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/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/umuscle/src/muscle/
H A Dhenikoffweightpb.cpp28 const unsigned uSeqCount = GetSeqCount(); in CalcHenikoffWeightsColPB() local
50 if (uCount == uSeqCount) in CalcHenikoffWeightsColPB()
82 const unsigned uSeqCount = GetSeqCount(); in SetUniformWeights() local
83 if (0 == uSeqCount) in SetUniformWeights()
94 const unsigned uSeqCount = GetSeqCount(); in SetHenikoffWeightsPB() local
96 if (0 == uSeqCount) in SetHenikoffWeightsPB()
98 else if (1 == uSeqCount) in SetHenikoffWeightsPB()
103 else if (2 == uSeqCount) in SetHenikoffWeightsPB()
123 if (VectorIsZero(m_Weights, uSeqCount)) in SetHenikoffWeightsPB()
124 VectorSet(m_Weights, uSeqCount, 1.0); in SetHenikoffWeightsPB()
[all …]
H A Dseqvect.cpp21 unsigned uSeqCount = Length(); in ToFASTAFile() local
59 unsigned uSeqCount = Length(); in PadToMSA() local
60 if (0 == uSeqCount) in PadToMSA()
106 unsigned uSeqCount = Length(); in StripGaps() local
116 unsigned uSeqCount = Length(); in StripGapsAndWhitespace() local
126 unsigned uSeqCount = Length(); in ToUpper() local
136 unsigned uSeqCount = Length(); in FindName() local
158 unsigned uSeqCount = Length(); in LogMe() local
239 if (0 == uSeqCount) in GuessAlpha()
254 if (uSeqIndex >= uSeqCount) in GuessAlpha()
[all …]
H A Dhenikoffweight.cpp22 const unsigned uSeqCount = GetSeqCount(); in CalcHenikoffWeightsCol() local
28 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in CalcHenikoffWeightsCol()
40 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in CalcHenikoffWeightsCol()
56 const unsigned uSeqCount = GetSeqCount(); in SetHenikoffWeights() local
58 if (0 == uSeqCount) in SetHenikoffWeights()
60 else if (1 == uSeqCount) in SetHenikoffWeights()
65 else if (2 == uSeqCount) in SetHenikoffWeights()
72 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in SetHenikoffWeights()
79 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in SetHenikoffWeights()
83 Normalize(m_Weights, uSeqCount); in SetHenikoffWeights()
H A Dmsa2.cpp27 const unsigned uSeqCount = GetSeqCount(); in GetFractionalWeightedCounts() local
187 const unsigned uSeqCount = msa.GetColCount(); in MSAColIsConservative() local
188 if (0 == uSeqCount) in MSAColIsConservative()
213 msaOut.SetSize(uSeqCount, uColCount); in MSAFromSeqRange()
231 const unsigned uSeqCount = msaIn.GetSeqCount(); in MSAFromColRange() local
237 msaOut.SetSize(uSeqCount, uColCount); in MSAFromColRange()
257 const unsigned uSeqCount = msa.GetSeqCount(); in SeqVectFromMSA() local
292 msaOut.SetSize(uSeqCount, uColCount); in MSAFromSeqSubset()
445 const unsigned uSeqCount = msa.GetSeqCount(); in SetClustalWWeightsMuscle() local
503 const unsigned uSeqCount = msa1.GetSeqCount(); in MSAAppend() local
[all …]
H A Dfastdistmafft.cpp126 const unsigned uSeqCount = v.Length(); in DistKmer6_6() local
128 DF.SetCount(uSeqCount); in DistKmer6_6()
129 if (0 == uSeqCount) in DistKmer6_6()
133 for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1) in DistKmer6_6()
141 unsigned **Letters = new unsigned *[uSeqCount]; in DistKmer6_6()
157 for (unsigned n = 0; n < uSeqCount; ++n) in DistKmer6_6()
159 uCommonTupleCount[n] = new unsigned[uSeqCount]; in DistKmer6_6()
163 const unsigned uPairCount = (uSeqCount*(uSeqCount + 1))/2; in DistKmer6_6()
165 for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1) in DistKmer6_6()
245 for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1) in DistKmer6_6()
[all …]
H A Dfastdistnuc.cpp114 const unsigned uSeqCount = v.Length(); in DistKmer4_6() local
116 DF.SetCount(uSeqCount); in DistKmer4_6()
117 if (0 == uSeqCount) in DistKmer4_6()
121 for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1) in DistKmer4_6()
129 unsigned **Letters = new unsigned *[uSeqCount]; in DistKmer4_6()
146 for (unsigned n = 0; n < uSeqCount; ++n) in DistKmer4_6()
