import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
-import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
import jalview.datamodel.PDBEntry.Type;
import jalview.gui.JvOptionPane;
newDs = PA.getValue(sq, "datasetSequence");
assertNotNull(newDs);
assertNotSame(ds, newDs);
- SequenceFeature[] sfs = sq.getSequenceFeatures();
- assertNotNull(sfs);
- assertEquals(1, sfs.length);
- assertNotSame(sf1, sfs[0]);
- assertEquals(sf1, sfs[0]);
+ List<SequenceFeature> sfs = sq.getSequenceFeatures();
+ assertEquals(1, sfs.size());
+ assertNotSame(sf1, sfs.get(0));
+ assertEquals(sf1, sfs.get(0));
/*
* delete at start - no new dataset sequence created
assertSame(ds, PA.getValue(sq, "datasetSequence"));
sfs = sq.getSequenceFeatures();
assertNotNull(sfs);
- assertEquals(1, sfs.length);
- assertSame(sf1, sfs[0]);
+ assertEquals(1, sfs.size());
+ assertSame(sf1, sfs.get(0));
/*
* delete at end - no new dataset sequence created
SequenceI sq = new Sequence("test", "GATCAT");
sq.createDatasetSequence();
- assertNull(sq.getSequenceFeatures());
+ assertTrue(sq.getSequenceFeatures().isEmpty());
/*
* SequenceFeature on sequence
*/
SequenceFeature sf = new SequenceFeature("Cath", "desc", 2, 4, 2f, null);
sq.addSequenceFeature(sf);
- SequenceFeature[] sfs = sq.getSequenceFeatures();
- assertEquals(1, sfs.length);
- assertSame(sf, sfs[0]);
+ List<SequenceFeature> sfs = sq.getSequenceFeatures();
+ assertEquals(1, sfs.size());
+ assertSame(sf, sfs.get(0));
/*
* SequenceFeature on sequence and dataset sequence; returns that on
null);
sq.getDatasetSequence().addSequenceFeature(sf2);
sfs = sq.getSequenceFeatures();
- assertEquals(1, sfs.length);
- assertSame(sf, sfs[0]);
+ assertEquals(1, sfs.size());
+ assertSame(sf, sfs.get(0));
/*
* SequenceFeature on dataset sequence only
* Note JAL-2046: spurious: we have no use case for setting a non-dataset sequence's feature array to null at the moment.
*/
sq.setSequenceFeatures(null);
- assertNull(sq.getDatasetSequence().getSequenceFeatures());
+ assertTrue(sq.getDatasetSequence().getSequenceFeatures().isEmpty());
/*
* Corrupt case - no SequenceFeature, dataset's dataset is the original
assertTrue(e.getMessage().toLowerCase()
.contains("implementation error"));
}
- assertNull(sq.getSequenceFeatures());
+ assertTrue(sq.getSequenceFeatures().isEmpty());
}
/**
"group"));
sq.addDBRef(new DBRefEntry("source", "version", "accession"));
assertNull(sq.getDatasetSequence());
- assertNotNull(PA.getValue(sq, "sequenceFeatures")); // to be removed!
assertNotNull(PA.getValue(sq, "sequenceFeatureStore"));
assertNotNull(PA.getValue(sq, "dbrefs"));
assertSame(sq.getDatasetSequence(), rds);
// sequence features and dbrefs transferred to dataset sequence
- assertNull(PA.getValue(sq, "sequenceFeatures"));
assertNull(PA.getValue(sq, "sequenceFeatureStore"));
assertNull(PA.getValue(sq, "dbrefs"));
- assertNotNull(PA.getValue(rds, "sequenceFeatures"));
assertNotNull(PA.getValue(rds, "sequenceFeatureStore"));
assertNotNull(PA.getValue(rds, "dbrefs"));
}
assertEquals("CD", derived.getSequenceAsString());
assertSame(sq.getDatasetSequence(), derived.getDatasetSequence());
- assertNull(sq.sequenceFeatures);
- assertNull(derived.sequenceFeatures);
// derived sequence should access dataset sequence features
assertNotNull(sq.getSequenceFeatures());
- assertArrayEquals(sq.getSequenceFeatures(),
- derived.getSequenceFeatures());
+ assertEquals(sq.getSequenceFeatures(), derived.getSequenceFeatures());
/*
* verify we have primary db refs *just* for PDB IDs with associated
assertEquals(anns[0].score, seq1.getAnnotation()[0].score);
// copy has a copy of the sequence feature:
- SequenceFeature[] sfs = copy.getSequenceFeatures();
- assertEquals(1, sfs.length);
+ List<SequenceFeature> sfs = copy.getSequenceFeatures();
+ assertEquals(1, sfs.size());
if (seq1.getDatasetSequence() != null
&& copy.getDatasetSequence() == seq1.getDatasetSequence())
{
- assertTrue(sfs[0] == seq1.getSequenceFeatures()[0]);
+ assertSame(sfs.get(0), seq1.getSequenceFeatures().get(0));
}
else
{
- assertFalse(sfs[0] == seq1.getSequenceFeatures()[0]);
+ assertNotSame(sfs.get(0), seq1.getSequenceFeatures().get(0));
}
- assertTrue(sfs[0].equals(seq1.getSequenceFeatures()[0]));
+ assertEquals(sfs.get(0), seq1.getSequenceFeatures().get(0));
// copy has a copy of the PDB entry
Vector<PDBEntry> pdbs = copy.getAllPDBEntries();