@Test(dataProvider = "CompleteCycleData")
public void testSplitterCompleteCycle(
final List<String> strings, final boolean hasTop, final boolean hasBot) {
final SeqGraph graph = new SeqGraph(11);
int edgeWeight = 1;
final SeqVertex top = hasTop ? new SeqVertex("AAAAAAAA") : null;
final SeqVertex bot = hasBot ? new SeqVertex("GGGGGGGG") : null;
final List<SeqVertex> v = new ArrayList<>();
for (final String s : strings) {
v.add(new SeqVertex(s));
}
graph.addVertices(v.toArray(new SeqVertex[v.size()]));
final SeqVertex first = v.get(0);
if (hasTop) {
graph.addVertex(top);
for (final SeqVertex vi : v) graph.addEdge(top, vi, new BaseEdge(vi == first, edgeWeight++));
}
if (hasBot) {
graph.addVertex(bot);
for (final SeqVertex vi : v) graph.addEdge(vi, bot, new BaseEdge(vi == first, edgeWeight++));
}
final Set<String> haplotypes = new HashSet<>();
final KBestHaplotypeFinder originalPaths =
new KBestHaplotypeFinder((SeqGraph) graph.clone(), graph.getSources(), graph.getSinks());
for (final KBestHaplotype path : originalPaths) haplotypes.add(new String(path.bases()));
final SharedVertexSequenceSplitter splitter = new SharedVertexSequenceSplitter(graph, v);
splitter.split();
if (PRINT_GRAPHS)
graph.printGraph(
new File(Utils.join("_", strings) + "_" + hasTop + "_" + hasBot + ".original.dot"), 0);
if (PRINT_GRAPHS)
splitter.splitGraph.printGraph(
new File(Utils.join("_", strings) + "_" + hasTop + "_" + hasBot + ".split.dot"), 0);
splitter.updateGraph(top, bot);
if (PRINT_GRAPHS)
graph.printGraph(
new File(Utils.join("_", strings) + "_" + hasTop + "_" + hasBot + ".updated.dot"), 0);
final KBestHaplotypeFinder splitPaths =
new KBestHaplotypeFinder(graph, graph.getSources(), graph.getSinks());
for (final KBestHaplotype path : splitPaths) {
final String h = new String(path.bases());
Assert.assertTrue(haplotypes.contains(h), "Failed to find haplotype " + h);
}
final List<byte[]> sortedOriginalPaths = new ArrayList<>(originalPaths.size());
for (final KBestHaplotype kbh : originalPaths.unique()) sortedOriginalPaths.add(kbh.bases());
Collections.sort(sortedOriginalPaths, BaseUtils.BASES_COMPARATOR);
final List<byte[]> sortedSplitPaths = new ArrayList<>(splitPaths.size());
for (final KBestHaplotype kbh : splitPaths.unique()) sortedSplitPaths.add(kbh.bases());
Collections.sort(sortedSplitPaths, BaseUtils.BASES_COMPARATOR);
Assert.assertEquals(
sortedSplitPaths,
sortedOriginalPaths,
Utils.join("_", strings) + "_" + hasTop + "_" + hasBot);
}
