@Override public PositionalBufferedStream makeSourceFromStream(final InputStream bufferedInputStream) { if (bufferedInputStream instanceof PositionalBufferedStream) return (PositionalBufferedStream) bufferedInputStream; else return new PositionalBufferedStream(bufferedInputStream); }
@Override public PositionalBufferedStream makeSourceFromStream(final InputStream bufferedInputStream) { return new PositionalBufferedStream(bufferedInputStream); } }
@Override public PositionalBufferedStream makeSourceFromStream(final InputStream bufferedInputStream) { if (bufferedInputStream instanceof PositionalBufferedStream) return (PositionalBufferedStream) bufferedInputStream; else return new PositionalBufferedStream(bufferedInputStream); }
/** * Note: This class implements LocationAware, which requires preservation of virtual file pointers on BGZF inputs. * However, if the inputStream wrapped by this class is a BlockCompressedInputStream, it violates that contract by * wrapping the stream and returning positional file offsets instead. * * @deprecated 8/8/2017 use {@link #from} */ @Deprecated public AsciiLineReader(final InputStream is){ // NOTE: This will wrap the input stream in a PositionalBufferedStream even if its already a PositionalBufferedStream this(new PositionalBufferedStream(is)); }
/** * Note: This class implements LocationAware, which requires preservation of virtual file pointers on BGZF inputs. * However, if the inputStream wrapped by this class is a BlockCompressedInputStream, it violates that contract by * wrapping the stream and returning positional file offsets instead. * * @deprecated 8/8/2017 use {@link #from} */ @Deprecated public AsciiLineReader(final InputStream is){ // NOTE: This will wrap the input stream in a PositionalBufferedStream even if its already a PositionalBufferedStream this(new PositionalBufferedStream(is)); }
EmblTableIterator(InputStream stream) { if(stream instanceof PositionalBufferedStream) { is = (PositionalBufferedStream) stream; } else { is = new PositionalBufferedStream(stream); } reader = new BufferedReader(new InputStreamReader(stream)); // Advance to first record next(); }
private static PositionalBufferedStream initIndexablePositionalStream(final File inputFile) { try { final FileInputStream fileStream = new FileInputStream(inputFile); return new PositionalBufferedStream(fileStream); } catch (final FileNotFoundException e) { throw new TribbleException.FeatureFileDoesntExist("Unable to open the input file, most likely the file doesn't exist.", inputFile.getAbsolutePath()); } }
private PositionalBufferedStream initStream(final File inputFile, final long skip) { try { final FileInputStream is = new FileInputStream(inputFile); final PositionalBufferedStream pbs = new PositionalBufferedStream(is); if ( skip > 0 ) pbs.skip(skip); return pbs; } catch (final FileNotFoundException e) { throw new TribbleException.FeatureFileDoesntExist("Unable to open the input file, most likely the file doesn't exist.", inputFile.getAbsolutePath()); } catch (final IOException e) { throw new TribbleException.MalformedFeatureFile("Error initializing stream", inputFile.getAbsolutePath(), e); } }
public void tstReadCorrectNumberBytes(int bufferSize) throws Exception{ InputStream is = new PositionalBufferedStream(FileIs, bufferSize); long count = 0; while(is.read() >= 0){ count++; } Assert.assertEquals(count, expectedBytes); }
@Override public LocationAware makeIndexableSourceFromStream(final InputStream bufferedInputStream) { final PositionalBufferedStream pbs; if (bufferedInputStream instanceof PositionalBufferedStream) { pbs = (PositionalBufferedStream) bufferedInputStream; } else { pbs = new PositionalBufferedStream(bufferedInputStream); } return new AsciiLineReaderIterator(new AsciiLineReader(pbs)); }
@Override public LocationAware makeIndexableSourceFromStream(final InputStream bufferedInputStream) { final PositionalBufferedStream pbs; if (bufferedInputStream instanceof PositionalBufferedStream) { pbs = (PositionalBufferedStream) bufferedInputStream; } else { pbs = new PositionalBufferedStream(bufferedInputStream); } return new AsciiLineReaderIterator(new AsciiLineReader(pbs)); }
public LineIterator getLineIterator() { try { return new LineIteratorImpl(new SynchronousLineReader(new PositionalBufferedStream(new FileInputStream(hapMapFile)))); } catch (FileNotFoundException e) { Assert.fail("Unable to open hapmap file : " + hapMapFile); } return null; // for intellij, it doesn't know that assert.fail is fatal }
@DataProvider(name = "fromStream") public Object[][] getFromStreamData() { return new Object[][]{ { new BlockCompressedInputStream(new ByteArrayInputStream(new byte[10])), BlockCompressedAsciiLineReader.class }, { new PositionalBufferedStream(new ByteArrayInputStream(new byte[10])), AsciiLineReader.class }, { new ByteArrayInputStream(new byte[10]), AsciiLineReader.class } }; }
@Test public void testLineReaderIterator_streamConstructor() throws Exception { final File filePath = new File(TestUtils.DATA_DIR + "gwas/smallp.gwas"); final LineIterator lineIterator = new LineIteratorImpl(new SynchronousLineReader(new PositionalBufferedStream(new FileInputStream(filePath)))); final BufferedReader br = new BufferedReader(new InputStreamReader(new FileInputStream(filePath))); while (lineIterator.hasNext()) { Assert.assertEquals(lineIterator.next(), br.readLine()); } Assert.assertNull(br.readLine()); }
@Test(expectedExceptions = UnsupportedOperationException.class) public void testRejectPositionalInputStream() throws IOException { final File multiBlockFile = File.createTempFile("BlockCompressedAsciiLineReaderTest", ".gz"); multiBlockFile.deleteOnExit(); populateMultiBlockCompressedFile(multiBlockFile); try (final BlockCompressedInputStream bcis = new BlockCompressedInputStream(multiBlockFile); final BlockCompressedAsciiLineReader asciiLineReader = new BlockCompressedAsciiLineReader(bcis)) { asciiLineReader.readLine(new PositionalBufferedStream(new ByteArrayInputStream(new byte[1100]))); } }
@Ignore //@Test public void rawTestFile() throws Exception { String path = "/path/to/myfile.bcf"; PositionalBufferedStream ps = new PositionalBufferedStream(new FileInputStream(path)); BCF2Codec codec = new BCF2Codec(); codec.readHeader(ps); }
@Override public Iterator<T> iterator() { return this; } }
@Override public Iterator<T> iterator() { return this; } }
@Test public void testIsDone() throws Exception{ PositionalBufferedStream is = new PositionalBufferedStream(FileIs); while(!is.isDone()){ is.read(); } Assert.assertTrue(is.isDone()); Assert.assertEquals(is.getPosition(), expectedBytes); }
@Test public void testPeek() throws Exception{ int trials = 10; PositionalBufferedStream is = new PositionalBufferedStream(FileIs); int bb = is.peek(); for(int ii=0; ii < trials; ii++){ Assert.assertEquals(is.peek(), bb); Assert.assertEquals(is.getPosition(), 0); } while((bb = is.peek()) >= 0){ Assert.assertEquals(is.read(), bb); } }