/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/umuscle/src/muscle/ |
H A D | msf.cpp | 39 const unsigned uColCount = GetColCount(); in GetGCGCheckSum() 52 const int ColCount = a.GetColCount(); in MSFFixGaps() 77 GetColCount(), seqtype); in ToMSFFile() 95 GetColCount(), GetGCGCheckSum(uSeqIndex), GetSeqWeight(uSeqIndex)); in ToMSFFile() 98 if (0 == GetColCount()) in ToMSFFile() 101 unsigned uLineCount = (GetColCount() - 1)/uCharsPerLine + 1; in ToMSFFile() 107 if (uEndColIndex >= GetColCount()) in ToMSFFile() 108 uEndColIndex = GetColCount() - 1; in ToMSFFile()
|
H A D | progalign.cpp | 67 Node.m_uLength = Node.m_MSA.GetColCount(); in ProgressiveAlignE() 135 unsigned uLength = Parent.m_MSA.GetColCount(); in ProgressiveAlignE() 143 ListProfile(Node1.m_Prof, Node1.m_MSA.GetColCount(), &Node1.m_MSA); in ProgressiveAlignE() 145 ListProfile(P1, Node1.m_MSA.GetColCount(), &Node1.m_MSA); in ProgressiveAlignE() 147 AssertProfsEq(Node1.m_Prof, Node1.m_uLength, P1, Node1.m_MSA.GetColCount()); in ProgressiveAlignE() 150 ListProfile(Node2.m_Prof, Node2.m_MSA.GetColCount(), &Node2.m_MSA); in ProgressiveAlignE() 156 ListProfile(P2, Node2.m_MSA.GetColCount(), &Node2.m_MSA); in ProgressiveAlignE() 158 AssertProfsEq(Node2.m_Prof, Node2.m_uLength, P2, Node2.m_MSA.GetColCount()); in ProgressiveAlignE() 169 ListProfile(TmpProf, Parent.m_MSA.GetColCount(), &Parent.m_MSA); in ProgressiveAlignE() 173 TmpProf, Parent.m_MSA.GetColCount()); in ProgressiveAlignE()
|
H A D | objscore2.cpp | 50 const unsigned uColCount = msa1.GetColCount(); in ScoreSeqPairLetters() 51 const unsigned uColCount2 = msa2.GetColCount(); in ScoreSeqPairLetters() 125 const unsigned uColCount = msa1.GetColCount(); in ScoreSeqPairGaps() 126 const unsigned uColCount2 = msa2.GetColCount(); in ScoreSeqPairGaps() 253 const unsigned uColCount = msa.GetColCount(); in ObjScoreSP() 319 const unsigned uColCount = msa1.GetColCount(); in ObjScoreDP() 320 if (msa2.GetColCount() != uColCount) in ObjScoreDP() 323 const unsigned uColCount1 = msa1.GetColCount(); in ObjScoreDP() 433 const unsigned uColCount = msa.GetColCount(); in ObjScorePS() 490 const unsigned uColCount1 = msa1.GetColCount(); in ObjScoreXP() [all …]
|
H A D | msa.cpp | 102 if (0 == GetColCount()) in LogMe() 114 unsigned iEnd = GetColCount(); in LogMe() 125 Log(" %-10u", GetColCount()); in LogMe() 292 for (unsigned n = 0; n < GetColCount(); ++n) in HasGap() 311 assert(uFromCol < GetColCount()); in CopyCol() 312 assert(uToCol < GetColCount()); in CopyCol() 478 assert(uColIndex < GetColCount()); in GetCharCount() 587 const unsigned uColCount = GetColCount(); in GetSeqLength() 603 const unsigned uColCount = GetColCount(); in GetPWID() 633 assert(uColIndex < GetColCount()); in UniqueResidueTypes() [all …]
|
