@Override public void testEquals() throws IOException { final File dir = FileHelper.createTempDirectory(mDir); final File otherDir = FileHelper.createTempDirectory(mDir); ReaderTestUtils.getReaderDNAFastq("", dir, false).close(); ReaderTestUtils.getReaderDNAFastq("", otherDir, false).close(); final CompressedMemorySequencesReader cmsr = new CompressedMemorySequencesReader( dir, new IndexFile(dir), 5, true, false, new LongRange(0, 0)); final CompressedMemorySequencesReader other = new CompressedMemorySequencesReader( otherDir, new IndexFile(dir), 5, true, false, new LongRange(0, 0)); assertTrue(cmsr.equals(cmsr)); assertFalse(cmsr.equals(null)); assertFalse(cmsr.equals(other)); assertFalse(cmsr.equals("FDSA")); }
@Override public void setUp() throws IOException { Diagnostic.setLogStream(); mDir = FileHelper.createTempDirectory(); }
public void testValidator() throws IOException { Diagnostic.setLogStream(); final MemoryPrintStream err = new MemoryPrintStream(); final CliDiagnosticListener listener = new CliDiagnosticListener(err.printStream()); Diagnostic.addListener(listener); final File tempDir = FileHelper.createTempDirectory(); try { final CFlags flags = new CFlags("PhyloTest", TestUtils.getNullPrintStream(), err.printStream()); SimilarityCli.initFlags(flags); checkErrorMessage( flags, new String[] {"-o", "blah", "-I", "ba", "-i", "humbug"}, err, "Only set one of --input or --input-list-file"); checkErrorMessage( flags, new String[] {"-o", "blah", "-i", "humbug"}, err, "The specified SDF, \"humbug\", does not exist."); final File fakePaired = new File(tempDir, "fakePaired"); assertTrue(fakePaired.mkdir()); final File left = new File(fakePaired, "left"); assertTrue(left.mkdir()); assertTrue(new File(fakePaired, "right").mkdir()); checkErrorMessage( flags, new String[] {"-o", "blah", "-i", fakePaired.getPath()}, err, "The specified SDF, \"" + fakePaired.getPath() + "\", is a paired end SDF."); checkErrorMessage( flags, new String[] {"-o", "blah"}, err, "Must set one of --input or --input-list-file"); checkErrorMessage( flags, new String[] {"-o", "blah", "-I", "ba"}, err, "The specified list file, \"ba\", does not exist."); checkErrorMessage( flags, new String[] {"-o", "blah", "-I", fakePaired.getPath()}, err, "The specified list file,", "\"" + fakePaired.getPath() + "\",", "directory."); final File fakeList = new File(tempDir, "fakeList.txt"); assertTrue(fakeList.createNewFile()); checkErrorMessage( flags, new String[] {"-o", fakePaired.getPath(), "-I", fakeList.getPath()}, err, "The directory", "\"" + fakePaired.getPath() + "\"", "already exists."); checkErrorMessage( flags, new String[] {"-o", "blah", "-I", fakeList.getPath(), "-w", "-1"}, err, "The specified flag \"--word\" has invalid value \"-1\". It should be greater than or equal to \"1\"."); checkErrorMessage( flags, new String[] {"-o", "blah", "-I", fakeList.getPath(), "-w", "0"}, err, "The specified flag \"--word\" has invalid value \"0\". It should be greater than or equal to \"1\"."); checkErrorMessage( flags, new String[] {"-o", "blah", "-I", fakeList.getPath(), "-w", "33"}, err, "The specified flag \"--word\" has invalid value \"33\". It should be less than or equal to \"32\"."); checkErrorMessage( flags, new String[] {"-o", "blah", "-I", fakeList.getPath(), "--max-reads", "0"}, err, "The --max-reads must be greater than 0"); checkErrorMessage( flags, new String[] {"-o", "blah", "-I", fakeList.getPath(), "-w", "20", "-s", "20"}, err); checkErrorMessage( flags, new String[] {"-o", "blah", "-i", left.getPath(), "--max-reads", "1"}, err, "Only set --max-reads when using --input-list-file"); checkErrorMessage(flags, new String[] {"-o", "blah", "-i", left.getPath()}, err); } finally { Diagnostic.removeListener(listener); err.close(); assertTrue(FileHelper.deleteAll(tempDir)); } }