@Test
public void testUserFriendlyList() {
Assert.assertTrue(
manager.userFriendlyListOfAvailableFeatures().length() > 0,
"Expected at least one codec to be listed");
Assert.assertTrue(
manager.userFriendlyListOfAvailableFeatures().split(",").length > 0,
"Expected at least two codecs, but only saw one");
}
@Test
public void testCodecCreation() {
FeatureManager.FeatureDescriptor descriptor = manager.getByName("vcf");
Assert.assertNotNull(descriptor, "Couldn't find VCF feature descriptor!");
FeatureCodec c = manager.createCodec(descriptor, "foo", genomeLocParser);
Assert.assertNotNull(c, "Couldn't create codec");
Assert.assertEquals(c.getClass(), descriptor.getCodecClass());
Assert.assertEquals(c.getFeatureType(), descriptor.getFeatureClass());
}
@Test(dataProvider = "tests")
public void testGetters(FMTest params) {
params.assertExpected(manager.getByCodec(params.codec));
params.assertExpected(manager.getByName(params.name));
params.assertExpected(manager.getByName(params.name.toLowerCase()));
params.assertExpected(manager.getByName(params.name.toUpperCase()));
Collection<FeatureManager.FeatureDescriptor> descriptors = manager.getByFeature(params.feature);
Assert.assertTrue(descriptors.size() > 0, "Look up by FeatureClass failed");
}
@Test
public void testGetByFileNoMatch() {
FeatureManager.FeatureDescriptor byFile = manager.getByFiletype(RANDOM_FILE);
Assert.assertNull(
byFile,
"Found type " + byFile + " associated with RANDOM, non-Tribble file " + RANDOM_FILE);
}
public void train(int startingIndex, ModelManager modelInfo, List data) {
Assert.a(allFeatureTypes.size() > 0, "No features types have been assigned.");
Assert.a(startIndexes == null, "FeatureManager has already been trained.");
startIx = startingIndex;
// Train each of the individual FeatureManagers and calculate offsets
startIndexes = new int[allFeatureTypes.size()];
totalFeatures = 0;
for (int i = 0; i < startIndexes.length; ++i) {
startIndexes[i] = totalFeatures + startIx;
FeatureManager fm = allFeatureTypes.get(i);
List compData =
fm.getInputComponent() == null ? data : new ComponentList(data, fm.getInputComponent());
fm.train(totalFeatures, modelInfo, compData);
totalFeatures += fm.getNumFeatures();
}
}
@Test(dataProvider = "tests")
public void testGetByFile(FMTest params) {
if (params.associatedFile != null) {
FeatureManager.FeatureDescriptor byFile = manager.getByFiletype(params.associatedFile);
Assert.assertNotNull(
byFile, "Couldn't find any type associated with file " + params.associatedFile);
params.assertExpected(byFile);
}
}
public void addFeatureManager(String name, String inputParams, FeatureManager fm) {
Assert.a(startIndexes == null, "Attempted to add a new FeatureManager after training.");
if (name != null) fm.setInputComponent(name);
allFeatureTypes.add(fm);
// Add each feature type into the right list for evalution
if (fm instanceof FeatureManagerNode) {
nodeFeatureTypes.add((FeatureManagerNode) fm);
}
if (fm instanceof FeatureManagerEdge) {
edgeFeatureTypes.add((FeatureManagerEdge) fm);
}
if (fm instanceof FeatureManagerNodeExplicitLength) {
explicitLengthNodeFeatureTypes.add((FeatureManagerNodeExplicitLength) fm);
}
if (fm instanceof FeatureManagerEdgeExplicitLength) {
explicitLengthEdgeFeatureTypes.add((FeatureManagerEdgeExplicitLength) fm);
}
}
@Test
public void testManagerCreation() {
Assert.assertTrue(manager.getFeatureDescriptors().size() > 0);
}
