/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/align/ngalign/ |
H A D | alignment_scorer.hpp | 75 void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope); 87 void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope); 96 void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope); 105 void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope); 114 void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope); 126 void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope); 138 void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope); 150 void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope); 162 void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope);
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H A D | sequence_set.hpp | 97 const CAlignResultsSet& Alignments, int Threshold); 120 const CAlignResultsSet& Alignments, int Threshold); 126 const CAlignResultsSet& Alignments, int Threshold); 145 const CAlignResultsSet& Alignments, int Threshold); 152 const CAlignResultsSet& Alignments, int Threshold); 175 const CAlignResultsSet& Alignments, int Threshold);
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/dports/security/clamav-lts/clamav-0.103.5/libclamav/c++/llvm/lib/Target/ |
H A D | TargetData.cpp | 244 if (Alignments[i].AlignType == align_type && in setAlignment() 247 Alignments[i].ABIAlign = abi_align; in setAlignment() 248 Alignments[i].PrefAlign = pref_align; in setAlignment() 266 if (Alignments[i].AlignType == AlignType && in getAlignmentInfo() 267 Alignments[i].TypeBitWidth == BitWidth) in getAlignmentInfo() 268 return ABIInfo ? Alignments[i].ABIAlign : Alignments[i].PrefAlign; in getAlignmentInfo() 276 Alignments[i].TypeBitWidth < Alignments[BestMatchIdx].TypeBitWidth)) in getAlignmentInfo() 281 Alignments[i].TypeBitWidth > Alignments[LargestInt].TypeBitWidth) in getAlignmentInfo() 429 const TargetAlignElem &AI = Alignments[i]; in getStringRepresentation() 551 if (Alignments[i].AlignType == STACK_ALIGN) in getCallFrameTypeAlignment() [all …]
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/dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/src/tigr/ |
H A D | postnuc.cc | 175 CurrAp = Alignments.end( ) - 1; in extendClusters() 182 assert(TargetAp >= Alignments.begin()); in extendClusters() 183 assert(TargetAp <= Alignments.end()); in extendClusters() 237 parseDelta(Alignments, Aseq, Bseq, Blen); in extendClusters() 267 if ( TargetAp != Alignments.end( ) ) in extendBackward() 315 Alignments.pop_back( ); in extendBackward() 606 (std::vector<Alignment> & Alignments, in parseDelta() argument 626 for ( Ap = Alignments.begin( ); Ap != Alignments.end( ); ++Ap) { in parseDelta() 768 for ( Ap = Alignments.begin( ); Ap < Alignments.end( ); Ap ++ ) { in validateData() 779 for ( Ap = Alignments.begin( ); Ap < Alignments.end( ); ++Ap) { in validateData() [all …]
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H A D | postpro.cc | 159 vector<Alignment> & Alignments, 184 vector<Alignment> & Alignments, 559 Alignments.push_back (Align); in addNewAlignment() 648 Alignments.pop_back( ); in extendBackward() 945 vector<Alignment> & Alignments, in flushAlignments() argument 962 for ( Ap = Alignments.begin( ); Ap < Alignments.end( ); Ap ++ ) in flushAlignments() 978 Alignments.clear( ); in flushAlignments() 1175 Ap = Alignments.end( ); in getReverseTargetAlignment() 1304 for ( Ap = Alignments.begin( ); Ap < Alignments.end( ); Ap ++ ) in parseDelta() 1643 for ( Ap = Alignments.begin( ); Ap < Alignments.end( ); Ap ++ ) in validateData() [all …]
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/dports/finance/weberp/webERP/ |
H A D | FormDesigner.php | 60 $Alignments = array(); // Possible alignments 61 $Alignments['left']['Caption'] = _('Left'); 62 $Alignments['left']['Title'] = _('Text lines are rendered flush left'); 63 $Alignments['centre']['Caption'] = _('Centre'); 64 $Alignments['centre']['Title'] = _('Text lines are centred'); 65 $Alignments['right']['Caption'] = _('Right'); 66 $Alignments['right']['Title'] = _('Text lines are rendered flush right'); 67 $Alignments['full']['Caption'] = _('Justify'); 68 $Alignments['full']['Title'] = _('Text lines are justified to both margins'); 70 foreach ($Alignments as $AlignmentValue => $AlignmentOption) {
