Examples of SeekableStream

Examples of com.sun.media.jai.codec.SeekableStream

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        try {
            // Create a SeekableStream from the file name (first parameter).
            String fileName = (String)args.getObjectParameter(0);

      SeekableStream src = null;
      try {
                src = new FileSeekableStream(fileName);
            } catch (FileNotFoundException fnfe) {
    // Try to get the file as an InputStream resource. This would
    // happen when the application and image file are packaged in
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Examples of com.sun.media.jai.codec.SeekableStream

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     * Creates an image from a SeekableStream.
     */
    public RenderedImage create(ParameterBlock paramBlock,
                                RenderingHints renderHints) {
        ImagingListener listener = ImageUtil.getImagingListener(renderHints);
        SeekableStream src = (SeekableStream)paramBlock.getObjectParameter(0);
        try {
            src.seek(0L);
        } catch (IOException e) {
            listener.errorOccurred(JaiI18N.getString("StreamRIF0"),
                                   e, this, false);
//            e.printStackTrace();
            return null;
        }

        ImageDecodeParam param = null;
        if (paramBlock.getNumParameters() > 1) {
            param = (ImageDecodeParam)paramBlock.getObjectParameter(1);
        }

        String[] names = ImageCodec.getDecoderNames(src);

        OperationRegistry registry =
            JAI.getDefaultInstance().getOperationRegistry();
        int bound = OpImage.OP_IO_BOUND;
        ImageLayout layout = RIFUtil.getImageLayoutHint(renderHints);

        if (renderHints != null) {
            RenderingHints.Key key;

            key = JAI.KEY_OPERATION_REGISTRY;
            if (renderHints.containsKey(key)) {
                registry = (OperationRegistry)renderHints.get(key);
            }

            key = JAI.KEY_OPERATION_BOUND;
            if (renderHints.containsKey(key)) {
                bound = ((Integer)renderHints.get(key)).intValue();
            }
        }

        // Try to create a JAI operation with the given name
        for (int i = 0; i < names.length; i++) {
            RenderedImageFactory rif = null;
            try {
                rif = RIFRegistry.get(registry, names[i]);
            } catch(IllegalArgumentException iae) {
                // ignore IAE.
            }
            if(rif != null) {
                RenderedImage im = RIFRegistry.create(registry, names[i],
                                                      paramBlock, renderHints);
                if (im != null) {
                    return im;
                }
            }
        }

        // Set flag indicating that a recovery may be attempted if
        // an OutOfMemoryError occurs during the decodeAsRenderedImage()
        // call - which is only possible if the stream can seek backwards.
        boolean canAttemptRecovery = src.canSeekBackwards();

        // Save the stream position prior to decodeAsRenderedImage().
        long streamPosition = Long.MIN_VALUE;
        if(canAttemptRecovery) {
            try {
                streamPosition = src.getFilePointer();
            } catch(IOException ioe) {
                listener.errorOccurred(JaiI18N.getString("StreamRIF1"),
                                       ioe, this, false);
                // Unset the recovery attempt flag but otherwise
                // ignore the exception.
                canAttemptRecovery = false;
            }
        }

        // Try to create an ImageDecoder directly
        for (int i = 0; i < names.length; i++) {
            ImageDecoder dec =
                ImageCodec.createImageDecoder(names[i], src, param);
            RenderedImage im = null;
            try {
                im = dec.decodeAsRenderedImage();
            } catch(OutOfMemoryError memoryError) {
                // Ran out of memory - may be due to the decoder being
                // obliged to read the entire image when it creates the
                // RenderedImage it returns.
                if(canAttemptRecovery) {
                    // First flush the cache if one is defined.
                    TileCache cache = RIFUtil.getTileCacheHint(renderHints);
                    if(cache != null) {
                        cache.flush();
                    }

                    // Force garbage collection.
                    System.gc(); //slow

                    try {
                        // Reposition the stream before the previous decoding.
                        src.seek(streamPosition);

                        // Retry image decoding.
                        im = dec.decodeAsRenderedImage();
                    } catch (IOException ioe) {
                        listener.errorOccurred(JaiI18N.getString("StreamRIF2"),
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Examples of com.sun.media.jai.codec.SeekableStream

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        {
            fract, fract,
            fract, fract,
            fract, fract
        };
        SeekableStream s = SeekableStream.wrapInputStream(stream, false);
        RenderedOp op = JAI.create("Stream", s);

        RenderingHints hints = new RenderingHints(
                RenderingHints.KEY_RENDERING,
                RenderingHints.VALUE_RENDER_QUALITY);
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Examples of htsjdk.samtools.seekablestream.SeekableStream

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        int startPosition = 500000;
        int length = 50000;

        byte[] buffer1 = new byte[length];
        SeekableStream unBufferedStream = new SeekableFileStream(BAM_FILE);
        unBufferedStream.seek(startPosition);
        int bytesRead = unBufferedStream.read(buffer1, 0, length);
        assertEquals(length, bytesRead);

        byte[] buffer2 = new byte[length];
        SeekableStream bufferedStream = new IGVSeekableBufferedStream(new SeekableHTTPStream(new URL(BAM_URL_STRING)));
        bufferedStream.seek(startPosition);
        bytesRead = bufferedStream.read(buffer2, 0, length);
        assertEquals(length, bytesRead);

        assertArraysEqual(buffer1, buffer2);
    }
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Examples of htsjdk.samtools.seekablestream.SeekableStream

