| /dports/biology/muscle/muscle-3.8.1551/ |
| H A D | params.cpp | 119 DISTANCE g_Distance1 = DISTANCE_Kmer6_6; variable
204 Log("Distance method (1) %s\n", DISTANCEToStr(g_Distance1)); in ListParams()
235 g_Distance1 = DISTANCE_Kmer6_6; in SetDefaultsLE()
252 g_Distance1 = DISTANCE_Kmer6_6; in SetDefaultsSP()
269 g_Distance1 = DISTANCE_Kmer6_6; in SetDefaultsSV()
304 g_Distance1 = DISTANCE_Kmer4_6; in SetDefaultsSPN_DNA()
322 g_Distance1 = DISTANCE_Kmer4_6; in SetDefaultsSPN_RNA()
420 EnumParam("Distance", DISTANCE_Opts, (int *) &g_Distance1); in SetPPCommandLineParams()
423 EnumParam("Distance1", DISTANCE_Opts, (int *) &g_Distance1); in SetPPCommandLineParams()
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| H A D | muscle.cpp | 43 g_Distance1 = DISTANCE_Kmer4_6; in MUSCLE()
88 TreeFromSeqVect(v, GuideTree, g_Cluster1, g_Distance1, g_Root1); in MUSCLE()
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| H A D | params.h | 101 extern DISTANCE g_Distance1;
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| H A D | local.cpp | 22 TreeFromMSA(msa, tree, g_Cluster1, g_Distance1, g_Root1); in ProfileFromMSALocal()
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| H A D | subfam.cpp | 260 g_Distance1 = DISTANCE_Kmer4_6; in ProgAlignSubFams()
306 TreeFromSeqVect(v, GuideTree, g_Cluster1, g_Distance1, g_Root1); in ProgAlignSubFams()
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| H A D | domuscle.cpp | 154 TreeFromSeqVect(v, GuideTree, g_Cluster1, g_Distance1, g_Root1, in DoMuscle()
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| /dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/umuscle/src/muscle/ |
| H A D | params.cpp | 114 ctx->params.g_Distance1 = DISTANCE_Kmer6_6; in SetDefaultsLE()
132 ctx->params.g_Distance1 = DISTANCE_Kmer6_6; in SetDefaultsSP()
150 ctx->params.g_Distance1 = DISTANCE_Kmer6_6; in SetDefaultsSV()
187 ctx->params.g_Distance1 = DISTANCE_Kmer4_6; in SetDefaultsSPN_DNA()
207 ctx->params.g_Distance1 = DISTANCE_Kmer4_6; in SetDefaultsSPN_RNA()
309 EnumParam("Distance", DISTANCE_Opts, (int *) &ctx->params.g_Distance1); in SetPPCommandLineParams()
312 EnumParam("Distance1", DISTANCE_Opts, (int *) &ctx->params.g_Distance1); in SetPPCommandLineParams()
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| H A D | muscle.cpp | 45 ctx->params.g_Distance1 = DISTANCE_Kmer4_6; in MUSCLE()
90 …TreeFromSeqVect(v, GuideTree, ctx->params.g_Cluster1, ctx->params.g_Distance1, ctx->params.g_Root1… in MUSCLE()
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| H A D | local.cpp | 24 TreeFromMSA(msa, tree, ctx->params.g_Cluster1, ctx->params.g_Distance1, ctx->params.g_Root1); in ProfileFromMSALocal()
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| H A D | subfam.cpp | 263 ctx->params.g_Distance1 = DISTANCE_Kmer4_6; in ProgAlignSubFams()
309 …TreeFromSeqVect(v, GuideTree, ctx->params.g_Cluster1, ctx->params.g_Distance1, ctx->params.g_Root1… in ProgAlignSubFams()
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| H A D | domuscle.cpp | 158 …TreeFromSeqVect(v, GuideTree, ctx->params.g_Cluster1, ctx->params.g_Distance1, ctx->params.g_Root1, in DoMuscle()
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| H A D | muscle_context.h | 58 DISTANCE g_Distance1; member
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| H A D | muscle_context.cpp | 199 params.g_Distance1 = DISTANCE_Kmer6_6; in MuscleContext()
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| /dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/umuscle/src/ |
| H A D | MuscleAdapter.cpp | 115 …TreeFromSeqVect(v, GuideTree, ctx->params.g_Cluster1, ctx->params.g_Distance1, ctx->params.g_Root1… in alignUnsafe()
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| H A D | MuscleParallel.cpp | 199 …TreeFromSeqVect(v, GuideTree, ctx->params.g_Cluster1, ctx->params.g_Distance1, ctx->params.g_Root1… in alignPrepareUnsafe()
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