| /dports/biology/jalview/jalview/test/jalview/analysis/ |
| H A D | CrossRefTest.java | 238 dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2")); in testFindXrefSequences_noDbrefs()
267 dna1.addDBRef(dbref); in testSearchDataset()
268 dna1.addDBRef(new DBRefEntry("EMBL", "0", "AF039662")); in testSearchDataset()
293 found = testee.searchDataset(!dna1.isProtein(), dna1, dbref, result, in testSearchDataset()
312 assertSame(dna1, result.get(0)); in testSearchDataset()
317 assertSame(dna1, mapping.getFromSeq()); in testSearchDataset()
352 dna1.createDatasetSequence(); in testFindXrefSequences_fromDbRefMap()
368 dna1.getDatasetSequence().addDBRef(dbRef1); in testFindXrefSequences_fromDbRefMap()
372 dna1.getDatasetSequence().addDBRef(dbRef2); in testFindXrefSequences_fromDbRefMap()
378 AlignmentI al = new Alignment(new SequenceI[] { dna1 }); in testFindXrefSequences_fromDbRefMap()
[all …]
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| H A D | AlignmentUtilsTests.java | 1008 dna1.createDatasetSequence(); in testMakeCdsAlignment()
1057 dna1.addDBRef(dna1xref); in testMakeCdsAlignment()
1119 assertEquals(3, dna1.getDBRefs().length); in testMakeCdsAlignment()
1243 dna1.createDatasetSequence(); in testMakeCdsAlignment_multipleProteins()
1651 dna1.createDatasetSequence(); in testMakeCdsAlignment_alternativeTranscripts()
2093 dna1.createDatasetSequence(); in testMakeCdsAlignment_filterProducts()
2224 SequenceI dna3 = new Sequence(dna1); in testAlignAsSameSequences()
2286 SequenceI uas1 = dna1.deriveSequence(); in testAlignAsSameSequencesMultipleSubSeq()
2471 dna1.createDatasetSequence(); in testFindCdsForProtein()
2540 dna1.createDatasetSequence(); in testFindCdsForProtein_noUTR()
[all …]
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| /dports/biology/jalview/jalview/test/jalview/datamodel/ |
| H A D | AlignedCodonFrameTest.java | 104 dna1.createDatasetSequence(); in testGetMappedRegion()
118 assertNull(acf.getMappedRegion(dna1, pep1, 3)); in testGetMappedRegion()
135 acf.getMappedRegion(dna1, pep1, 3)); in testGetMappedRegion()
137 acf.getMappedRegion(dna1, pep1, 4)); in testGetMappedRegion()
157 acf.getMappedRegion(pep1, dna1, 11)); in testGetMappedRegion()
159 acf.getMappedRegion(pep1, dna1, 12)); in testGetMappedRegion()
161 acf.getMappedRegion(pep1, dna1, 13)); in testGetMappedRegion()
572 dna1.createDatasetSequence(); in testMarkMappedRegion()
586 acf.markMappedRegion(dna1, 12, sr); in testMarkMappedRegion()
603 acf.markMappedRegion(dna1, 10, sr); in testMarkMappedRegion()
[all …]
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| H A D | AlignmentTest.java | 901 String dna1 = "A-Aa-gG-GCC-cT-TT"; in testAlignAs_dnaAsProtein_withIntrons() local
903 AlignmentI al1 = loadAlignment(">Dna1/6-17\n" + dna1 in testAlignAs_dnaAsProtein_withIntrons()
931 al1.getSequenceAt(0).setSequence(dna1); in testAlignAs_dnaAsProtein_withIntrons()
|
| /dports/biology/exonerate/exonerate-2.4.0/src/model/ |
| H A D | ungapped.test.c | 66 register Sequence *dna1 = Sequence_create("dna1", NULL, in Argument_main() local
80 run_ungapped_test(dna1, dna2, FALSE, 47); in Argument_main()
82 run_ungapped_test(dna1, protein1, FALSE, 7); in Argument_main()
84 run_ungapped_test(dna1, dna2, TRUE, 22); in Argument_main()
85 Sequence_destroy(dna1); in Argument_main()
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/index/ |
| H A D | test_shapes.h | 50 DnaString dna1, dna2; in testShape() local
74 unhash(dna1, H1, weight(shape1)); in testShape()
76 …"\t" << std::hex << H1 << " " << H2 << ' ' << H1b << ' ' << H2b <<"\t" << dna1 << " " << dna2 << "… in testShape()
94 unhash(dna1, H1, weight(shape1)); in testShape()
