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Searched refs:g_AlphaSize (Results 1 – 24 of 24) sorted by relevance

/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/umuscle/src/muscle/
H A Dprofilefrommsa.cpp62 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()
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H A Ddiffobjscore.cpp18 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()
H A Dwritescorefile.cpp12 unsigned &g_AlphaSize = d->alpha.g_AlphaSize; in GetColScore() local
23 if (uLetter1 >= g_AlphaSize) in GetColScore()
30 if (uLetter2 >= g_AlphaSize) in GetColScore()
H A Dcons.cpp34 unsigned &g_AlphaSize = ctx->alpha.g_AlphaSize; in GetCons() local
37 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in GetCons()
H A Dscorepp.cpp11 unsigned &g_AlphaSize = ctx->alpha.g_AlphaSize; in ConsensusChar() local
19 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in ConsensusChar()
H A Dobjscore2.cpp47 unsigned &g_AlphaSize = ctx->alpha.g_AlphaSize; in ScoreSeqPairLetters() local
106 if (uLetter1 >= g_AlphaSize) in ScoreSeqPairLetters()
109 if (uLetter2 >= g_AlphaSize) in ScoreSeqPairLetters()
H A Dmsa2.cpp30 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()
H A Daligngivenpath.cpp98 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()
H A Dmsa.cpp631 unsigned &g_AlphaSize = getMuscleContext()->alpha.g_AlphaSize; in UniqueResidueTypes() local
646 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in UniqueResidueTypes()
H A Dalpha.cpp213 ctx->alpha.g_AlphaSize = GetAlphaSize(Alpha); in SetAlpha()
H A Dmuscle_context.h186 unsigned g_AlphaSize; member
H A Dmuscle.h264 void SortCounts(const FCOUNT fcCounts[], unsigned SortOrder[], unsigned g_AlphaSize);
H A Dmuscle_context.cpp224 alpha.g_AlphaSize = 0; in MuscleContext()
/dports/biology/muscle/muscle-3.8.1551/
H A Dprofilefrommsa.cpp54 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()
H A Ddiffobjscore.cpp20 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()
H A Dwritescorefile.cpp18 if (uLetter1 >= g_AlphaSize) in GetColScore()
25 if (uLetter2 >= g_AlphaSize) in GetColScore()
H A Dalpha.cpp45 unsigned g_AlphaSize = 0; variable
214 g_AlphaSize = GetAlphaSize(Alpha); in SetAlpha()
H A Dalpha.h98 extern unsigned g_AlphaSize;
H A Dcons.cpp33 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in GetCons()
H A Dscorepp.cpp10 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in ConsensusChar()
H A Dobjscore2.cpp103 if (uLetter1 >= g_AlphaSize) in ScoreSeqPairLetters()
106 if (uLetter2 >= g_AlphaSize) in ScoreSeqPairLetters()
H A Dmsa2.cpp24 memset(fcCounts, 0, g_AlphaSize*sizeof(FCOUNT)); in GetFractionalWeightedCounts()
96 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in GetFractionalWeightedCounts()
H A Daligngivenpath.cpp121 for (unsigned i = 0; i < g_AlphaSize; ++i) in ScoresFromFreqsPos()
124 for (unsigned j = 0; j < g_AlphaSize; ++j) in ScoresFromFreqsPos()
H A Dmsa.cpp605 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) in UniqueResidueTypes()