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/dports/biology/py-biopython/biopython-1.79/Tests/Hmmer/ |
H A D | text_31b2_hmmscan_001.out | 136 Alignments for each domain: 148 Alignments for each domain: 165 Alignments for each domain: 183 Alignments for each domain: 202 Alignments for each domain: 221 Alignments for each domain: 240 Alignments for each domain: 259 Alignments for each domain: 278 Alignments for each domain: 302 Alignments for each domain: [all …]
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H A D | text_31b2_hmmsearch_002.out | 40 Alignments for each domain: 53 Alignments for each domain: 71 Alignments for each domain: 83 Alignments for each domain: 96 Alignments for each domain: 116 Alignments for each domain: 143 Alignments for each domain: 174 Alignments for each domain: 193 Alignments for each domain: 211 Alignments for each domain: [all …]
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/dports/biology/viennarna/ViennaRNA-2.4.18/doc/latex/ |
H A D | group__file__formats__msa.tex | 2 \label{group__file__formats__msa}\index{Multiple Sequence Alignments@{Multiple Sequence Alignments}} 13 Collaboration diagram for Multiple Sequence Alignments\+: 100 \index{Multiple Sequence Alignments@{Multiple Sequence Alignments}!VRNA\_FILE\_FORMAT\_MSA\_FASTA@{… 117 \index{Multiple Sequence Alignments@{Multiple Sequence Alignments}!VRNA\_FILE\_FORMAT\_MSA\_MAF@{VR… 118 …SA\_MAF@{VRNA\_FILE\_FORMAT\_MSA\_MAF}!Multiple Sequence Alignments@{Multiple Sequence Alignments}} 134 \index{Multiple Sequence Alignments@{Multiple Sequence Alignments}!VRNA\_FILE\_FORMAT\_MSA\_MIS@{VR… 135 …SA\_MIS@{VRNA\_FILE\_FORMAT\_MSA\_MIS}!Multiple Sequence Alignments@{Multiple Sequence Alignments}} 268 \index{Multiple Sequence Alignments@{Multiple Sequence Alignments}!vrna\_file\_msa\_read@{vrna\_fil… 269 …ile\_msa\_read@{vrna\_file\_msa\_read}!Multiple Sequence Alignments@{Multiple Sequence Alignments}} 428 \index{Multiple Sequence Alignments@{Multiple Sequence Alignments}!vrna\_file\_msa\_write@{vrna\_fi… [all …]
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/dports/devel/gh/cli-2.4.0/vendor/github.com/yuin/goldmark/extension/ast/ |
H A D | table.go | 45 Alignments []Alignment member 53 for i, alignment := range n.Alignments { 56 if i != len(n.Alignments)-1 { 75 Alignments: []Alignment{}, 82 Alignments []Alignment member 106 Alignments []Alignment member
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/dports/devel/liteide/liteide-x37.4/liteidex/vendor/github.com/yuin/goldmark/extension/ast/ |
H A D | table.go | 45 Alignments []Alignment member 53 for i, alignment := range n.Alignments { 56 if i != len(n.Alignments)-1 { 75 Alignments: []Alignment{}, 82 Alignments []Alignment member 106 Alignments []Alignment member
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/dports/sysutils/chezmoi/chezmoi-2.9.3/vendor/github.com/yuin/goldmark/extension/ast/ |
H A D | table.go | 45 Alignments []Alignment member 53 for i, alignment := range n.Alignments { 56 if i != len(n.Alignments)-1 { 75 Alignments: []Alignment{}, 82 Alignments []Alignment member 106 Alignments []Alignment member
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/dports/www/gohugo/hugo-0.91.2/vendor/github.com/yuin/goldmark/extension/ast/ |
H A D | table.go | 45 Alignments []Alignment member 53 for i, alignment := range n.Alignments { 56 if i != len(n.Alignments)-1 { 75 Alignments: []Alignment{}, 82 Alignments []Alignment member 106 Alignments []Alignment member
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/dports/www/gitea/gitea-1.16.5/vendor/github.com/yuin/goldmark/extension/ast/ |
H A D | table.go | 45 Alignments []Alignment member 53 for i, alignment := range n.Alignments { 56 if i != len(n.Alignments)-1 { 75 Alignments: []Alignment{}, 82 Alignments []Alignment member 106 Alignments []Alignment member
