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/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/umuscle/src/muscle/
H A Dobjscore2.cpp50 const unsigned uColCount = msa1.GetColCount(); in ScoreSeqPairLetters() local
52 if (uColCount != uColCount2) in ScoreSeqPairLetters()
60 msaTmp.SetSize(2, uColCount); in ScoreSeqPairLetters()
84 unsigned uColEnd = uColCount - 1; in ScoreSeqPairLetters()
125 const unsigned uColCount = msa1.GetColCount(); in ScoreSeqPairGaps() local
127 if (uColCount != uColCount2) in ScoreSeqPairGaps()
135 msaTmp.SetSize(2, uColCount); in ScoreSeqPairGaps()
161 unsigned uColEnd = uColCount - 1; in ScoreSeqPairGaps()
253 const unsigned uColCount = msa.GetColCount(); in ObjScoreSP() local
320 if (msa2.GetColCount() != uColCount) in ObjScoreDP()
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H A Dmsa.cpp68 m_uCacheSeqLength = uColCount; in SetSize()
71 if (0 == uSeqCount && 0 == uColCount) in SetSize()
86 m_szSeqs[uSeqIndex][uColCount] = 0; in SetSize()
328 SetSize(uSeqCount, uColCount); in Copy()
491 assert(m_uColCount == uColCount || in CopySeq()
497 m_uColCount = uColCount; in CopySeq()
766 msaOut.SetSize(uIdCount, uColCount); in MSASubsetByIds()
837 m_uCacheSeqLength = uColCount; in ExpandCache()
838 m_uColCount = uColCount; in ExpandCache()
882 unsigned uSeqIndex = i/uColCount; in GuessAlpha()
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H A Danchors.cpp90 const unsigned uColCount = msa.GetColCount(); in FindBestColsCombo() local
93 for (unsigned uIndex = 0; uIndex < uColCount; ++uIndex) in FindBestColsCombo()
192 const unsigned uColCount = msa.GetColCount(); in FindAnchorCols() local
193 if (uColCount < 16) in FindAnchorCols()
199 SCORE *MatchScore = new SCORE[uColCount]; in FindAnchorCols()
200 SCORE *SmoothScore = new SCORE[uColCount]; in FindAnchorCols()
201 unsigned *BestCols = new unsigned[uColCount]; in FindAnchorCols()
204 static_WindowSmooth(MatchScore, uColCount, ctx->params.g_uSmoothWindowLength, SmoothScore, in FindAnchorCols()
H A Dhenikoffweightpb.cpp73 const unsigned uColCount = GetColCount(); in IsGapSeq() local
74 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in IsGapSeq()
93 const unsigned uColCount = GetColCount(); in SetHenikoffWeightsPB() local
113 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in SetHenikoffWeightsPB()
H A Dobjscoreda.cpp89 const unsigned uColCount = msa1.GetColCount(); in ScoreSeqPair() local
91 if (uColCount != uColCount2) in ScoreSeqPair()
97 for (unsigned i = 0; i < uColCount; ++i) in ScoreSeqPair()
101 for (unsigned i = 0; i < uColCount; ++i) in ScoreSeqPair()
113 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in ScoreSeqPair()
158 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in ScoreSeqPair()
232 LogGap(uGapStartCol, uColCount - 1, uGapLength, false, true); in ScoreSeqPair()
H A Dstabilize.cpp7 const unsigned uColCount = msa.GetColCount(); in Stabilize() local
9 msaStable.SetSize(uSeqCount, uColCount); in Stabilize()
15 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in Stabilize()
H A Dmsa2.cpp28 const unsigned uColCount = GetColCount(); in GetFractionalWeightedCounts() local
127 if (uColCount - 1 == uColIndex) in GetFractionalWeightedCounts()
212 const unsigned uColCount = msaIn.GetColCount(); in MSAFromSeqRange() local
213 msaOut.SetSize(uSeqCount, uColCount); in MSAFromSeqRange()
220 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in MSAFromSeqRange()
234 if (uFromColIndex + uColCount - 1 > uInColCount) in MSAFromColRange()
237 msaOut.SetSize(uSeqCount, uColCount); in MSAFromColRange()
246 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in MSAFromColRange()
291 const unsigned uColCount = msaIn.GetColCount(); in MSAFromSeqSubset() local
292 msaOut.SetSize(uSeqCount, uColCount); in MSAFromSeqSubset()