148 uCommonTupleCount[n] = new unsigned[uSeqCount]; in DistKmer4_6()
152 const unsigned uPairCount = (uSeqCount*(uSeqCount + 1))/2; in DistKmer4_6()
154 for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1) in DistKmer4_6()
234 for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1) in DistKmer4_6()
[all …]
H A Dfastdistjones.cpp22 const unsigned uSeqCount = v.Length(); in DistKmer20_3() local
24 DF.SetCount(uSeqCount); in DistKmer20_3()
25 if (0 == uSeqCount) in DistKmer20_3()
27 for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1) in DistKmer20_3()
43 const unsigned uBytes = uSeqCount*sizeof(int); in DistKmer20_3()
48 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in DistKmer20_3()
97 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in DistKmer20_3()
113 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in DistKmer20_3()
124 const unsigned uSeqListBytes = uSeqCount*sizeof(unsigned); in DistKmer20_3()
166 const unsigned uTotal = (uSeqCount*(uSeqCount - 1))/2; in DistKmer20_3()
[all …]
H A Dmuscle.cpp12 const unsigned uSeqCount = v.Length(); in MUSCLE() local
14 if (0 == uSeqCount) in MUSCLE()
51 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in MUSCLE()
63 SetSeqStats(uSeqCount, uMinL, uMaxL, uTotL/uSeqCount); in MUSCLE()
65 MSA::SetIdCount(uSeqCount); in MUSCLE()
72 if (uSeqCount > 1) in MUSCLE()
75 if (0 == uSeqCount) in MUSCLE()
81 if (1 == uSeqCount && ALPHA_Amino == Alpha) in MUSCLE()
101 if (1 == ctx->params.g_uMaxIters || 2 == uSeqCount) in MUSCLE()
H A Dmsa.cpp67 m_uSeqCount = uSeqCount; in SetSize()
71 if (0 == uSeqCount && 0 == uColCount) in SetSize()
74 m_szSeqs = new char *[uSeqCount]; in SetSize()
75 m_szNames = new char *[uSeqCount]; in SetSize()
76 m_Weights = new WEIGHT[uSeqCount]; in SetSize()
328 SetSize(uSeqCount, uColCount); in Copy()
658 unsigned uSeqCount = GetSeqCount(); in GetOcc() local
659 return (double) (uSeqCount - uGapCount) / (double) uSeqCount; in GetOcc()
836 m_uCacheSeqCount = uSeqCount; in ExpandCache()
873 if (0 == uSeqCount) in GuessAlpha()
[all …]
H A Dmhack.cpp22 const unsigned uSeqCount = v.Length(); in MHackStart() local
23 M = new bool[uSeqCount]; in MHackStart()
24 memset(M, 0, uSeqCount*sizeof(bool)); in MHackStart()
25 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in MHackStart()
50 const unsigned uSeqCount = msa.GetSeqCount(); in MHackEnd() local
52 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in MHackEnd()
H A Drefinew.cpp18 const unsigned uSeqCount = msa1.GetSeqCount(); in AppendMSA() local
25 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in AppendMSA()
64 const unsigned uSeqCount = msa.GetSeqCount(); in SeqVectFromMSACols() local
65 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in SeqVectFromMSACols()
82 const unsigned uSeqCount = msaIn.GetSeqCount(); in RefineW() local
87 msaOut.SetSize(uSeqCount, uReserveColCount); in RefineW()
89 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in RefineW()
189 const unsigned uSeqCount = msa.GetSeqCount(); in DoRefineW() local
190 if (0 == uSeqCount) in DoRefineW()
193 MSA::SetIdCount(uSeqCount); in DoRefineW()
[all …]
/dports/biology/muscle/muscle-3.8.1551/
H A Dhenikoffweightpb.cpp25 const unsigned uSeqCount = GetSeqCount(); in CalcHenikoffWeightsColPB() local
47 if (uCount == uSeqCount) in CalcHenikoffWeightsColPB()
79 const unsigned uSeqCount = GetSeqCount(); in SetUniformWeights() local
80 if (0 == uSeqCount) in SetUniformWeights()
91 const unsigned uSeqCount = GetSeqCount(); in SetHenikoffWeightsPB() local
93 if (0 == uSeqCount) in SetHenikoffWeightsPB()
95 else if (1 == uSeqCount) in SetHenikoffWeightsPB()
100 else if (2 == uSeqCount) in SetHenikoffWeightsPB()
120 if (VectorIsZero(m_Weights, uSeqCount)) in SetHenikoffWeightsPB()
121 VectorSet(m_Weights, uSeqCount, 1.0); in SetHenikoffWeightsPB()
[all …]
H A Dseqvect.cpp21 unsigned uSeqCount = Length(); in ToFASTAFile() local