H A D | msa2.cpp | 28 const unsigned uColCount = GetColCount(); in GetFractionalWeightedCounts() 166 if (uColIndex > 0 && uColIndex < GetColCount() - 1) in GetFractionalWeightedCounts() 187 const unsigned uSeqCount = msa.GetColCount(); in MSAColIsConservative() 212 const unsigned uColCount = msaIn.GetColCount(); in MSAFromSeqRange() 232 const unsigned uInColCount = msaIn.GetColCount(); in MSAFromColRange() 279 if (uColIndex >= msa.GetColCount()) in DeleteGappedCols() 291 const unsigned uColCount = msaIn.GetColCount(); in MSAFromSeqSubset() 505 const unsigned uColCount1 = msa1.GetColCount(); in MSAAppend() 506 const unsigned uColCount2 = msa2.GetColCount(); in MSAAppend() 529 const unsigned uColCount1 = msa1.GetColCount(); in MSACat() [all …]
|
H A D | html.cpp | 16 const unsigned uColCount = a.GetColCount(); in MakeColors() 87 unsigned uLineCount = (GetColCount() - 1)/uCharsPerLine + 1; in ToHTMLFile() 94 if (uEndColIndex >= GetColCount()) in ToHTMLFile() 95 uEndColIndex = GetColCount() - 1; in ToHTMLFile()
|
H A D | profile.cpp | 68 uLength1 = msa1.GetColCount(); in ProfileProfile() 69 uLength2 = msa2.GetColCount(); in ProfileProfile() 105 Progress("%u seqs %u cols", msa1.GetSeqCount(), msa1.GetColCount()); in Profile() 109 Progress("%u seqs %u cols", msa2.GetSeqCount(), msa2.GetColCount()); in Profile()
|
H A D | cons.cpp | 17 for (unsigned uColIndex = 0; uColIndex < GetColCount(); ++uColIndex) in GetAvgCons() 72 const unsigned uColCount = GetColCount(); in GetPctIdentityPair() 97 const unsigned uColCount = GetColCount(); in GetPctGroupIdentityPair()
|
H A D | aligntwomsas.cpp | 11 const unsigned uLengthA = msa1.GetColCount(); in AlignTwoMSAs() 12 const unsigned uLengthB = msa2.GetColCount(); in AlignTwoMSAs()
|
H A D | fasta.cpp | 28 const unsigned uColCount = GetColCount(); in ToFASTAFile() 30 const unsigned uLinesPerSeq = (GetColCount() - 1)/FASTA_BLOCK + 1; in ToFASTAFile()
|
/dports/biology/muscle/muscle-3.8.1551/ |
H A D | msf.cpp | 36 const unsigned uColCount = GetColCount(); in GetGCGCheckSum() 49 const int ColCount = a.GetColCount(); in MSFFixGaps() 73 GetColCount(), seqtype); in ToMSFFile() 91 GetColCount(), GetGCGCheckSum(uSeqIndex), GetSeqWeight(uSeqIndex)); in ToMSFFile() 94 if (0 == GetColCount()) in ToMSFFile() 97 unsigned uLineCount = (GetColCount() - 1)/uCharsPerLine + 1; in ToMSFFile() 103 if (uEndColIndex >= GetColCount()) in ToMSFFile() 104 uEndColIndex = GetColCount() - 1; in ToMSFFile()
|
H A D | progalign.cpp | 64 Node.m_uLength = Node.m_MSA.GetColCount(); in ProgressiveAlignE() 132 unsigned uLength = Parent.m_MSA.GetColCount(); in ProgressiveAlignE() 140 ListProfile(Node1.m_Prof, Node1.m_MSA.GetColCount(), &Node1.m_MSA); in ProgressiveAlignE() 142 ListProfile(P1, Node1.m_MSA.GetColCount(), &Node1.m_MSA); in ProgressiveAlignE() 144 AssertProfsEq(Node1.m_Prof, Node1.m_uLength, P1, Node1.m_MSA.GetColCount()); in ProgressiveAlignE() 147 ListProfile(Node2.m_Prof, Node2.m_MSA.GetColCount(), &Node2.m_MSA); in ProgressiveAlignE() 153 ListProfile(P2, Node2.m_MSA.GetColCount(), &Node2.m_MSA); in ProgressiveAlignE() 155 AssertProfsEq(Node2.m_Prof, Node2.m_uLength, P2, Node2.m_MSA.GetColCount()); in ProgressiveAlignE() 166 ListProfile(TmpProf, Parent.m_MSA.GetColCount(), &Parent.m_MSA); in ProgressiveAlignE() 170 TmpProf, Parent.m_MSA.GetColCount()); in ProgressiveAlignE()
