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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/align/ngalign/
H A Dalignment_scorer.hpp75 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);
H A Dsequence_set.hpp97 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);
/dports/security/clamav-lts/clamav-0.103.5/libclamav/c++/llvm/lib/Target/
H A DTargetData.cpp244 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()
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/dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/src/tigr/
H A Dpostnuc.cc175 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()
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H A Dpostpro.cc159 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()
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/dports/finance/weberp/webERP/
H A DFormDesigner.php60 $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) {
/dports/biology/py-biopython/biopython-1.79/Tests/Hmmer/
H A Dtext_31b2_hmmscan_001.out136 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:
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H A Dtext_31b2_hmmsearch_002.out40 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:
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/dports/biology/viennarna/ViennaRNA-2.4.18/doc/latex/
H A Dgroup__file__formats__msa.tex2 \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…
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/dports/devel/gh/cli-2.4.0/vendor/github.com/yuin/goldmark/extension/ast/
H A Dtable.go45 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
/dports/devel/liteide/liteide-x37.4/liteidex/vendor/github.com/yuin/goldmark/extension/ast/
H A Dtable.go45 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
/dports/sysutils/chezmoi/chezmoi-2.9.3/vendor/github.com/yuin/goldmark/extension/ast/
H A Dtable.go45 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
/dports/www/gohugo/hugo-0.91.2/vendor/github.com/yuin/goldmark/extension/ast/
H A Dtable.go45 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
/dports/www/gitea/gitea-1.16.5/vendor/github.com/yuin/goldmark/extension/ast/
H A Dtable.go45 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
/dports/www/mattermost-server/mattermost-server-6.0.2/vendor/github.com/yuin/goldmark/extension/ast/
H A Dtable.go45 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
/dports/sysutils/glow/glow-0.2.0/vendor/github.com/yuin/goldmark/extension/ast/
H A Dtable.go45 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
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/id_mapper/app/
H A Did_mapper_app.cpp415 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()
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/dports/biology/hmmer/hmmer-3.3/easel/demotic/examples/
H A Dexample.phmmer.out43 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:
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/dports/biology/infernal/infernal-1.1.3/easel/demotic/examples/
H A Dexample.phmmer.out43 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:
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/ngalign/
H A Dsequence_set.cpp167 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()
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/dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/include/mummer/
H A Dpostnuc.hh235 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()
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/dports/devel/llvm-devel/llvm-project-f05c95f10fc1d8171071735af8ad3a9e87633120/llvm/tools/llvm-lipo/
H A Dllvm-lipo.cpp532 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()
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/dports/lang/rust/rustc-1.58.1-src/src/llvm-project/llvm/tools/llvm-lipo/
H A Dllvm-lipo.cpp532 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()
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/dports/devel/wasi-compiler-rt12/llvm-project-12.0.1.src/llvm/tools/llvm-lipo/
H A Dllvm-lipo.cpp532 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()
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/dports/devel/wasi-compiler-rt13/llvm-project-13.0.1.src/llvm/tools/llvm-lipo/
H A Dllvm-lipo.cpp532 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()
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