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H A Dmakerootmsa.cpp166 unsigned uColCount = uInsane; in MakeRootMSA() local
208 if (uInsane == uColCount) in MakeRootMSA()
210 uColCount = sRootE.Length(); in MakeRootMSA()
211 a.SetSize(uSeqCount, uColCount); in MakeRootMSA()
215 assert(uColCount == sRootE.Length()); in MakeRootMSA()
219 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in MakeRootMSA()
H A Drefinevert.cpp18 static void ListVertSavings(unsigned uColCount, unsigned uAnchorColCount, in ListVertSavings() argument
24 double dTotalArea = uColCount*uColCount; in ListVertSavings()
37 unsigned uColCount, Range Ranges[]) in ColsToRanges() argument
47 unsigned uBestColRight = uColCount; in ColsToRanges()
H A Dcons.cpp72 const unsigned uColCount = GetColCount(); in GetPctIdentityPair() local
75 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in GetPctIdentityPair()
97 const unsigned uColCount = GetColCount(); in GetPctGroupIdentityPair() local
100 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in GetPctGroupIdentityPair()
H A Dfasta.cpp28 const unsigned uColCount = GetColCount(); in ToFASTAFile() local
29 assert(uColCount > 0); in ToFASTAFile()
42 unsigned uLetters = uColCount - uLine*FASTA_BLOCK; in ToFASTAFile()
/dports/biology/muscle/muscle-3.8.1551/
H A Dobjscore2.cpp44 const unsigned uColCount = msa1.GetColCount(); in ScoreSeqPairLetters() local
46 if (uColCount != uColCount2) in ScoreSeqPairLetters()
54 msaTmp.SetSize(2, uColCount); in ScoreSeqPairLetters()
81 unsigned uColEnd = uColCount - 1; in ScoreSeqPairLetters()
118 const unsigned uColCount = msa1.GetColCount(); in ScoreSeqPairGaps() local
120 if (uColCount != uColCount2) in ScoreSeqPairGaps()
128 msaTmp.SetSize(2, uColCount); in ScoreSeqPairGaps()
154 unsigned uColEnd = uColCount - 1; in ScoreSeqPairGaps()
243 const unsigned uColCount = msa.GetColCount(); in ObjScoreSP() local
310 if (msa2.GetColCount() != uColCount) in ObjScoreDP()
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H A Dmsa.cpp62 m_uCacheSeqLength = uColCount; in SetSize()
65 if (0 == uSeqCount && 0 == uColCount) in SetSize()
80 m_szSeqs[uSeqIndex][uColCount] = 0; in SetSize()
289 SetSize(uSeqCount, uColCount); in Copy()
452 assert(m_uColCount == uColCount || in CopySeq()
458 m_uColCount = uColCount; in CopySeq()
771 char *Seq = new char[uColCount]; in ExpandCache()
774 memset(Seq, '?', uColCount); in ExpandCache()
787 m_uCacheSeqLength = uColCount; in ExpandCache()
788 m_uColCount = uColCount; in ExpandCache()
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H A Danchors.cpp88 const unsigned uColCount = msa.GetColCount(); in FindBestColsCombo() local
91 for (unsigned uIndex = 0; uIndex < uColCount; ++uIndex) in FindBestColsCombo()
108 const unsigned uColCount = msa.GetColCount(); in ListBestCols() local
116 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in ListBestCols()
189 const unsigned uColCount = msa.GetColCount(); in FindAnchorCols() local
190 if (uColCount < 16) in FindAnchorCols()
196 SCORE *MatchScore = new SCORE[uColCount]; in FindAnchorCols()
197 SCORE *SmoothScore = new SCORE[uColCount]; in FindAnchorCols()
198 unsigned *BestCols = new unsigned[uColCount]; in FindAnchorCols()
201 WindowSmooth(MatchScore, uColCount, g_uSmoothWindowLength, SmoothScore, in FindAnchorCols()
H A Dfasta.cpp16 unsigned uColCount = uInsane; in FromFASTAFile() local
30 const unsigned uColCount = GetColCount(); in ToFASTAFile() local
31 assert(uColCount > 0); in ToFASTAFile()
44 unsigned uLetters = uColCount - uLine*FASTA_BLOCK; in ToFASTAFile()
H A Dmsa2.cpp22 const unsigned uColCount = GetColCount(); in GetFractionalWeightedCounts() local
116 if (uColCount - 1 == uColIndex) in GetFractionalWeightedCounts()
200 const unsigned uColCount = msaIn.GetColCount(); in MSAFromSeqRange() local
201 msaOut.SetSize(uSeqCount, uColCount); in MSAFromSeqRange()