|
H A D | objscore2.cpp | 44 const unsigned uColCount = msa1.GetColCount(); in ScoreSeqPairLetters() 45 const unsigned uColCount2 = msa2.GetColCount(); in ScoreSeqPairLetters() 118 const unsigned uColCount = msa1.GetColCount(); in ScoreSeqPairGaps() 119 const unsigned uColCount2 = msa2.GetColCount(); in ScoreSeqPairGaps() 243 const unsigned uColCount = msa.GetColCount(); in ObjScoreSP() 309 const unsigned uColCount = msa1.GetColCount(); in ObjScoreDP() 310 if (msa2.GetColCount() != uColCount) in ObjScoreDP() 313 const unsigned uColCount1 = msa1.GetColCount(); in ObjScoreDP() 314 const unsigned uColCount2 = msa2.GetColCount(); in ObjScoreDP() 415 const unsigned uColCount = msa.GetColCount(); in ObjScorePS() [all …]
|
H A D | msa.cpp | 96 if (0 == GetColCount()) in LogMe() 108 unsigned iEnd = GetColCount(); in LogMe() 119 Log(" %-10u", GetColCount()); in LogMe() 253 for (unsigned n = 0; n < GetColCount(); ++n) in HasGap() 272 assert(uFromCol < GetColCount()); in CopyCol() 273 assert(uToCol < GetColCount()); in CopyCol() 439 assert(uColIndex < GetColCount()); in GetCharCount() 548 const unsigned uColCount = GetColCount(); in GetSeqLength() 564 const unsigned uColCount = GetColCount(); in GetPWID() 592 assert(uColIndex < GetColCount()); in UniqueResidueTypes() [all …]
|
H A D | msa2.cpp | 22 const unsigned uColCount = GetColCount(); in GetFractionalWeightedCounts() 155 if (uColIndex > 0 && uColIndex < GetColCount() - 1) in GetFractionalWeightedCounts() 176 const unsigned uSeqCount = msa.GetColCount(); in MSAColIsConservative() 200 const unsigned uColCount = msaIn.GetColCount(); in MSAFromSeqRange() 220 const unsigned uInColCount = msaIn.GetColCount(); in MSAFromColRange() 267 if (uColIndex >= msa.GetColCount()) in DeleteGappedCols() 279 const unsigned uColCount = msaIn.GetColCount(); in MSAFromSeqSubset() 474 const unsigned uColCount1 = msa1.GetColCount(); in MSAAppend() 475 const unsigned uColCount2 = msa2.GetColCount(); in MSAAppend() 499 const unsigned uColCount1 = msa1.GetColCount(); in MSACat() [all …]
|
H A D | profile.cpp | 66 uLength1 = msa1.GetColCount(); in ProfileProfile() 67 uLength2 = msa2.GetColCount(); in ProfileProfile() 101 Progress("%u seqs %u cols", msa1.GetSeqCount(), msa1.GetColCount()); in Profile() 105 Progress("%u seqs %u cols", msa2.GetSeqCount(), msa2.GetColCount()); in Profile()
|
H A D | html.cpp | 16 const unsigned uColCount = a.GetColCount(); in MakeColors() 87 unsigned uLineCount = (GetColCount() - 1)/uCharsPerLine + 1; in ToHTMLFile() 94 if (uEndColIndex >= GetColCount()) in ToHTMLFile() 95 uEndColIndex = GetColCount() - 1; in ToHTMLFile()
|
H A D | cons.cpp | 16 for (unsigned uColIndex = 0; uColIndex < GetColCount(); ++uColIndex) in GetAvgCons() 68 const unsigned uColCount = GetColCount(); in GetPctIdentityPair() 93 const unsigned uColCount = GetColCount(); in GetPctGroupIdentityPair()
