/dports/textproc/py-textdistance/textdistance-4.2.2/textdistance/algorithms/ |
H A D | base.py | 19 def __call__(self, *sequences): argument 23 def maximum(*sequences): argument 28 def distance(self, *sequences): argument 31 return self(*sequences) 38 return self.maximum(*sequences) - self.distance(*sequences) 86 if not sequences: 92 if not all(sequences): 125 return sequences 134 return sequences 172 return self.maximum(*sequences) - self.similarity(*sequences) [all …]
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H A D | token_based.py | 43 sequences = self._get_counters(*sequences) # sets 74 sequences = self._get_counters(*sequences) # sets 102 sequences = self._get_counters(*sequences) # sets 105 sequences = [self._count_counters(s) for s in sequences] # ints 114 s1, s2 = sequences 142 sequences = self._get_counters(*sequences) # sets 145 sequences = [self._count_counters(s) for s in sequences] # ints 169 sequences = self._get_counters(*sequences) # sets 172 sequences = [self._count_counters(s) for s in sequences] # ints 228 sequences = self._get_sequences(*sequences) [all …]
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H A D | sequence_based.py | 67 if not all(sequences): 70 c = sequences[0][-1] 71 sequences = [s[:-1] for s in sequences] 75 ss = sequences[:i] + (s[:-1], ) + sequences[i + 1:] 80 if not sequences: 82 sequences = self._get_sequences(*sequences) 83 if len(sequences) == 2: 114 if not all(sequences): 116 length = len(sequences) 122 sequences = self._get_sequences(*sequences) [all …]
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H A D | simple.py | 21 def __call__(self, *sequences): argument 22 if not sequences: 24 sequences = self._get_sequences(*sequences) 28 s = sequences[0] 36 return len(self(*sequences)) 42 def __call__(self, *sequences): argument 43 s = sequences[0] 44 sequences = [reversed(s) for s in sequences] 65 def maximum(self, *sequences): argument 93 if sequences in self.mat: [all …]
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/dports/biology/py-biopython/biopython-1.79/Tests/ |
H A D | test_SeqIO.py | 636 sequences = [ 657 sequences, 664 sequences = [ 711 sequences = [ 765 sequences = [ 819 sequences = [ 1367 sequences = [ 1417 sequences = [ 1492 sequences = [ 1544 sequences = [ [all …]
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/dports/biology/emboss/EMBOSS-6.6.0/doc/programs/master/emboss/apps/inc/ |
H A D | needleall.output | 7 Alignment score (21.5) is less than minimum score(40.0) for sequences Illumina_Genomici_DNA_Adapter… 8 Alignment score (24.5) is less than minimum score(40.0) for sequences Illumina_Genomic_DNA_Adapters… 9 Alignment score (31.0) is less than minimum score(40.0) for sequences Illumina_Genomic_DNA_PCR_Prim… 10 Alignment score (25.5) is less than minimum score(40.0) for sequences Illumina_Genomic_DNA_PCR_Prim… 18 Alignment score (14.5) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters1_… 19 Alignment score (24.5) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters1_… 20 Alignment score (12.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters2_… 21 Alignment score (12.0) is less than minimum score(40.0) for sequences Illumina_DpnII_Gex_Adapters2_… 30 Alignment score (12.0) is less than minimum score(40.0) for sequences Illumina_Small_RNA_RT_Primer … 31 Alignment score (23.5) is less than minimum score(40.0) for sequences Illumina_Small_RNA_5p_Adapter… [all …]
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/dports/math/reduce/Reduce-svn5758-src/jlisp/android/AndroidReduce/src/uk/ac/cam/aa582/structures/reducible/ |
H A D | WrapperExpression.java | 17 return sequences[0]; in getLeftmostSequence() 20 return sequences[sequences.length-1]; in getRightmostSequence() 23 Sequence[] sequences; field in WrapperExpression 26 this.sequences = sequences; in WrapperExpression() 28 for(int i=0; i<sequences.length-1;i++){ in WrapperExpression() 29 sequences[i].setRightSequence(sequences[i+1]); in WrapperExpression() 30 sequences[i+1].setLeftSequence(sequences[i]); in WrapperExpression() 44 if(sequences == null) return ll.iterator(); in iterator() 45 for(int i=0; i<sequences.length; i++){ in iterator() 46 ll.add(sequences[i]); in iterator() [all …]
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Tools/ |
