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/dports/textproc/py-textdistance/textdistance-4.2.2/textdistance/algorithms/
H A Dbase.py19 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 …]
H A Dtoken_based.py43 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)
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H A Dsequence_based.py67 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 …]
H A Dsimple.py21 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:
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/dports/biology/py-biopython/biopython-1.79/Tests/
H A Dtest_SeqIO.py636 sequences = [
657 sequences,
664 sequences = [
711 sequences = [
765 sequences = [
819 sequences = [
1367 sequences = [
1417 sequences = [
1492 sequences = [
1544 sequences = [
[all …]
/dports/biology/emboss/EMBOSS-6.6.0/doc/programs/master/emboss/apps/inc/
H A Dneedleall.output7 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 …]
/dports/math/reduce/Reduce-svn5758-src/jlisp/android/AndroidReduce/src/uk/ac/cam/aa582/structures/reducible/
H A DWrapperExpression.java17 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()
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Tools/
H A DLucy.pm279 $self->{sequences}{$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};
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/dports/biology/cd-hit/cdhit-4.8.1/cd-hit-auxtools/
H A DbioSequence.hxx55 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 …]
H A DbioSequence.cxx112 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()
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/dports/biology/velvet/velvet_1.2.10/src/
H A Drun2.c81 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()
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/dports/graphics/blender/blender-2.91.0/release/scripts/addons/power_sequencer/operators/utils/
H A Dfunctions.py55 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:
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/dports/databases/pgloader3/lparallel-20160825-git/src/cognate/
H A Dpquantifier.lisp33 (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))
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/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/VelvetAPI/
H A DVelvetGraph.cc4 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 …]
/dports/games/libretro-scummvm/scummvm-7b1e929/engines/lastexpress/game/
H A Dbeetle.cpp65 _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 …]
/dports/games/scummvm/scummvm-2.5.1/engines/lastexpress/game/
H A Dbeetle.cpp65 _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 …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/alignment_free/
H A Dtest_alignment_free.cpp63 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 …]
/dports/biology/py-biopython/biopython-1.79/Tests/Emboss/
H A Dno_oligo.primer35 # 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 …]
/dports/www/firefox-esr/firefox-91.8.0/testing/web-platform/meta/encoding/streams/
H A Ddecode-non-utf8.any.js.ini2 [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 …]
/dports/www/firefox/firefox-99.0/testing/web-platform/meta/encoding/streams/
H A Ddecode-non-utf8.any.js.ini2 [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 …]
/dports/mail/thunderbird/thunderbird-91.8.0/testing/web-platform/meta/encoding/streams/
H A Ddecode-non-utf8.any.js.ini2 [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 …]
/dports/math/gambit/gambit-16.0.1/src/tools/enumpoly/
H A Dsfstrat.cc49 : 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 …]
/dports/lang/spidermonkey78/firefox-78.9.0/testing/web-platform/meta/encoding/streams/
H A Ddecode-non-utf8.any.js.ini2 [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 …]
/dports/math/py-theano/Theano-1.0.5/theano/scan_module/
H A Dscan_views.py32 sequences, argument
64 sequences=sequences,
75 sequences, argument
109 sequences=sequences,
124 sequences, argument
153 sequences=sequences,
163 sequences, argument
192 sequences=sequences,
/dports/devel/py-pyrsistent/pyrsistent-0.14.11/tests/
H A Dhypothesis_vector_test.py100 @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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