import jalview.io.gff.SequenceOntologyI;
import jalview.util.MapList;
import jalview.util.MappingUtils;
+import jalview.ws.params.InvalidArgumentException;
import java.io.IOException;
import java.util.ArrayList;
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
// now the other way round
- seq1.setDBRefs(null);
+ seq1.setDBRefs(null);
seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1",
new Mapping(mapfordna1));
dna1.addDBRef(dna1xref);
- assertEquals(2, dna1.getDBRefs().length); // to self and to pep1
+ assertEquals(2, dna1.getDBRefs().size()); // to self and to pep1
DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2",
new Mapping(mapfordna2));
dna2.addDBRef(dna2xref);
- assertEquals(2, dna2.getDBRefs().length); // to self and to pep2
+ assertEquals(2, dna2.getDBRefs().size()); // to self and to pep2
/*
* execute method under test:
* verify CDS has a dbref with mapping to peptide
*/
assertNotNull(cds1Dss.getDBRefs());
- assertEquals(2, cds1Dss.getDBRefs().length);
- dbref = cds1Dss.getDBRefs()[0];
+ assertEquals(2, cds1Dss.getDBRefs().size());
+ dbref = cds1Dss.getDBRefs().get(0);
assertEquals(dna1xref.getSource(), dbref.getSource());
// version is via ensembl's primary ref
assertEquals(dna1xref.getVersion(), dbref.getVersion());
*/
assertNotNull(pep1.getDBRefs());
// FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ?
- assertEquals(2, pep1.getDBRefs().length);
- dbref = pep1.getDBRefs()[1];
+ assertEquals(2, pep1.getDBRefs().size());
+ dbref = pep1.getDBRefs().get(1);
assertEquals("ENSEMBL", dbref.getSource());
assertEquals("0", dbref.getVersion());
assertEquals("CDS|dna1", dbref.getAccessionId());
/*
* verify cDNA has added a dbref with mapping to CDS
*/
- assertEquals(3, dna1.getDBRefs().length);
- DBRefEntry dbRefEntry = dna1.getDBRefs()[2];
+ assertEquals(3, dna1.getDBRefs().size());
+ DBRefEntry dbRefEntry = dna1.getDBRefs().get(2);
assertSame(cds1Dss, dbRefEntry.getMap().getTo());
MapList dnaToCdsMapping = new MapList(new int[] { 4, 6, 10, 12 },
new int[] { 1, 6 }, 1, 1);
assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
- assertEquals(3, dna2.getDBRefs().length);
- dbRefEntry = dna2.getDBRefs()[2];
+ assertEquals(3, dna2.getDBRefs().size());
+ dbRefEntry = dna2.getDBRefs().get(2);
assertSame(cds2Dss, dbRefEntry.getMap().getTo());
dnaToCdsMapping = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
new int[] { 1, 9 }, 1, 1);
/*
* verify CDS has added a dbref with mapping to cDNA
*/
- assertEquals(2, cds1Dss.getDBRefs().length);
- dbRefEntry = cds1Dss.getDBRefs()[1];
+ assertEquals(2, cds1Dss.getDBRefs().size());
+ dbRefEntry = cds1Dss.getDBRefs().get(1);
assertSame(dna1.getDatasetSequence(), dbRefEntry.getMap().getTo());
MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 }, new int[] {
4, 6, 10, 12 }, 1, 1);
assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
- assertEquals(2, cds2Dss.getDBRefs().length);
- dbRefEntry = cds2Dss.getDBRefs()[1];
+ assertEquals(2, cds2Dss.getDBRefs().size());
+ dbRefEntry = cds2Dss.getDBRefs().get(1);
assertSame(dna2.getDatasetSequence(), dbRefEntry.getMap().getTo());
cdsToDnaMapping = new MapList(new int[] { 1, 9 }, new int[] { 1, 3, 7,
9, 13, 15 }, 1, 1);