H A D | Lucy.pm | 279 $self->{sequences}{$name}{beg_clear} = $5; 280 $self->{sequences}{$name}{end_clear} = $6; 317 …@slice = @vals[$self->{sequences}{$name}{beg_clear} - 1 .. $self->{sequences}{$name}{end_clear} - … 319 $self->{sequences}{$name}{quality} = $vals; 352 …$self->{sequences}{$1}{full_length} = 1 if $self->{sequences}{$1}; # will show cleavage info for r… 382 delete $self->{sequences}{$1}; 448 my @keys = sort keys %{$self->{sequences}}; 464 return $self->{sequences}{$key}{sequence}; 480 return $self->{sequences}{$key}{quality}; 513 return $self->{sequences}{$key}{direction} if $self->{sequences}{$key}{direction}; [all …]
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/dports/biology/cd-hit/cdhit-4.8.1/cd-hit-auxtools/ |
H A D | bioSequence.hxx | 55 Min::Array<Sequence*> sequences; member in SequenceCache 76 for(int i=0,n=sequences.Size(); i<n; i++) delete sequences[i]; in Clear() 77 sequences.Clear(); in Clear() 82 size_t Count()const{ return sequences.Size(); } in Count() 88 Min::Array<Sequence*> sequences; member in SequenceList 100 for(int i=0,n=sequences.Size(); i<n; i++) delete sequences[i]; in Clear() 101 sequences.Clear(); in Clear() 109 int i, N = sequences.Size(); in MaxLength() 112 if( sequences[i]->Length() > max_length ) max_length = sequences[i]->Length(); in MaxLength() 117 int i, N = sequences.Size(); in MinLength() [all …]
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H A D | bioSequence.cxx | 112 if( max > 0 && (int)sequences.Size() >= max ) return sequences.Size(); in Update() 125 return sequences.Size(); in Update() 201 int N = sequences.Size(); in SortByLength() 214 sorting[id] = sequences[i]; in SortByLength() 217 sequences.Swap( sorting ); in SortByLength() 224 delete sequences[i]; in RemoveEmptySequences() 227 sequences[M++] = sequences[i]; in RemoveEmptySequences() 229 sequences.Resize( M ); in RemoveEmptySequences() 233 int i, N = sequences.Size(); in Shuffle() 238 sequences[i] = sequences[rnd]; in Shuffle() [all …]
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/dports/biology/velvet/velvet_1.2.10/src/ |
H A D | run2.c | 81 ReadSet *sequences = NULL; in main() local 445 convertSequences(sequences); in main() 463 convertSequences(sequences); in main() 518 convertSequences(sequences); in main() 570 if (sequences == NULL) { in main() 575 convertSequences(sequences); in main() 588 sequences, in main() 595 sequences, in main() 604 if (sequences->readCount > 0 && sequences->categories[0] == REFERENCE) in main() 611 sequences); in main() [all …]
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/dports/graphics/blender/blender-2.91.0/release/scripts/addons/power_sequencer/operators/utils/ |
H A D | functions.py | 55 for s in sequences: 114 for s in context.sequences: 145 sequences = [ 158 return sequences 180 def get_channel_range(sequences): argument 238 if not sequences: 323 context.sequences, 331 context.sequences, 375 for s in sequences: 399 for s in sequences: [all …]
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/dports/databases/pgloader3/lparallel-20160825-git/src/cognate/ |
H A D | pquantifier.lisp | 33 (defun pquantifier (quantifier predicate sequences bail) 34 (with-parsed-options (sequences size parts-hint) 44 (defun pevery (predicate &rest sequences) 52 (defun psome (predicate &rest sequences) 59 (pquantifier #'some (ensure-function predicate) sequences t)) 61 (defun pnotevery (predicate &rest sequences) 67 (declare (dynamic-extent sequences)) 68 (not (apply #'pevery predicate sequences))) 70 (defun pnotany (predicate &rest sequences) 76 (declare (dynamic-extent sequences)) [all …]
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/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/VelvetAPI/ |
H A D | VelvetGraph.cc | 4 sequences = importReadSet( VUtils::getCharFileName(seqFileName) ); in VelvetGraph() 5 convertSequences( sequences ); in VelvetGraph() 10 sequences = importReadSet( VUtils::getCharFileName(seqFileName) ); in VelvetGraph() 11 convertSequences( sequences ); in VelvetGraph() 37 ShortLength* sequenceLengths = getSequenceLengths( sequences, getWordLength(graph) ); in correct() 38 correctGraph( graph, sequenceLengths, sequences->categories ); in correct() 56 if (sequences->readCount > 0 && sequences->categories[0] == REFERENCE){ in removeNodes() 87 readCoherentGraph( graph, isUniqueSolexa, expectedCoverage, sequences ); in scaffoldingWithSinglePeakMode() 90 createReadPairingArray(sequences); in scaffoldingWithSinglePeakMode() 93 detachDubiousReads( sequences, dubious ); in scaffoldingWithSinglePeakMode() [all …]
