* first with no dbrefs to search
*/
sources = new CrossRef(new SequenceI[] { seq }, al)
- .findXrefSourcesForSequences();
+ .findXrefSourcesForSequences(false);
assertTrue(sources.isEmpty());
/*
seq.addDBRef(new DBRefEntry("ENSEMBL", "0", "E2349"));
seq.addDBRef(new DBRefEntry("ENSEMBLGENOMES", "0", "E2350"));
sources = new CrossRef(new SequenceI[] { seq }, al)
- .findXrefSourcesForSequences();
+ .findXrefSourcesForSequences(false);
assertEquals(4, sources.size());
assertEquals("[EMBL, EMBLCDS, GENEDB, ENSEMBL]",
sources.toString());
// TODO include ENSEMBLGENOMES in DBRefSource.DNACODINGDBS ?
al.addSequence(seq2);
sources = new CrossRef(new SequenceI[] { seq }, al)
- .findXrefSourcesForSequences();
+ .findXrefSourcesForSequences(false);
assertEquals(3, sources.size());
assertEquals("[EMBLCDS, EMBL, GENEDB]", sources.toString());
}
*/
AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq });
Alignment xrefs = new CrossRef(new SequenceI[] { emblSeq }, al)
- .findXrefSequences("UNIPROT");
+ .findXrefSequences("UNIPROT", true);
assertEquals(1, xrefs.getHeight());
assertSame(uniprotSeq, xrefs.getSequenceAt(0));
}
*/
AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq });
Alignment xrefs = new CrossRef(new SequenceI[] { uniprotSeq },
- al).findXrefSequences("EMBL");
+ al)
+ .findXrefSequences("EMBL", true);
assertEquals(1, xrefs.getHeight());
assertSame(emblSeq, xrefs.getSequenceAt(0));
}
*/
AlignmentI al = new Alignment(new SequenceI[] { dna1, dna2 });
Alignment xrefs = new CrossRef(new SequenceI[] { dna2 }, al)
- .findXrefSequences("UNIPROT");
+ .findXrefSequences("UNIPROT", true);
assertNull(xrefs);
}
*/
DBRefEntry dbref = new DBRefEntry("UNIPROT", "0", "P30419");
CrossRef testee = new CrossRef(al.getSequencesArray(), al);
- boolean found = testee.searchDataset(dna1, dbref, result, null, true);
+ boolean found = testee.searchDataset(true, dna1, dbref, result, null,
+ true);
assertFalse(found);
assertTrue(result.isEmpty());
* search for a protein sequence with dbref UNIPROT:Q9ZTS2
*/
dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
- found = testee.searchDataset(dna1, dbref, result, null, true);
+ found = testee.searchDataset(true, dna1, dbref, result, null, true);
assertTrue(found);
assertEquals(1, result.size());
assertSame(pep1, result.get(0));
*/
result.clear();
dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
- found = testee.searchDataset(pep1, dbref, result, null, false);
+ found = testee.searchDataset(false, pep1, dbref, result, null, false);
assertTrue(found);
assertEquals(1, result.size());
assertSame(dna1, result.get(0));
*/
AlignmentI al = new Alignment(new SequenceI[] { dna1 });
Alignment xrefs = new CrossRef(new SequenceI[] { dna1 }, al)
- .findXrefSequences("UNIPROT");
+ .findXrefSequences("UNIPROT", true);
assertEquals(2, xrefs.getHeight());
/*
*/
AlignmentI al = new Alignment(new SequenceI[] { dna1 });
Alignment xrefs = new CrossRef(new SequenceI[] { dna1 }, al)
- .findXrefSequences("UNIPROT");
+ .findXrefSequences("UNIPROT", true);
assertEquals(2, xrefs.getHeight());
assertSame(pep1, xrefs.getSequenceAt(0));
assertSame(pep2, xrefs.getSequenceAt(1));
SequenceI[] seqs = new SequenceI[] { gene, braf001, braf002 };
AlignmentI al = new Alignment(seqs);
Alignment xrefs = new CrossRef(seqs, al)
- .findXrefSequences("UNIPROT");
+.findXrefSequences("UNIPROT",
+ true);
assertEquals(2, xrefs.getHeight());
assertSame(pep1, xrefs.getSequenceAt(0));
assertSame(pep2, xrefs.getSequenceAt(1));
*/
SequenceI[] seqs = new SequenceI[] { p0ce19, p0ce20 };
AlignmentI al = new Alignment(seqs);
- Alignment xrefs = new CrossRef(seqs, al)
- .findXrefSequences("EMBL");
+ Alignment xrefs = new CrossRef(seqs, al).findXrefSequences("EMBL",
+ false);
/*
* verify retrieved sequences