@Test public void testNexusReader() throws IOException { File testFile = FileUtils.toFile(NexusReaderTest.class.getResource("/bees.nex")); DistanceMatrix distanceMatrix = new NexusReader().readDistanceMatrix(testFile); assertTrue(distanceMatrix.size() == 6); }
@Override public DistanceMatrix readDistanceMatrix(File file) throws IOException { return this.parse(file).getDistanceMatrix(); }
NexusReader extends AbstractSpectreReader { @Override public DistanceMatrix readDistanceMatrix(File file) throws IOException { return this.parse(file).getDistanceMatrix(); } }
NexusReader extends AbstractSpectreReader { @Override public DistanceMatrix readDistanceMatrix(File file) throws IOException { return this.parse(file).getDistanceMatrix(); }  }
NexusReader extends AbstractSpectreReader { @Override public DistanceMatrix readDistanceMatrix(File file) throws IOException { return this.parse(file).getDistanceMatrix(); }  Nexus parse(File file); @Override DistanceMatrix readDistanceMatrix(File file); @Override Sequences readAlignment(File file); @Override Locations readLocations(File file); @Override List<NewickTree> readTrees(File input, double weight); @Override SplitSystem readSplitSystem(File file); @Override String[] commonFileExtensions(); @Override String getIdentifier(); @Override boolean acceptsDataType(SpectreDataType spectreDataType); IdentifierList extractCircOrdering(File file); List<String> extractBlock(File file, String blockName); Nexus readNexusData(File inFile); }
NexusReader extends AbstractSpectreReader { @Override public DistanceMatrix readDistanceMatrix(File file) throws IOException { return this.parse(file).getDistanceMatrix(); }  Nexus parse(File file); @Override DistanceMatrix readDistanceMatrix(File file); @Override Sequences readAlignment(File file); @Override Locations readLocations(File file); @Override List<NewickTree> readTrees(File input, double weight); @Override SplitSystem readSplitSystem(File file); @Override String[] commonFileExtensions(); @Override String getIdentifier(); @Override boolean acceptsDataType(SpectreDataType spectreDataType); IdentifierList extractCircOrdering(File file); List<String> extractBlock(File file, String blockName); Nexus readNexusData(File inFile);  }