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/dports/biology/py-biopython/biopython-1.79/Tests/
H A Dtest_AlignIO_FastaIO.py23 alignments[0][0].seq,
32 alignments[0][1].seq,
43 alignments[1][0].seq,
51 alignments[1][1].seq,
92 alignments[0][0].seq,
101 alignments[0][1].seq,
112 alignments[1][0].seq,
118 alignments[1][1].seq,
126 alignments[2][0].seq,
135 alignments[2][1].seq,
[all …]
H A Dtest_NCBITextParser.py75 self.assertEqual(len(record.alignments), 3)
184 self.assertEqual(len(record.alignments), 0)
247 self.assertEqual(len(record.alignments), 6)
14459 for ali in record.alignments:
14523 for ali in record.alignments:
14585 for ali in record.alignments:
14649 for ali in record.alignments:
14713 for ali in record.alignments:
14754 h = record.alignments[0].hsps[0]
14756 h = record.alignments[0].hsps[1]
[all …]
H A Dtest_AlignIO.py98 alignments.reverse()
156 return alignments
760 alignments[0],
767 alignments[1],
774 alignments[2],
781 alignments[3],
788 alignments[4],
872 alignments[0],
879 alignments[1],
883 alignments[2],
[all …]
H A Dtest_AlignIO_EmbossIO.py373 self.assertEqual(len(alignments), 1)
374 self.assertEqual(len(alignments[0]), 2)
379 self.assertEqual(len(alignments), 1)
380 self.assertEqual(len(alignments[0]), 4)
387 self.assertEqual(len(alignments), 2)
388 self.assertEqual(len(alignments[0]), 2)
389 self.assertEqual(len(alignments[1]), 4)
397 self.assertEqual(len(alignments), 5)
398 self.assertEqual(len(alignments[0]), 2)
408 self.assertEqual(len(alignments), 1)
[all …]
H A Dtest_pairwise_aligner.py230 alignment = alignments[0]
242 alignment = alignments[1]
258 alignment = alignments[0]
2955 alignments = list(alignments)
2958 alignments = list(alignments)
2966 alignments = list(alignments)
2969 alignments = list(alignments)
2979 alignments = list(alignments)
2982 alignments = list(alignments)
2990 alignments = list(alignments)
[all …]
H A Dtest_AlignIO_ClustalIO.py160 self.assertEqual(1, len(alignments))
161 self.assertEqual(alignments[0]._version, "1.81")
162 alignment = alignments[0]
177 self.assertEqual(1, len(alignments))
179 alignment = alignments[0]
191 self.assertEqual(2, len(alignments))
192 self.assertEqual(9, len(alignments[0]))
194 self.assertEqual(2, len(alignments[1]))
203 alignments = (
229 self.assertEqual(1, len(alignments))
[all …]
H A Dtest_NCBIXML.py26 alignments = record.alignments
31 alignment = alignments[0]
52 alignment = alignments[1]
73 alignment = alignments[2]
94 alignment = alignments[3]
2033 alignments = record.alignments
2065 alignments = record.alignments
2087 alignments = record.alignments
2105 alignments = record.alignments
2125 alignments = record.alignments
[all …]
/dports/biology/bedtools/bedtools2-2.30.0/src/bamToFastq/
H A DbamToFastq.cpp89 vector<BamAlignment> alignments; in PairedFastq() local
97 WritePairs(alignments); in PairedFastq()
98 alignments.clear(); in PairedFastq()
99 alignments.push_back(curr); in PairedFastq()
109 if (alignments.size() != 0) WritePairs(alignments); in PairedFastq()
118 if (alignments.size() == 1) in WritePairs()
125 else if (alignments.size() == 2) in WritePairs()
127 queryName = alignments[0].Name; in WritePairs()
129 if (alignments[0].IsFirstMate() && alignments[1].IsSecondMate()) in WritePairs()
144 else if (alignments[0].IsSecondMate() && alignments[1].IsFirstMate()) in WritePairs()
[all …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/bam_io/
H A Dtest_read_sam.h128 String<BamAlignmentRecord> alignments; in SEQAN_DEFINE_TEST() local
131 resize(alignments, length(alignments) + 1); in SEQAN_DEFINE_TEST()
139 SEQAN_ASSERT_EQ(length(alignments), 3u); in SEQAN_DEFINE_TEST()
