@Test public void testEmbossReaderAsh() throws IOException { File testFile = FileUtils.toFile(EmbossReaderTest.class.getResource("/ash.distmat")); DistanceMatrix distanceMatrix = new EmbossReader().readDistanceMatrix(testFile); assertTrue(distanceMatrix.size() == 58); }
@Override public DistanceMatrix readDistanceMatrix(File file) throws IOException { if (file == null) { throw new NullPointerException("Must specify an emboss distmat file to read"); } if (!file.exists()) { throw new IOException("Emboss distmat file does not exist: " + file.getAbsolutePath()); } if (!file.canRead()) { throw new IOException("Emboss distmat file cannot be read: " + file.getAbsolutePath()); } List<String> inLines = FileUtils.readLines(file, "UTF-8"); return alternativeParser(inLines); }
EmbossReader extends AbstractSpectreReader { @Override public DistanceMatrix readDistanceMatrix(File file) throws IOException { if (file == null) { throw new NullPointerException("Must specify an emboss distmat file to read"); } if (!file.exists()) { throw new IOException("Emboss distmat file does not exist: " + file.getAbsolutePath()); } if (!file.canRead()) { throw new IOException("Emboss distmat file cannot be read: " + file.getAbsolutePath()); } List<String> inLines = FileUtils.readLines(file, "UTF-8"); return alternativeParser(inLines); } }
EmbossReader extends AbstractSpectreReader { @Override public DistanceMatrix readDistanceMatrix(File file) throws IOException { if (file == null) { throw new NullPointerException("Must specify an emboss distmat file to read"); } if (!file.exists()) { throw new IOException("Emboss distmat file does not exist: " + file.getAbsolutePath()); } if (!file.canRead()) { throw new IOException("Emboss distmat file cannot be read: " + file.getAbsolutePath()); } List<String> inLines = FileUtils.readLines(file, "UTF-8"); return alternativeParser(inLines); }  }
EmbossReader extends AbstractSpectreReader { @Override public DistanceMatrix readDistanceMatrix(File file) throws IOException { if (file == null) { throw new NullPointerException("Must specify an emboss distmat file to read"); } if (!file.exists()) { throw new IOException("Emboss distmat file does not exist: " + file.getAbsolutePath()); } if (!file.canRead()) { throw new IOException("Emboss distmat file cannot be read: " + file.getAbsolutePath()); } List<String> inLines = FileUtils.readLines(file, "UTF-8"); return alternativeParser(inLines); }  @Override DistanceMatrix readDistanceMatrix(File file); @Override String[] commonFileExtensions(); @Override String getIdentifier(); @Override boolean acceptsDataType(SpectreDataType spectreDataType); }
EmbossReader extends AbstractSpectreReader { @Override public DistanceMatrix readDistanceMatrix(File file) throws IOException { if (file == null) { throw new NullPointerException("Must specify an emboss distmat file to read"); } if (!file.exists()) { throw new IOException("Emboss distmat file does not exist: " + file.getAbsolutePath()); } if (!file.canRead()) { throw new IOException("Emboss distmat file cannot be read: " + file.getAbsolutePath()); } List<String> inLines = FileUtils.readLines(file, "UTF-8"); return alternativeParser(inLines); }  @Override DistanceMatrix readDistanceMatrix(File file); @Override String[] commonFileExtensions(); @Override String getIdentifier(); @Override boolean acceptsDataType(SpectreDataType spectreDataType);  }