|
H A D | refinew.cpp | 19 const unsigned uColCount1 = msa1.GetColCount(); in AppendMSA() 20 const unsigned uColCount2 = msa2.GetColCount(); in AppendMSA() 75 const unsigned uColCount = msaIn.GetColCount(); in RefineW() 125 unsigned uOutCols = msaOut.GetColCount(); in RefineW()
|
H A D | aligntwomsas.cpp | 11 const unsigned uLengthA = msa1.GetColCount(); in AlignTwoMSAs() 12 const unsigned uLengthB = msa2.GetColCount(); in AlignTwoMSAs()
|
H A D | fasta.cpp | 30 const unsigned uColCount = GetColCount(); in ToFASTAFile() 32 const unsigned uLinesPerSeq = (GetColCount() - 1)/FASTA_BLOCK + 1; in ToFASTAFile()
|
/dports/editors/libreoffice/libreoffice-7.2.6.2/sw/source/uibase/table/ |
H A D | tablemgr.cxx | 64 if(aCols.Count() == GetColCount()) in GetColWidth() 78 SwTwips nRValid = nNum < GetColCount() ? in GetColWidth() 96 if ( GetColCount() > 0 ) in GetMaxColWidth() 106 if(nNum == GetColCount()) in GetMaxColWidth() 125 if(aCols.Count() != GetColCount()) in SetColWidth() 132 else if( nNum < GetColCount() ) in SetColWidth() 329 sal_uInt16 SwTableFUNC::GetColCount() const in GetColCount() function in SwTableFUNC 340 OSL_ENSURE( nNum < static_cast<int>(GetColCount()) ,"Index out of range"); in GetRightSeparator()
|
/dports/editors/libreoffice6/libreoffice-6.4.7.2/sw/source/uibase/table/ |
H A D | tablemgr.cxx | 71 if(aCols.Count() == GetColCount()) in GetColWidth() 85 SwTwips nRValid = nNum < GetColCount() ? in GetColWidth() 103 if ( GetColCount() > 0 ) in GetMaxColWidth() 113 if(nNum == GetColCount()) in GetMaxColWidth() 132 if(aCols.Count() != GetColCount()) in SetColWidth() 139 else if( nNum < GetColCount() ) in SetColWidth() 340 sal_uInt16 SwTableFUNC::GetColCount() const in GetColCount() function in SwTableFUNC 351 OSL_ENSURE( nNum < static_cast<int>(GetColCount()) ,"Index out of range"); in GetRightSeparator()
|
/dports/editors/libreoffice/libreoffice-7.2.6.2/sw/source/ui/vba/ |
H A D | vbatablehelper.cxx | 165 sal_Int32 SwVbaTableHelper::GetColCount( SwTabCols const & rCols ) in GetColCount() function in SwVbaTableHelper 176 OSL_ENSURE( nNum < GetColCount( rCols ) ,"Index out of range"); in GetRightSeparator() 205 if(rCols.Count() == static_cast<size_t>(GetColCount( rCols ))) in GetColWidth() 220 SwTwips nRValid = nNum < GetColCount( rCols ) ? in GetColWidth() 255 else if( nCol < GetColCount( aCols ) ) in SetColWidth()
|
/dports/editors/libreoffice6/libreoffice-6.4.7.2/sw/source/ui/vba/ |
H A D | vbatablehelper.cxx | 165 sal_Int32 SwVbaTableHelper::GetColCount( SwTabCols const & rCols ) in GetColCount() function in SwVbaTableHelper 176 OSL_ENSURE( nNum < GetColCount( rCols ) ,"Index out of range"); in GetRightSeparator() 205 if(rCols.Count() == static_cast<size_t>(GetColCount( rCols ))) in GetColWidth() 220 SwTwips nRValid = nNum < GetColCount( rCols ) ? in GetColWidth() 255 else if( nCol < GetColCount( aCols ) ) in SetColWidth()
|