208 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in MSAFromSeqRange()
222 if (uFromColIndex + uColCount - 1 > uInColCount) in MSAFromColRange()
225 msaOut.SetSize(uSeqCount, uColCount); in MSAFromColRange()
234 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in MSAFromColRange()
279 const unsigned uColCount = msaIn.GetColCount(); in MSAFromSeqSubset() local
280 msaOut.SetSize(uSeqCount, uColCount); in MSAFromSeqSubset()
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H A Dhenikoffweightpb.cpp70 const unsigned uColCount = GetColCount(); in IsGapSeq() local
71 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in IsGapSeq()
90 const unsigned uColCount = GetColCount(); in SetHenikoffWeightsPB() local
110 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in SetHenikoffWeightsPB()
H A Dobjscoreda.cpp89 const unsigned uColCount = msa1.GetColCount(); in ScoreSeqPair() local
91 if (uColCount != uColCount2) in ScoreSeqPair()
97 for (unsigned i = 0; i < uColCount; ++i) in ScoreSeqPair()
101 for (unsigned i = 0; i < uColCount; ++i) in ScoreSeqPair()
113 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in ScoreSeqPair()
158 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in ScoreSeqPair()
232 LogGap(uGapStartCol, uColCount - 1, uGapLength, false, true); in ScoreSeqPair()
H A Drefinevert.cpp17 static void ListVertSavings(unsigned uColCount, unsigned uAnchorColCount, in ListVertSavings() argument
22 double dTotalArea = uColCount*uColCount; in ListVertSavings()
35 unsigned uColCount, Range Ranges[]) in ColsToRanges() argument
45 unsigned uBestColRight = uColCount; in ColsToRanges()
H A Dstabilize.cpp7 const unsigned uColCount = msa.GetColCount(); in Stabilize() local
9 msaStable.SetSize(uSeqCount, uColCount); in Stabilize()
15 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in Stabilize()
H A Dmakerootmsa.cpp166 unsigned uColCount = uInsane; in MakeRootMSA() local
207 if (uInsane == uColCount) in MakeRootMSA()
209 uColCount = sRootE.Length(); in MakeRootMSA()
210 a.SetSize(uSeqCount, uColCount); in MakeRootMSA()
214 assert(uColCount == sRootE.Length()); in MakeRootMSA()
218 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in MakeRootMSA()
H A Dcons.cpp68 const unsigned uColCount = GetColCount(); in GetPctIdentityPair() local
71 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in GetPctIdentityPair()
93 const unsigned uColCount = GetColCount(); in GetPctGroupIdentityPair() local
96 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in GetPctGroupIdentityPair()
H A Drefinew.cpp75 const unsigned uColCount = msaIn.GetColCount(); in RefineW() local
78 const unsigned uReserveColCount = (uColCount*120)/100; in RefineW()
87 const unsigned uWindowCount = (uColCount + g_uRefineWindow - 1)/g_uRefineWindow; in RefineW()
107 if (uColTo >= uColCount) in RefineW()
108 uColTo = uColCount - 1; in RefineW()
/dports/biology/ugene/ugene-40.1/src/libs_3rdparty/qscore/src/qscore/
H A Dqscore_msa_qscore.cpp57 void MSA_QScore::ExpandCache(unsigned uSeqCount, unsigned uColCount) in ExpandCache() argument
59 if (m_uSeqCount > 0 && uColCount != m_uColCount) in ExpandCache()
73 char *Seq = new char[uColCount]; in ExpandCache()
76 memset(Seq, '?', uColCount); in ExpandCache()
87 m_uColCount = uColCount; in ExpandCache()
132 const unsigned uColCount = GetColCount(); in GetPairMap() local
133 for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) in GetPairMap()
/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/umuscle/src/
H A DrefinevertP.cpp38 static void ListVertSavings(unsigned uColCount, unsigned uAnchorColCount, in ListVertSavings() argument
44 double dTotalArea = uColCount*uColCount; in ListVertSavings()
57 unsigned uColCount, Range Ranges[]) in ColsToRanges() argument
67 unsigned uBestColRight = uColCount; in ColsToRanges()

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