96 …::cout << std::dec << i << "\t" << std::hex << H1 << " " << H2 << "\t" << dna1 << " " << dna2 << "… in testShape()
|
| /dports/biology/jalview/jalview/test/jalview/io/gff/ |
| H A D | GffTests.java | 102 SequenceI dna1 = new Sequence("dna1", "AAACCCGGGTTTAAACCCGGGTTT"); in testResolveExonerateGff() local
103 AlignmentI al = new Alignment(new SequenceI[] { dna1 }); in testResolveExonerateGff()
111 mapping.realiseWith(dna1); in testResolveExonerateGff()
113 assertSame(dna1.getDatasetSequence(), in testResolveExonerateGff()
|
| /dports/biology/jalview/jalview/test/jalview/schemes/ |
| H A D | ResidueColourSchemeTest.java | 60 SequenceI dna1 = new Sequence("dna1", "ACTGAC"); in testIsApplicableTo() local
63 AlignmentI nucleotide = new Alignment(new SequenceI[] { dna1, dna2 }); in testIsApplicableTo()
|
| /dports/biology/p5-BioPerl/BioPerl-1.7.7/t/LocalDB/ |
| H A D | Qual.t | 85 my (%h,$dna1,$dna2);
88 ok $dna1 = $h{"$seqid:1,10"};
|
| /dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/t/ |
| H A D | EMBOSS.t | 46 -sequence => test_input_file('dna1.fa'),
184 '-sequence' => test_input_file('dna1.fa'),
|
| /dports/biology/p5-Bio-FeatureIO/Bio-FeatureIO-1.6.905/ |
| H A D | MANIFEST | 24 t/data/dna1.fa
|
| /dports/biology/fasta/fasta/ |
| H A D | lx_align3.c | 565 char *dna1, c1, c2, c3; variable
567 dna1 = ckalloc(ld);
568 for (st = dna, i = 0; i < ld; i++, st++) dna1[i] = aa[*st];
580 strncpy(&line1[len], &dna1[y], i); y+=i;
|
| /dports/biology/ncbi-toolkit/ncbi/api/ |
| H A D | txalign.c | 6064 char *dna1, c1, c2, c3; in OOFDisplayTraceBack1() local
6066 dna1 = Malloc(ld+2); in OOFDisplayTraceBack1()
6067 MemCpy(dna1+1, dna, ld); in OOFDisplayTraceBack1()
6068 dna1[0] = ' '; dna1[1] = ' '; in OOFDisplayTraceBack1()
6100 line1[len] = dna1[y+1]; y+= 3; in OOFDisplayTraceBack1()
6127 MemFree(dna1); in OOFDisplayTraceBack1()
6138 char *dna1, c1, c2, c3; in OOFDisplayTraceBack2() local
6140 dna1 = Malloc(ld+2); in OOFDisplayTraceBack2()
6143 MemCpy(dna1+1, dna, ld); in OOFDisplayTraceBack2()
6144 dna1[0] = ' '; dna1[1] = ' '; in OOFDisplayTraceBack2()
[all …]
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| /dports/misc/orange3/orange3-3.29.1/Orange/widgets/data/tests/ |
| H A D | test_owconcatenate.py | 412 dna1, dna2, dna3, dna4, dnc1 = dtable_n.domain.variables
417 self.assertIs(na1, dna1)
|
| /dports/biology/p5-Bio-FeatureIO/Bio-FeatureIO-1.6.905/t/ |
| H A D | gff.t | 21 ok( $io = Bio::FeatureIO->new( -file => test_input_file('dna1.fa') ) );
|
| /dports/www/firefox-esr/firefox-91.8.0/intl/locales/sl/hyphenation/ |
| H A D | hyph_sl.dic | 276 dna1
|
| /dports/lang/spidermonkey78/firefox-78.9.0/intl/locales/sl/hyphenation/ |
| H A D | hyph_sl.dic | 276 dna1
|
| /dports/www/firefox/firefox-99.0/intl/locales/sl/hyphenation/ |
| H A D | hyph_sl.dic | 276 dna1
|
| /dports/mail/thunderbird/thunderbird-91.8.0/intl/locales/sl/hyphenation/ |
| H A D | hyph_sl.dic | 276 dna1
|
| /dports/www/firefox-legacy/firefox-52.8.0esr/intl/locales/sl/hyphenation/ |
| H A D | hyph_sl.dic | 276 dna1
|
| /dports/lang/spidermonkey60/firefox-60.9.0/intl/locales/sl/hyphenation/ |
| H A D | hyph_sl.dic | 276 dna1
|
| /dports/textproc/sl-hunspell/sl-hunspell-2020.12.31/ |
| H A D | hyph_sl_SI.dic | 278 dna1
|
| /dports/textproc/py-pyphen/Pyphen-0.10.0/pyphen/dictionaries/ |
| H A D | hyph_sl_SI.dic | 278 dna1
|
| /dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/ |
| H A D | MANIFEST | 151 t/data/dna1.fa
|
| /dports/biology/fasta3/fasta-36.3.8/src/ |
| H A D | dropfx2.c | 2077 unsigned char *dna1, c1, c2, c3, *st; local
2079 dna1 = ckalloc((size_t)ld);
2080 for (st = dna, i = 0; i < ld; i++, st++) dna1[i] = NCBIstdaa[*st];
2092 strncpy(&line1[len], (const char *)&dna1[y], i); y+=i;
|