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/dports/www/mattermost-server/mattermost-server-6.0.2/vendor/github.com/yuin/goldmark/extension/ast/ |
H A D | table.go | 45 Alignments []Alignment member 53 for i, alignment := range n.Alignments { 56 if i != len(n.Alignments)-1 { 75 Alignments: []Alignment{}, 82 Alignments []Alignment member 106 Alignments []Alignment member
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/dports/sysutils/glow/glow-0.2.0/vendor/github.com/yuin/goldmark/extension/ast/ |
H A D | table.go | 45 Alignments []Alignment member 53 for i, alignment := range n.Alignments { 56 if i != len(n.Alignments)-1 { 75 Alignments: []Alignment{}, 82 Alignments []Alignment member 106 Alignments []Alignment member
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/id_mapper/app/ |
H A D | id_mapper_app.cpp | 415 CRef<CSeq_align_set> Alignments(new CSeq_align_set); in x_HandleAlignments() local 435 Alignments->Set().insert(Alignments->Set().end(), in x_HandleAlignments() 445 Alignments->Set().insert(Alignments->Set().end(), in x_HandleAlignments() 455 Alignments->Set().push_back(Align); in x_HandleAlignments() 466 Alignments->Set().insert(Alignments->Set().end(), in x_HandleAlignments() 477 Alignments->Set().insert(Alignments->Set().end(), in x_HandleAlignments() 487 Alignments->Set().push_back(Align); in x_HandleAlignments() 492 if(Alignments->Get().empty()) { in x_HandleAlignments() 500 if(Alignments->Get().empty()) in x_HandleAlignments() 505 Alignments->Set()) { in x_HandleAlignments() [all …]
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/dports/biology/hmmer/hmmer-3.3/easel/demotic/examples/ |
H A D | example.phmmer.out | 43 Alignments for each domain: 66 Alignments for each domain: 85 Alignments for each domain: 104 Alignments for each domain: 123 Alignments for each domain: 142 Alignments for each domain: 160 Alignments for each domain: 173 Alignments for each domain: 192 Alignments for each domain: 211 Alignments for each domain: [all …]
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/dports/biology/infernal/infernal-1.1.3/easel/demotic/examples/ |
H A D | example.phmmer.out | 43 Alignments for each domain: 66 Alignments for each domain: 85 Alignments for each domain: 104 Alignments for each domain: 123 Alignments for each domain: 142 Alignments for each domain: 160 Alignments for each domain: 173 Alignments for each domain: 192 Alignments for each domain: 211 Alignments for each domain: [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/ngalign/ |
H A D | sequence_set.cpp | 167 const CAlignResultsSet& Alignments, int Threshold) in GetGiList() argument 171 if(Alignments.QueryExists(**IdIter)) { in GetGiList() 172 CConstRef<CQuerySet> QuerySet = Alignments.GetQuerySet(**IdIter); in GetGiList() 416 if(Alignments.QueryExists(**IdIter)) { in CreateQueryFactory() 417 CConstRef<CQuerySet> QuerySet = Alignments.GetQuerySet(**IdIter); in CreateQueryFactory() 498 const CAlignResultsSet& Alignments, int Threshold) in GetGiList() argument 507 if(Alignments.QueryExists(*Id)) { in GetGiList() 508 CConstRef<CQuerySet> QuerySet = Alignments.GetQuerySet(*Id); in GetGiList() 595 if(Alignments.QueryExists(*Id)) { in CreateQueryFactory() 596 CConstRef<CQuerySet> QuerySet = Alignments.GetQuerySet(*Id); in CreateQueryFactory() [all …]
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/dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/include/mummer/ |
H A D | postnuc.hh | 235 std::vector<Alignment>& Alignments) const; 250 std::vector<Alignment>::iterator getReverseTargetAlignment(std::vector<Alignment> & Alignments, 252 void parseDelta(std::vector<Alignment> & Alignments, 264 void printDeltaAlignments(const std::vector<Alignment>& Alignments, 270 inline void printDeltaAlignments(const std::vector<Alignment>& Alignments, in printDeltaAlignments() argument 273 printDeltaAlignments(Alignments, Af.Id(), Af.len(), Bf.Id(), Bf.len(), DeltaFile); in printDeltaAlignments() 278 void printSAMAlignments(const std::vector<Alignment>& Alignments, 290 const std::vector<Alignment> & Alignments, std::vector<Alignment>::const_iterator Ap); 416 void printSAMAlignments(const std::vector<Alignment>& Alignments, in printSAMAlignments() argument 420 const char* mapq = Alignments.size() > 1 ? "\t10\t" : "\t30\t"; in printSAMAlignments() [all …]