141 SEQAN_ASSERT_EQ(alignments[0].qName, "READ0"); in SEQAN_DEFINE_TEST()
142 SEQAN_ASSERT_EQ(alignments[0].flag, 2u); in SEQAN_DEFINE_TEST()
143 SEQAN_ASSERT_EQ(alignments[0].rID, 0); in SEQAN_DEFINE_TEST()
144 SEQAN_ASSERT_EQ(alignments[0].beginPos, 0); in SEQAN_DEFINE_TEST()
145 SEQAN_ASSERT_EQ(alignments[0].mapQ, 8u); in SEQAN_DEFINE_TEST()
153 SEQAN_ASSERT_EQ(alignments[0].rNextId, 0); in SEQAN_DEFINE_TEST()
154 SEQAN_ASSERT_EQ(alignments[0].pNext, 30); in SEQAN_DEFINE_TEST()
[all …]
H A Dtest_bam_file.h130 resize(alignments, length(alignments) + 1); in testBamIOBamFileReadRecords()
131 readRecord(back(alignments), bamIO); in testBamIOBamFileReadRecords()
133 SEQAN_ASSERT_EQ(length(alignments), 3u); in testBamIOBamFileReadRecords()
136 SEQAN_ASSERT_EQ(alignments[0].flag, 2u); in testBamIOBamFileReadRecords()
137 SEQAN_ASSERT_EQ(alignments[0].rID, 0); in testBamIOBamFileReadRecords()
139 SEQAN_ASSERT_EQ(alignments[0].mapQ, 8u); in testBamIOBamFileReadRecords()
149 SEQAN_ASSERT_EQ(alignments[0].tLen, 40); in testBamIOBamFileReadRecords()
155 SEQAN_ASSERT_EQ(alignments[1].flag, 1u); in testBamIOBamFileReadRecords()
156 SEQAN_ASSERT_EQ(alignments[1].rID, 0); in testBamIOBamFileReadRecords()
175 SEQAN_ASSERT_EQ(alignments[2].rID, 0); in testBamIOBamFileReadRecords()
[all …]
H A Dtest_read_bam.h125 String<BamAlignmentRecord> alignments; in SEQAN_DEFINE_TEST() local
128 resize(alignments, length(alignments) + 1); in SEQAN_DEFINE_TEST()
136 SEQAN_ASSERT_EQ(length(alignments), 3u); in SEQAN_DEFINE_TEST()
138 SEQAN_ASSERT_EQ(alignments[0].qName, "READ0"); in SEQAN_DEFINE_TEST()
139 SEQAN_ASSERT_EQ(alignments[0].flag, 2u); in SEQAN_DEFINE_TEST()
140 SEQAN_ASSERT_EQ(alignments[0].rID, 0); in SEQAN_DEFINE_TEST()
141 SEQAN_ASSERT_EQ(alignments[0].beginPos, 0); in SEQAN_DEFINE_TEST()
142 SEQAN_ASSERT_EQ(alignments[0].mapQ, 8u); in SEQAN_DEFINE_TEST()
150 SEQAN_ASSERT_EQ(alignments[0].rNextId, 0); in SEQAN_DEFINE_TEST()
151 SEQAN_ASSERT_EQ(alignments[0].pNext, 30); in SEQAN_DEFINE_TEST()
[all …]
/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/tasks/
H A Dalignments.bf7 * @name alignments.ReadCodonDataSet
17 * @name alignments.LoadGeneticCode
148 * @name alignments.GetIthSequence
221 * @name alignments.FilterType
276 * @name alignments.AlphabetType
378 …for (alignments.LoadCodonDataFile.i = 0; alignments.LoadCodonDataFile.i < ^"`dataset_name`.species…
381 …alignments.LoadCodonDataFile.name = alignments.GetIthSequenceOriginalName (dataset_name, alignment…
424 …for (alignments.LoadCodonDataFile.i = 0; alignments.LoadCodonDataFile.i < ^"`dataset_name`.species…
427 …alignments.LoadCodonDataFile.name = alignments.GetIthSequenceOriginalName (dataset_name, alignment…
898 * @name alignments.StripGaps
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/bwa/
H A DBwaMemAlignmentUtilsTest.java19 final List<BwaMemAlignment> alignments = new ArrayList<>(7); in testSATags() local
20 …alignments.add(new BwaMemAlignment(0,4,71180,71338,404,568,40,20,78,48,"404S94M3I10M5I54M66S","11G… in testSATags()
21 …alignments.add(new BwaMemAlignment(2064,1,49146596,49146678,517,599,0,2,72,71,"517H82M37H","60C10T… in testSATags()
22 …alignments.add(new BwaMemAlignment(2048,4,70496,70594,98,192,18,8,58,48,"98H98M440H","10A10G21T14G… in testSATags()
23 …alignments.add(new BwaMemAlignment(2048,0,790150,790188,283,321,8,0,38,35,"283H38M315H","38",null,… in testSATags()
24 …alignments.add(new BwaMemAlignment(2048,3,31231128,31231162,345,379,0,0,34,34,"345H34M257H","34",n… in testSATags()
25 …alignments.add(new BwaMemAlignment(2048,2,97988540,97988587,250,297,0,3,32,30,"250H47M339H","29G2A… in testSATags()
