* sequence
*/
DBRefEntry dbref = new DBRefEntry("ENSEMBL", "0", "dna1");
- dna1.getDatasetSequence().setSourceDBRef(dbref);
+ dna1.getDatasetSequence().addDBRef(dbref);
+ org.testng.Assert.assertEquals(dbref, dna1.getPrimaryDBRefs().get(0));
dbref = new DBRefEntry("ENSEMBL", "0", "dna2");
- dna2.getDatasetSequence().setSourceDBRef(dbref);
+ dna2.getDatasetSequence().addDBRef(dbref);
+ org.testng.Assert.assertEquals(dbref, dna2.getPrimaryDBRefs().get(0));
/*
* CDS sequences are 'discovered' from dna-to-protein mappings on the alignment
* verify peptide has added a dbref with reverse mapping to CDS
*/
assertNotNull(pep1.getDBRefs());
+ // FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ?
assertEquals(2, pep1.getDBRefs().length);
dbref = pep1.getDBRefs()[1];
assertEquals("ENSEMBL", dbref.getSource());
{
SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
- SequenceI as1 = dna1.deriveSequence(), as2 = dna1.deriveSequence()
- .getSubSequence(3, 7), as3 = dna2.deriveSequence();
+ SequenceI as1 = dna1.deriveSequence();
+ SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7);
+ SequenceI as3 = dna2.deriveSequence();
as1.insertCharAt(6, 5, '-');
String s_as1 = as1.getSequenceAsString();
as2.insertCharAt(6, 5, '-');
// why do we need to cast this still ?
((Alignment) aligned).createDatasetAlignment();
- SequenceI uas1 = dna1.deriveSequence(), uas2 = dna1.deriveSequence()
- .getSubSequence(3, 7), uas3 = dna2.deriveSequence();
+ SequenceI uas1 = dna1.deriveSequence();
+ SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
+ SequenceI uas3 = dna2.deriveSequence();
AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2,
uas3 });
((Alignment) tobealigned).createDatasetAlignment();