/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/umuscle/src/muscle/ |
H A D | objscore2.cpp | 50 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() [all …]
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H A D | msa.cpp | 68 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() [all …]
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H A D | anchors.cpp | 90 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()
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H A D | henikoffweightpb.cpp | 73 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()
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H A D | objscoreda.cpp | 89 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()
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H A D | stabilize.cpp | 7 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()
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H A D | msa2.cpp | 28 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() [all …]
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H A D | makerootmsa.cpp | 166 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()
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H A D | refinevert.cpp | 18 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()
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H A D | cons.cpp | 72 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()
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H A D | fasta.cpp | 28 const unsigned uColCount = GetColCount(); in ToFASTAFile() local 29 assert(uColCount > 0); in ToFASTAFile() 42 unsigned uLetters = uColCount - uLine*FASTA_BLOCK; in ToFASTAFile()
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/dports/biology/muscle/muscle-3.8.1551/ |
H A D | objscore2.cpp | 44 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() [all …]
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H A D | msa.cpp | 62 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() [all …]
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H A D | anchors.cpp | 88 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()
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H A D | fasta.cpp | 16 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()
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H A D | msa2.cpp | 22 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() [all …]
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H A D | henikoffweightpb.cpp | 70 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()
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H A D | objscoreda.cpp | 89 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()
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H A D | refinevert.cpp | 17 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()
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H A D | stabilize.cpp | 7 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()
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H A D | makerootmsa.cpp | 166 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()
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H A D | cons.cpp | 68 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()
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H A D | refinew.cpp | 75 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()
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/dports/biology/ugene/ugene-40.1/src/libs_3rdparty/qscore/src/qscore/ |
H A D | qscore_msa_qscore.cpp | 57 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()
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/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/umuscle/src/ |
H A D | refinevertP.cpp | 38 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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