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/dports/devel/llvm-devel/llvm-project-f05c95f10fc1d8171071735af8ad3a9e87633120/llvm/tools/llvm-lipo/ |
H A D | llvm-lipo.cpp | 532 auto Alignment = Alignments.find(Slice.getArchString()); in updateAlignments() 533 if (Alignment != Alignments.end()) in updateAlignments() 544 for (StringRef Arch : Alignments.keys()) in checkUnusedAlignments() 555 const StringMap<const uint32_t> &Alignments, in buildSlices() argument 598 updateAlignments(Slices, Alignments); in buildSlices() 611 buildSlices(InputBinaries, Alignments, ExtractedObjects); in createUniversalBinary() 613 checkUnusedAlignments(Slices, Alignments); in createUniversalBinary() 677 updateAlignments(SlicesMapRange, Alignments); in buildReplacementSlices() 683 const StringMap<const uint32_t> &Alignments, in replaceSlices() argument 697 buildReplacementSlices(ReplacementBinaries, Alignments); in replaceSlices() [all …]
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/dports/lang/rust/rustc-1.58.1-src/src/llvm-project/llvm/tools/llvm-lipo/ |
H A D | llvm-lipo.cpp | 532 auto Alignment = Alignments.find(Slice.getArchString()); in updateAlignments() 533 if (Alignment != Alignments.end()) in updateAlignments() 544 for (StringRef Arch : Alignments.keys()) in checkUnusedAlignments() 555 const StringMap<const uint32_t> &Alignments, in buildSlices() argument 598 updateAlignments(Slices, Alignments); in buildSlices() 611 buildSlices(InputBinaries, Alignments, ExtractedObjects); in createUniversalBinary() 613 checkUnusedAlignments(Slices, Alignments); in createUniversalBinary() 639 buildSlices(InputBinaries, Alignments, ExtractedObjects); in extractSlice() 677 updateAlignments(SlicesMapRange, Alignments); in buildReplacementSlices() 698 buildReplacementSlices(ReplacementBinaries, Alignments); in replaceSlices() [all …]
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/dports/devel/wasi-compiler-rt12/llvm-project-12.0.1.src/llvm/tools/llvm-lipo/ |
H A D | llvm-lipo.cpp | 532 auto Alignment = Alignments.find(Slice.getArchString()); in updateAlignments() 533 if (Alignment != Alignments.end()) in updateAlignments() 544 for (StringRef Arch : Alignments.keys()) in checkUnusedAlignments() 555 const StringMap<const uint32_t> &Alignments, in buildSlices() argument 598 updateAlignments(Slices, Alignments); in buildSlices() 611 buildSlices(InputBinaries, Alignments, ExtractedObjects); in createUniversalBinary() 613 checkUnusedAlignments(Slices, Alignments); in createUniversalBinary() 639 buildSlices(InputBinaries, Alignments, ExtractedObjects); in extractSlice() 677 updateAlignments(SlicesMapRange, Alignments); in buildReplacementSlices() 698 buildReplacementSlices(ReplacementBinaries, Alignments); in replaceSlices() [all …]
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/dports/devel/wasi-compiler-rt13/llvm-project-13.0.1.src/llvm/tools/llvm-lipo/ |
H A D | llvm-lipo.cpp | 532 auto Alignment = Alignments.find(Slice.getArchString()); in updateAlignments() 533 if (Alignment != Alignments.end()) in updateAlignments() 544 for (StringRef Arch : Alignments.keys()) in checkUnusedAlignments() 555 const StringMap<const uint32_t> &Alignments, in buildSlices() argument 598 updateAlignments(Slices, Alignments); in buildSlices() 611 buildSlices(InputBinaries, Alignments, ExtractedObjects); in createUniversalBinary() 613 checkUnusedAlignments(Slices, Alignments); in createUniversalBinary() 639 buildSlices(InputBinaries, Alignments, ExtractedObjects); in extractSlice() 677 updateAlignments(SlicesMapRange, Alignments); in buildReplacementSlices() 698 buildReplacementSlices(ReplacementBinaries, Alignments); in replaceSlices() [all …]
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