ++i) in ScoresFromFreqsPos() 124 for (unsigned j = 0; j < g_AlphaSize; ++j) in ScoresFromFreqsPos()
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H A D | msa.cpp | 605 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in UniqueResidueTypes()
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