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/dports/games/libretro-scummvm/scummvm-7b1e929/engines/lastexpress/game/ |
H A D | beetle.cpp | 65 _data->sequences.push_back(loadSequence("BW045.seq")); in load() 68 _data->sequences.push_back(loadSequence("BW090.seq")); in load() 71 _data->sequences.push_back(loadSequence("BW135.seq")); in load() 74 _data->sequences.push_back(loadSequence("BW180.seq")); in load() 80 _data->sequences.push_back(loadSequence("BW270.seq")); in load() 83 _data->sequences.push_back(loadSequence("BW315.seq")); in load() 97 for (uint i = 0; i < _data->sequences.size(); i++) { in load() 98 if (!_data->sequences[i]->isLoaded()) { in load() 476 _data->currentSequence = _data->sequences[index]; in updateData() 480 if (!_data->sequences[index]) in updateData() [all …]
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/dports/games/scummvm/scummvm-2.5.1/engines/lastexpress/game/ |
H A D | beetle.cpp | 65 _data->sequences.push_back(loadSequence("BW045.seq")); in load() 68 _data->sequences.push_back(loadSequence("BW090.seq")); in load() 71 _data->sequences.push_back(loadSequence("BW135.seq")); in load() 74 _data->sequences.push_back(loadSequence("BW180.seq")); in load() 80 _data->sequences.push_back(loadSequence("BW270.seq")); in load() 83 _data->sequences.push_back(loadSequence("BW315.seq")); in load() 97 for (uint i = 0; i < _data->sequences.size(); i++) { in load() 98 if (!_data->sequences[i]->isLoaded()) { in load() 476 _data->currentSequence = _data->sequences[index]; in updateData() 480 if (!_data->sequences[index]) in updateData() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/alignment_free/ |
H A D | test_alignment_free.cpp | 63 clear(sequences); in alfTestHelperGetSequences() 64 appendValue(sequences, seqIID1); in alfTestHelperGetSequences() 65 appendValue(sequences, seqIID2); in alfTestHelperGetSequences() 72 StringSet<Dna5String> sequences; in SEQAN_DEFINE_TEST() local 90 clear(sequences); in SEQAN_DEFINE_TEST() 91 appendValue(sequences, seq1); in SEQAN_DEFINE_TEST() 92 appendValue(sequences, seq2); in SEQAN_DEFINE_TEST() 143 modelMM0.build(sequences); in SEQAN_DEFINE_TEST() 147 modelMM1.build(sequences); in SEQAN_DEFINE_TEST() 170 modelMM0.build(sequences); in SEQAN_DEFINE_TEST() [all …]
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/dports/biology/py-biopython/biopython-1.79/Tests/Emboss/ |
H A D | no_oligo.primer3 | 5 # primer_0377 sequences/draft_stitched.fasta 13 # primer_0274 sequences/draft_stitched.fasta 21 # primer_0579 sequences/draft_stitched.fasta 29 # primer_0681 sequences/draft_stitched.fasta 37 # primer_0244 sequences/draft_stitched.fasta 45 # primer_0099 sequences/draft_stitched.fasta 53 # primer_0095 sequences/draft_stitched.fasta 61 # primer_0399 sequences/draft_stitched.fasta 69 # primer_0022 sequences/draft_stitched.fasta 77 # primer_0354 sequences/draft_stitched.fasta [all …]
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/dports/www/firefox-esr/firefox-91.8.0/testing/web-platform/meta/encoding/streams/ |
H A D | decode-non-utf8.any.js.ini | 2 [TextDecoderStream should be able to reject invalid sequences in Shift_JIS] 5 [TextDecoderStream should be able to decode invalid sequences in Shift_JIS] 8 [TextDecoderStream should be able to reject invalid sequences in UTF-16LE] 11 [TextDecoderStream should be able to reject invalid sequences in UTF-16BE] 17 [TextDecoderStream should be able to decode invalid sequences in UTF-16LE] 23 [TextDecoderStream should be able to decode invalid sequences in UTF-16BE] 46 [TextDecoderStream should be able to reject invalid sequences in Shift_JIS] 52 [TextDecoderStream should be able to reject invalid sequences in UTF-16LE] 55 [TextDecoderStream should be able to reject invalid sequences in UTF-16BE] 61 [TextDecoderStream should be able to decode invalid sequences in UTF-16LE] [all …]
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/dports/www/firefox/firefox-99.0/testing/web-platform/meta/encoding/streams/ |