26 …alignments.add(new BwaMemAlignment(2064,1,49141579,49141624,583,628,0,3,30,30,"583H45M8H","19C0A4A… in testSATags()
27 final String[] expectedTags = new String[alignments.size()]; in testSATags()
35 … Map<BwaMemAlignment,String> actualTagMap = BwaMemAlignmentUtils.createSATags(alignments,refNames); in testSATags()
[all …]
/dports/biology/biolibc/biolibc-0.2.1/
H A Dsam-buff.c124 sam_buff->alignments = in bl_sam_buff_init()
128 sam_buff->alignments[c] = NULL; in bl_sam_buff_init()
171 sam_buff->alignments[sam_buff->buffered_count] = in bl_sam_buff_add_alignment()
214 sam_buff->alignments = in bl_sam_buff_add_alignment()
219 sam_buff->alignments[c] = NULL; in bl_sam_buff_add_alignment()
284 bl_sam_free(sam_buff->alignments[c]); in bl_sam_buff_free_alignment()
286 if ( sam_buff->alignments[c] != NULL ) in bl_sam_buff_free_alignment()
288 free(sam_buff->alignments[c]); in bl_sam_buff_free_alignment()
289 sam_buff->alignments[c] = NULL; in bl_sam_buff_free_alignment()
334 sam_buff->alignments[c] = sam_buff->alignments[c + nelem]; in bl_sam_buff_shift()
[all …]
/dports/print/lilypond-devel/lilypond-2.23.5/input/regression/
H A Ddynamics-hairpin-endpoint-alignment.ly6 @code{endpoint-alignments}, which is a pair of numbers representing
40 \tempo \markup { "endpoint-alignments = #`(,LEFT . ,RIGHT)" }
42 \tempo \markup { "endpoint-alignments = #`(,LEFT . ,LEFT)" }
43 \override Hairpin.endpoint-alignments = #`(,LEFT . ,LEFT)
45 \tempo \markup { "endpoint-alignments = #`(,RIGHT . ,LEFT)" }
46 \override Hairpin.endpoint-alignments = #`(,RIGHT . ,LEFT)
49 \override Hairpin.endpoint-alignments = #`(,RIGHT . ,RIGHT)
52 \override Hairpin.endpoint-alignments = #`(,CENTER . ,CENTER)
57 "influenced by endpoint-alignments"
59 \override Hairpin.endpoint-alignments = #`(,LEFT . ,RIGHT)
[all …]
/dports/x11-toolkits/pango/pango-1.48.11/tests/
H A Dtesttabs.c49 PangoTabAlign *alignments; in test_tabs_copy() local
57 pango_tab_array_get_tabs (tabs2, &alignments, &locations); in test_tabs_copy()
58 g_assert_true (alignments[0] == PANGO_TAB_LEFT); in test_tabs_copy()
59 g_assert_true (alignments[1] == PANGO_TAB_LEFT); in test_tabs_copy()
63 g_free (alignments); in test_tabs_copy()
74 PangoTabAlign *alignments; in test_tabs_resize() local
88 pango_tab_array_get_tabs (tabs, &alignments, &locations); in test_tabs_resize()
89 g_assert_true (alignments[0] == PANGO_TAB_LEFT); in test_tabs_resize()
90 g_assert_true (alignments[1] == PANGO_TAB_LEFT); in test_tabs_resize()
94 g_free (alignments); in test_tabs_resize()
/dports/sysutils/glow/glow-0.2.0/vendor/github.com/yuin/goldmark/extension/
H A Dtable.go41 if alignments == nil {
49 table.Alignments = alignments
75 if i >= len(alignments) {
80 alignment = alignments[i]
95 for ; i < len(alignments); i++ {
114 var alignments []ast.Alignment
117 alignments = append(alignments, ast.AlignLeft)
119 alignments = append(alignments, ast.AlignRight)
121 alignments = append(alignments, ast.AlignCenter)
123 alignments = append(alignments, ast.AlignNone)
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/
H A DBwaMemTestUtils.java22 final List<BwaMemAlignment> alignments = allAlignments.get(0); in assertCorrectSingleReadAlignment() local
23 Assert.assertEquals(alignments.size(), 1); in assertCorrectSingleReadAlignment()
24 final BwaMemAlignment alignment = alignments.get(0); in assertCorrectSingleReadAlignment()
39 final List<BwaMemAlignment> alignments = allAlignments.get(0); in assertCorrectChimericContigAlignment() local
40 Assert.assertEquals(alignments.size(), 2); in assertCorrectChimericContigAlignment()
43 if ( alignments.get(0).getRefStart() < alignments.get(1).getRefStart() ) { in assertCorrectChimericContigAlignment()