59 unsigned uSeqCount = Length(); in PadToMSA() local
60 if (0 == uSeqCount) in PadToMSA()
106 unsigned uSeqCount = Length(); in StripGaps() local
116 unsigned uSeqCount = Length(); in StripGapsAndWhitespace() local
126 unsigned uSeqCount = Length(); in ToUpper() local
136 unsigned uSeqCount = Length(); in FindName() local
158 unsigned uSeqCount = Length(); in LogMe() local
239 if (0 == uSeqCount) in GuessAlpha()
254 if (uSeqIndex >= uSeqCount) in GuessAlpha()
[all …]
H A Dhenikoffweight.cpp22 const unsigned uSeqCount = GetSeqCount(); in CalcHenikoffWeightsCol() local
28 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in CalcHenikoffWeightsCol()
40 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in CalcHenikoffWeightsCol()
56 const unsigned uSeqCount = GetSeqCount(); in SetHenikoffWeights() local
58 if (0 == uSeqCount) in SetHenikoffWeights()
60 else if (1 == uSeqCount) in SetHenikoffWeights()
65 else if (2 == uSeqCount) in SetHenikoffWeights()
72 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in SetHenikoffWeights()
79 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in SetHenikoffWeights()
83 Normalize(m_Weights, uSeqCount); in SetHenikoffWeights()
H A Dmsa2.cpp21 const unsigned uSeqCount = GetSeqCount(); in GetFractionalWeightedCounts() local
176 const unsigned uSeqCount = msa.GetColCount(); in MSAColIsConservative() local
177 if (0 == uSeqCount) in MSAColIsConservative()
201 msaOut.SetSize(uSeqCount, uColCount); in MSAFromSeqRange()
219 const unsigned uSeqCount = msaIn.GetSeqCount(); in MSAFromColRange() local
225 msaOut.SetSize(uSeqCount, uColCount); in MSAFromColRange()
245 const unsigned uSeqCount = msa.GetSeqCount(); in SeqVectFromMSA() local
280 msaOut.SetSize(uSeqCount, uColCount); in MSAFromSeqSubset()
419 const unsigned uSeqCount = msa.GetSeqCount(); in SetClustalWWeightsMuscle() local
472 const unsigned uSeqCount = msa1.GetSeqCount(); in MSAAppend() local
[all …]
H A Dmuscle.cpp10 const unsigned uSeqCount = v.Length(); in MUSCLE() local
12 if (0 == uSeqCount) in MUSCLE()
49 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in MUSCLE()
61 SetSeqStats(uSeqCount, uMinL, uMaxL, uTotL/uSeqCount); in MUSCLE()
63 MSA::SetIdCount(uSeqCount); in MUSCLE()
70 if (uSeqCount > 1) in MUSCLE()
73 if (0 == uSeqCount) in MUSCLE()
79 if (1 == uSeqCount && ALPHA_Amino == Alpha) in MUSCLE()
99 if (1 == g_uMaxIters || 2 == uSeqCount) in MUSCLE()
H A Dfastdistjones.cpp18 const unsigned uSeqCount = v.Length(); in DistKmer20_3() local
20 DF.SetCount(uSeqCount); in DistKmer20_3()
21 if (0 == uSeqCount) in DistKmer20_3()
23 for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1) in DistKmer20_3()
39 const unsigned uBytes = uSeqCount*sizeof(int); in DistKmer20_3()
44 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in DistKmer20_3()
93 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in DistKmer20_3()
109 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in DistKmer20_3()
120 const unsigned uSeqListBytes = uSeqCount*sizeof(unsigned); in DistKmer20_3()
162 const unsigned uTotal = (uSeqCount*(uSeqCount - 1))/2; in DistKmer20_3()
[all …]
H A Dmsa.cpp61 m_uSeqCount = uSeqCount; in SetSize()
65 if (0 == uSeqCount && 0 == uColCount) in SetSize()
68 m_szSeqs = new char *[uSeqCount]; in SetSize()
69 m_szNames = new char *[uSeqCount]; in SetSize()
70 m_Weights = new WEIGHT[uSeqCount]; in SetSize()
289 SetSize(uSeqCount, uColCount); in Copy()
617 unsigned uSeqCount = GetSeqCount(); in GetOcc() local
618 return (double) (uSeqCount - uGapCount) / (double) uSeqCount; in GetOcc()
786 m_uCacheSeqCount = uSeqCount; in ExpandCache()
821 if (0 == uSeqCount) in GuessAlpha()
[all …]
H A Dfastdistmafft.cpp116 const unsigned uSeqCount = v.Length(); in DistKmer6_6() local
118 DF.SetCount(uSeqCount); in DistKmer6_6()
119 if (0 == uSeqCount) in DistKmer6_6()
123 for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1) in DistKmer6_6()