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        return new SAMQueryIterator(iter);
    }

    private SAMFileReader getSAMFileReader(String samFile, long startPosition) {
        try {
            SeekableStream stream = IGVSeekableStreamFactory.getInstance().getStreamFor(samFile);
            if (startPosition >= 0) {
                stream.seek(startPosition);
            }
            SAMFileReader reader = new SAMFileReader(stream);
            reader.setValidationStringency(ValidationStringency.SILENT);

            //Need to keep the file source, if loading lazily
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Examples of htsjdk.samtools.seekablestream.SeekableStream

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            indexFile = getIndexFile(locator);
            if (indexFile == null) {
                throw new RuntimeException("Could not load index file for file: " + url.getPath());
            }

            SeekableStream ss = new IGVSeekableBufferedStream(IGVSeekableStreamFactory.getInstance().getStreamFor(url), 128000);
            //SeekableStream ss = getSeekableStream(url);
            log.debug("Initializing SAMFileReader");

            reader = new SAMFileReader(ss, indexFile, false);
        } else {
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Examples of htsjdk.samtools.seekablestream.SeekableStream

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    }

    public CloseableIterator<PicardAlignment> query(String sequence, int start, int end, boolean contained) {
        try {
            if (reader == null) {
                SeekableStream ss = new IGVSeekableBufferedStream(IGVSeekableStreamFactory.getInstance().getStreamFor(url));
                reader = new SAMFileReader(ss, indexFile, false);
            }
            CloseableIterator<SAMRecord> iter = reader.query(sequence, start + 1, end, contained);
            return new WrappedIterator(iter);
        } catch (IOException e) {
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Examples of htsjdk.samtools.seekablestream.SeekableStream

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        loadHeader();
        compressionUtils = new CompressionUtils();
    }

    private void loadHeader() throws IOException {
        SeekableStream ss = null;
        try {
            ss = IGVSeekableStreamFactory.getInstance().getStreamFor(path);
            LittleEndianInputStream is = new LittleEndianInputStream(new BufferedInputStream(ss));

            long indexPosition = is.readLong();
            trackLine = is.readString();
            nTimePoints = is.readInt();
            times = new int[nTimePoints];
            for (int t = 0; t < nTimePoints; t++) {
                times[t] = is.readInt();
            }
            signalsPath = is.readString();
            timeSignalsPath = new String[nTimePoints];
            for (int t = 0; t < nTimePoints; t++) {
                timeSignalsPath[t] = is.readString();
            }

            chrIndex = new HashMap<String, Long>();

            ss.seek(indexPosition);
            is = new LittleEndianInputStream(new BufferedInputStream(ss));
            int nChrs = is.readInt();
            for (int i = 0; i < nChrs; i++) {
                String chr = is.readString();
                long pos = is.readLong();
                chrIndex.put(chr, pos);
            }

        } finally {
            if (ss != null) ss.close();
        }

    }
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Examples of htsjdk.samtools.seekablestream.SeekableStream

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        if (chrPos == null) {
            return new ArrayList<Peak>();
        } else {
            List<Peak> peaks = new ArrayList<Peak>(10000);
            LittleEndianInputStream reader = null;
            SeekableStream ss = null;
            try {

                ss = IGVSeekableStreamFactory.getInstance().getStreamFor(path);
                int bufferSize = 512000;
                long contentLength = ss.length();
                if(contentLength > 0) {
                    bufferSize = (int) Math.min(contentLength, bufferSize);
                }

                IGVSeekableBufferedStream bufferedStream = new IGVSeekableBufferedStream(ss, bufferSize);
                bufferedStream.seek(chrPos);

                reader = new LittleEndianInputStream(bufferedStream);
                int nBytes = reader.readInt();

                byte[] compressedBytes = new byte[nBytes];
                bufferedStream.readFully(compressedBytes);

                byte[] bytes = compressionUtils.decompress(compressedBytes);

                ByteArrayInputStream bis = new ByteArrayInputStream(bytes);
                reader = new LittleEndianInputStream(bis);

                String chrRecorded = reader.readString();
                if (!chrRecorded.equals(chr)) {
                    throw new RuntimeException("Error paring peak file: " + path +
                            "<br>Expected: " + chr + "  found: " + chrRecorded);
                }

                int nDataPoints = reader.readInt();
                for (int n = 0; n < nDataPoints; n++) {
                    int start = reader.readInt();
                    int end = reader.readInt();
                    float combinedScore = reader.readFloat();
                    float[] timePointScores = new float[nTimePoints];
                    for (int i = 0; i < nTimePoints; i++) {
                        timePointScores[i] = reader.readFloat();
                    }
                    peaks.add(new Peak(chr, start, end, "", combinedScore, timePointScores));

                }
                return peaks;

            } finally {
                if (ss != null) ss.close();
            }
        }

    }
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Examples of htsjdk.samtools.seekablestream.SeekableStream

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        long startPosition = fileLength - remainder;
        int length = 1000;


        byte[] buffer = new byte[length];
        SeekableStream bufferedStream = new IGVSeekableBufferedStream(new SeekableHTTPStream(new URL(BAM_URL_STRING)));
        bufferedStream.seek(startPosition);
        int bytesRead = bufferedStream.read(buffer, 0, length);
        assertEquals(remainder, bytesRead);

        // Subsequent reads should return -1
        bytesRead = bufferedStream.read(buffer, 0, length);
        assertEquals(-1, bytesRead);
    }
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