44 alignment1 = alignments.get(0); in assertCorrectChimericContigAlignment()
45 alignment2 = alignments.get(1); in assertCorrectChimericContigAlignment()
48 alignment1 = alignments.get(1); in assertCorrectChimericContigAlignment()
49 alignment2 = alignments.get(0); in assertCorrectChimericContigAlignment()
/dports/games/py-fife/fifengine-0.4.2/engine/python/fife/extensions/pychan/widgets/
H A Dadjustingcontainer.py82 alignments = None):
123 if alignments is not None:
124 self.alignments = alignments
159 self.alignments)
176 def _setColumnAlignments(self, alignments): argument
178 if alignments is not None:
179 for a in alignments:
188 alignments = []
192 alignments.append(self.column_alignment(i))
194 return alignments
[all …]
/dports/lang/ruby26/ruby-2.6.9/test/fiddle/
H A Dtest_c_struct_entry.rb15 alignments = types.map { |type| PackInfo::ALIGN_MAP[type] }
17 expected = PackInfo.align 0, alignments[0]
20 expected = PackInfo.align expected, alignments[1]
23 expected = PackInfo.align expected, alignments.max
32 alignments = types.map { |type| PackInfo::ALIGN_MAP[type] }
34 expected = PackInfo.align 0, alignments[0]
37 expected = PackInfo.align expected, alignments[1]
40 expected = PackInfo.align expected, alignments.max
/dports/devel/liteide/liteide-x37.4/liteidex/vendor/github.com/yuin/goldmark/extension/
H A Dtable.go148 if alignments == nil {
156 table.Alignments = alignments
190 if i >= len(alignments) {
195 alignment = alignments[i]
210 for ; i < len(alignments); i++ {
229 var alignments []ast.Alignment
232 alignments = append(alignments, ast.AlignLeft)
234 alignments = append(alignments, ast.AlignRight)
236 alignments = append(alignments, ast.AlignCenter)
238 alignments = append(alignments, ast.AlignNone)
[all …]
/dports/audio/cantata/cantata-2.4.2/models/
H A Dsearchmodel.cpp58 …alignments[COL_TITLE]=alignments[COL_ARTIST]=alignments[COL_ALBUM]=alignments[COL_GENRE]=alignment… in SearchModel()
59 …alignments[COL_TRACK]=alignments[COL_LENGTH]=alignments[COL_DISC]=alignments[COL_YEAR]=alignments[… in SearchModel()
60 alignments[COL_RATING]=int(Qt::AlignVCenter|Qt::AlignHCenter); in SearchModel()
92 return alignments[section]; in headerData()
124 if (al!=alignments[section]) { in setHeaderData()
125 alignments[section]=al; in setHeaderData()
160 return alignments[index.column()]; in data()
/dports/biology/py-biopython/biopython-1.79/Bio/AlignIO/
H A D__init__.py183 def write(alignments, handle, format): argument
207 if isinstance(alignments, MultipleSeqAlignment):
209 alignments = [alignments]
215 count = writer_class(fp).write_file(alignments)
220 for alignment in alignments:
462 alignments = parse(in_file, in_format, None)
473 alignments = (over_ride(_) for _ in alignments)
474 return write(alignments, out_file, out_format)
/dports/biology/hisat2/hisat2-2.2.1/
H A Drepeat_kmer.h304 alignments.clear();
347 alignments.expand();
391 alignments.sort();
402 if(alignments.empty())
406 alignments[i].pos -= alignments[i].off;
408 alignments.sort();
415 if(alignments[i].pos != alignments[j].pos) {
418 alignments[i+1] = alignments[j];
429 alignments.resize(alignments.size() - remove_count);
431 if(alignments.size() > 1) {
[all …]
/dports/textproc/p5-RTF-Writer/RTF-Writer-1.11/lib/RTF/Writer/
H A DTableRowDecl.pm136 my($it,@alignments) = @_;
141 unless(@alignments and grep defined($_), @alignments) {
148 if( @alignments != 1) {
150 } elsif( ref $alignments[0] ) {
151 @alignments = @{$alignments[0]}
154 @alignments = grep length($_), split m/(?:\s*,\s*)|\s+/, $alignments[0];
159 foreach my $spec (@alignments) {

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