if (raiseAssert)
{
Assert.fail(message
- + " DBRefEntry for sequence in alignment had map to sequence not in dataset");
+ + " DBRefEntry " + dbr + " for sequence "
+ + seqds
+ + " in alignment has map to sequence not in dataset");
}
return false;
}
// third found.. so
assertFalse(iter.hasNext());
+ // search for annotation on one sequence with a particular label - expect
+ // one
+ SequenceI sqfound;
+ anns = al.findAnnotations(sqfound = al.getSequenceAt(1), null,
+ "Secondary Structure");
+ iter = anns.iterator();
+ assertTrue(iter.hasNext());
+ // expect reference to sequence 1 in the alignment
+ assertTrue(sqfound == iter.next().sequenceRef);
+ assertFalse(iter.hasNext());
+
// null on all parameters == find all annotations
anns = al.findAnnotations(null, null, null);
iter = anns.iterator();
/*
* verify peptide.cdsdbref.peptidedbref is now mapped to peptide dataset
*/
- DBRefEntry[] dbRefs = pep.getDBRefs();
- assertEquals(2, dbRefs.length);
- assertSame(dna, dbRefs[0].map.to);
- assertSame(cds, dbRefs[1].map.to);
- assertEquals(1, dna.getDBRefs().length);
- assertSame(pep.getDatasetSequence(), dna.getDBRefs()[0].map.to);
- assertEquals(1, cds.getDBRefs().length);
- assertSame(pep.getDatasetSequence(), cds.getDBRefs()[0].map.to);
+ List<DBRefEntry> dbRefs = pep.getDBRefs();
+ assertEquals(2, dbRefs.size());
+ assertSame(dna, dbRefs.get(0).map.to);
+ assertSame(cds, dbRefs.get(1).map.to);
+ assertEquals(1, dna.getDBRefs().size());
+ assertSame(pep.getDatasetSequence(), dna.getDBRefs().get(0).map.to);
+ assertEquals(1, cds.getDBRefs().size());
+ assertSame(pep.getDatasetSequence(), cds.getDBRefs().get(0).map.to);
}
@Test(groups = { "Functional" })
// hidden sequences, properties
}
+ /**
+ * test that calcId == null on findOrCreate doesn't raise an NPE, and yields
+ * an annotation with a null calcId
+ *
+ */
+ @Test(groups = "Functional")
+ public void testFindOrCreateForNullCalcId()
+ {
+ SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-");
+ AlignmentI alignment = new Alignment(new SequenceI[] { seq });
+
+ AlignmentAnnotation ala = alignment.findOrCreateAnnotation(
+ "Temperature Factor", null, false, seq, null);
+ assertNotNull(ala);
+ assertEquals(seq, ala.sequenceRef);
+ assertEquals("", ala.calcId);
+ }
+
@Test(groups = "Functional")
public void testPropagateInsertions()
{
assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
}
+
+ @Test(groups = { "Functional" })
+ public void testPadGaps()
+ {
+ SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+ SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+ SequenceI seq3 = new Sequence("seq2", "-PQR");
+ AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+ a.setGapCharacter('.'); // this replaces existing gaps
+ assertEquals("ABCDEF..", seq1.getSequenceAsString());
+ a.padGaps();
+ // trailing gaps are pruned, short sequences padded with gap character
+ assertEquals("ABCDEF.", seq1.getSequenceAsString());
+ assertEquals(".JKLMNO", seq2.getSequenceAsString());
+ assertEquals(".PQR...", seq3.getSequenceAsString());
+ }
+
+ /**
+ * Test for setHiddenColumns, to check it returns true if the hidden columns
+ * have changed, else false
+ */
+ @Test(groups = { "Functional" })
+ public void testSetHiddenColumns()
+ {
+ AlignmentI al = new Alignment(new SequenceI[] {});
+ assertFalse(al.getHiddenColumns().hasHiddenColumns());
+
+ HiddenColumns hc = new HiddenColumns();
+ assertFalse(al.setHiddenColumns(hc)); // no change
+ assertSame(hc, al.getHiddenColumns());
+
+ hc.hideColumns(2, 4);
+ assertTrue(al.getHiddenColumns().hasHiddenColumns());
+
+ /*
+ * set a different object but with the same columns hidden
+ */
+ HiddenColumns hc2 = new HiddenColumns();
+ hc2.hideColumns(2, 4);
+ assertFalse(al.setHiddenColumns(hc2)); // no change
+ assertSame(hc2, al.getHiddenColumns());
+
+ assertTrue(al.setHiddenColumns(null));
+ assertNull(al.getHiddenColumns());
+ assertTrue(al.setHiddenColumns(hc));
+ assertSame(hc, al.getHiddenColumns());
+
+ al.getHiddenColumns().hideColumns(10, 12);
+ hc2.hideColumns(10, 12);
+ assertFalse(al.setHiddenColumns(hc2)); // no change
+
+ /*
+ * hide columns 15-16 then 17-18 in hc
+ * hide columns 15-18 in hc2
+ * these are not now 'equal' objects even though they
+ * represent the same set of columns
+ */
+ assertSame(hc2, al.getHiddenColumns());
+ hc.hideColumns(15, 16);
+ hc.hideColumns(17, 18);
+ hc2.hideColumns(15, 18);
+ assertFalse(hc.equals(hc2));
+ assertTrue(al.setHiddenColumns(hc)); // 'changed'
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetWidth()
+ {
+ SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+ SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+ SequenceI seq3 = new Sequence("seq2", "-PQR");
+ AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+ assertEquals(9, a.getWidth());
+
+ // width includes hidden columns
+ a.getHiddenColumns().hideColumns(2, 5);
+ assertEquals(9, a.getWidth());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetVisibleWidth()
+ {
+ SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+ SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+ SequenceI seq3 = new Sequence("seq2", "-PQR");
+ AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+ assertEquals(9, a.getVisibleWidth());
+
+ // width excludes hidden columns
+ a.getHiddenColumns().hideColumns(2, 5);
+ assertEquals(5, a.getVisibleWidth());
+ }
}