131 unsigned **Letters = new unsigned *[uSeqCount]; in DistKmer6_6()
147 for (unsigned n = 0; n < uSeqCount; ++n) in DistKmer6_6()
149 uCommonTupleCount[n] = new unsigned[uSeqCount]; in DistKmer6_6()
153 const unsigned uPairCount = (uSeqCount*(uSeqCount + 1))/2; in DistKmer6_6()
155 for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1) in DistKmer6_6()
235 for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1) in DistKmer6_6()
[all …]
H A Dfastdistnuc.cpp100 const unsigned uSeqCount = v.Length(); in DistKmer4_6() local
102 DF.SetCount(uSeqCount); in DistKmer4_6()
103 if (0 == uSeqCount) in DistKmer4_6()
107 for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1) in DistKmer4_6()
115 unsigned **Letters = new unsigned *[uSeqCount]; in DistKmer4_6()
132 for (unsigned n = 0; n < uSeqCount; ++n) in DistKmer4_6()
134 uCommonTupleCount[n] = new unsigned[uSeqCount]; in DistKmer4_6()
138 const unsigned uPairCount = (uSeqCount*(uSeqCount + 1))/2; in DistKmer4_6()
140 for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1) in DistKmer4_6()
220 for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1) in DistKmer4_6()
[all …]
H A Ddomuscle.cpp29 const unsigned uSeqCount = v.Length(); in DoMuscle() local
31 if (0 == uSeqCount) in DoMuscle()
85 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in DoMuscle()
97 SetSeqStats(uSeqCount, uMinL, uMaxL, uTotL/uSeqCount); in DoMuscle()
101 MSA::SetIdCount(uSeqCount); in DoMuscle()
105 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in DoMuscle()
108 if (0 == uSeqCount) in DoMuscle()
110 if (1 == uSeqCount) in DoMuscle()
117 if (uSeqCount > 1) in DoMuscle()
136 if (GuideTree.GetLeafCount() != uSeqCount) in DoMuscle()
[all …]
H A Dmhack.cpp20 const unsigned uSeqCount = v.Length(); in MHackStart() local
21 M = new bool[uSeqCount]; in MHackStart()
22 memset(M, 0, uSeqCount*sizeof(bool)); in MHackStart()
23 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in MHackStart()
44 const unsigned uSeqCount = msa.GetSeqCount(); in MHackEnd() local
46 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in MHackEnd()
H A Drefinew.cpp17 const unsigned uSeqCount = msa1.GetSeqCount(); in AppendMSA() local
24 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in AppendMSA()
63 const unsigned uSeqCount = msa.GetSeqCount(); in SeqVectFromMSACols() local
64 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in SeqVectFromMSACols()
74 const unsigned uSeqCount = msaIn.GetSeqCount(); in RefineW() local
79 msaOut.SetSize(uSeqCount, uReserveColCount); in RefineW()
81 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in RefineW()
179 const unsigned uSeqCount = msa.GetSeqCount(); in DoRefineW() local
180 if (0 == uSeqCount) in DoRefineW()
183 MSA::SetIdCount(uSeqCount); in DoRefineW()
[all …]
H A Dsubfam.cpp138 const unsigned uSeqCount = vAll.GetSeqCount(); in AlignSubFam() local
143 unsigned *Leaves = new unsigned[uSeqCount]; in AlignSubFam()
204 const unsigned uSeqCount = v.Length(); in ProgAlignSubFams() local
206 if (0 == uSeqCount) in ProgAlignSubFams()
278 SetSeqStats(uSeqCount, uMinL, uMaxL, uTotL/uSeqCount); in ProgAlignSubFams()
282 MSA::SetIdCount(uSeqCount); in ProgAlignSubFams()
289 if (uSeqCount > 1) in ProgAlignSubFams()
292 if (0 == uSeqCount) in ProgAlignSubFams()
298 if (1 == uSeqCount && ALPHA_Amino == Alpha) in ProgAlignSubFams()
322 unsigned *SubFams = new unsigned[uSeqCount]; in ProgAlignSubFams()
[all …]
H A Dfastdistkbit.cpp70 const unsigned uSeqCount = v.Length(); in DistKbit20_3() local
71 DF.SetCount(uSeqCount); in DistKbit20_3()
77 const unsigned uBytes = uSeqCount*1000; in DistKbit20_3()
82 for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) in DistKbit20_3()
86 const unsigned uTotal = (uSeqCount*(uSeqCount - 1))/2; in DistKbit20_3()
87 for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount; ++uSeqIndex1) in DistKbit20_3()

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