H A D | decode-non-utf8.any.js.ini | 2 [TextDecoderStream should be able to reject invalid sequences in Shift_JIS] 5 [TextDecoderStream should be able to decode invalid sequences in Shift_JIS] 8 [TextDecoderStream should be able to reject invalid sequences in UTF-16LE] 11 [TextDecoderStream should be able to reject invalid sequences in UTF-16BE] 17 [TextDecoderStream should be able to decode invalid sequences in UTF-16LE] 23 [TextDecoderStream should be able to decode invalid sequences in UTF-16BE] 46 [TextDecoderStream should be able to reject invalid sequences in Shift_JIS] 52 [TextDecoderStream should be able to reject invalid sequences in UTF-16LE] 55 [TextDecoderStream should be able to reject invalid sequences in UTF-16BE] 61 [TextDecoderStream should be able to decode invalid sequences in UTF-16LE] [all …]
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/dports/mail/thunderbird/thunderbird-91.8.0/testing/web-platform/meta/encoding/streams/ |
H A D | decode-non-utf8.any.js.ini | 2 [TextDecoderStream should be able to reject invalid sequences in Shift_JIS] 5 [TextDecoderStream should be able to decode invalid sequences in Shift_JIS] 8 [TextDecoderStream should be able to reject invalid sequences in UTF-16LE] 11 [TextDecoderStream should be able to reject invalid sequences in UTF-16BE] 17 [TextDecoderStream should be able to decode invalid sequences in UTF-16LE] 23 [TextDecoderStream should be able to decode invalid sequences in UTF-16BE] 46 [TextDecoderStream should be able to reject invalid sequences in Shift_JIS] 52 [TextDecoderStream should be able to reject invalid sequences in UTF-16LE] 55 [TextDecoderStream should be able to reject invalid sequences in UTF-16BE] 61 [TextDecoderStream should be able to decode invalid sequences in UTF-16LE] [all …]
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/dports/math/gambit/gambit-16.0.1/src/tools/enumpoly/ |
H A D | sfstrat.cc | 49 : efp(p), sequences() in SFSequenceSet() 57 : efp(s.efp), sequences(s.sequences) in SFSequenceSet() 68 delete sequences[i]; in ~SFSequenceSet() 75 sequences = s.sequences; in operator =() 83 if (sequences.Length() != s.sequences.Length()) return (false); in operator ==() 86 && sequences[i] == s.sequences[i]; i++); in operator ==() 101 sequences.Append(s); in AddSequence() 112 t = sequences.Find(s); in RemoveSequence() 123 if(sequences[t]->GetNumber() == j) return sequences[t]; in Find() 132 return (sequences.Length()); in NumSequences() [all …]
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/dports/lang/spidermonkey78/firefox-78.9.0/testing/web-platform/meta/encoding/streams/ |
H A D | decode-non-utf8.any.js.ini | 2 [TextDecoderStream should be able to reject invalid sequences in Shift_JIS] 5 [TextDecoderStream should be able to decode invalid sequences in Shift_JIS] 8 [TextDecoderStream should be able to reject invalid sequences in UTF-16LE] 11 [TextDecoderStream should be able to reject invalid sequences in UTF-16BE] 17 [TextDecoderStream should be able to decode invalid sequences in UTF-16LE] 23 [TextDecoderStream should be able to decode invalid sequences in UTF-16BE] 37 [TextDecoderStream should be able to reject invalid sequences in Shift_JIS] 40 [TextDecoderStream should be able to decode invalid sequences in Shift_JIS] 43 [TextDecoderStream should be able to reject invalid sequences in UTF-16LE] 46 [TextDecoderStream should be able to reject invalid sequences in UTF-16BE] [all …]
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/dports/math/py-theano/Theano-1.0.5/theano/scan_module/ |
H A D | scan_views.py | 32 sequences, argument 64 sequences=sequences, 75 sequences, argument 109 sequences=sequences, 124 sequences, argument 153 sequences=sequences, 163 sequences, argument 192 sequences=sequences,
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/dports/devel/py-pyrsistent/pyrsistent-0.14.11/tests/ |
H A D | hypothesis_vector_test.py | 100 @rule(target=sequences, former=sequences) 112 @rule(target=sequences, start=sequences, end=sequences) 126 @rule(target=sequences, former=sequences, data=st.data()) 139 @rule(target=sequences, former=sequences, data=st.data()) 153 @rule(target=sequences, former=sequences, data=st.data()) 167 @rule(target=sequences, former=sequences, data=st.data()) 180 @rule(target=sequences, former=sequences, data=st.data()) 192 @rule(pair=sequences) 234 @rule(item=sequences) 243 @rule(start=sequences, end=sequences) [all …]
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