@Test(dataProvider = "assemblyResults")
public void testAddManyHaplotypes(
final java.util.List<AssemblyResult> assemblyResults,
final java.util.List<java.util.List<Haplotype>> haplotypes) {
final AssemblyResultSet subject = new AssemblyResultSet();
for (int i = 0; i < haplotypes.size(); i++) {
final int haplotypeCountBefore = subject.getHaplotypeCount();
final java.util.List<Haplotype> haplos = haplotypes.get(i);
final AssemblyResult ar = assemblyResults.get(i);
for (final Haplotype h : haplos) {
Assert.assertTrue(subject.add(h, ar));
Assert.assertFalse(subject.add(h, ar));
if (h.isReference()) Assert.assertEquals(subject.getReferenceHaplotype(), h);
}
final int haplotypeCountAfter = subject.getHaplotypeCount();
Assert.assertEquals(haplos.size(), haplotypeCountAfter - haplotypeCountBefore);
Assert.assertTrue(subject.getMaximumKmerSize() >= ar.getKmerSize());
Assert.assertTrue(subject.getMinimumKmerSize() <= ar.getKmerSize());
Assert.assertEquals(
subject.getUniqueReadThreadingGraph(ar.getKmerSize()), ar.getThreadingGraph());
}
}
@Test
public void testEmptyResultSet() {
final AssemblyResultSet subject = new AssemblyResultSet();
Assert.assertEquals(subject.getHaplotypeList().size(), 0);
Assert.assertEquals(subject.getHaplotypeCount(), 0);
Assert.assertEquals(subject.getReferenceHaplotype(), null);
Assert.assertEquals(subject.getFullReferenceWithPadding(), null);
Assert.assertEquals(subject.getPaddedReferenceLoc(), null);
Assert.assertEquals(subject.getRegionForGenotyping(), null);
Assert.assertEquals(subject.getUniqueReadThreadingGraph(10), null);
Assert.assertFalse(subject.hasMultipleKmerSizes());
}
@Test
public void testAddReferenceHaplotype() {
final Haplotype ref = new Haplotype("ACGT".getBytes(), true);
ref.setGenomeLocation(genomeLocParser.createGenomeLoc("1", 1, ref.length() + 1));
final AssemblyResultSet subject = new AssemblyResultSet();
Assert.assertTrue(subject.add(ref));
Assert.assertFalse(subject.add(ref));
Assert.assertEquals(subject.getReferenceHaplotype(), ref);
Assert.assertEquals(subject.getHaplotypeCount(), 1);
Assert.assertEquals(subject.getHaplotypeList().size(), 1);
}