Examples of org.broad.igv.util.stream.IGVSeekableHTTPStream

org.broad.igv.util.stream.IGVSeekableHTTPStream
TODO Get rid of this class Temporary workaround to let us use IGVUrlHelper, think it's what's causing the issue with reading TDF from web start over http

    @Test
    public void testRead() throws Exception {


        String tdfFile = "http://www.broadinstitute.org/igvdata/annotations/hg18/conservation/omega.12mer.tdf";


        IGVSeekableHTTPStream hs = new IGVSeekableHTTPStream(new URL(tdfFile));
        final int position = 100;
        hs.seek(position);
        final int range = 1000;
        byte[] expectedBytes = new byte[range];
        hs.read(expectedBytes, 0, expectedBytes.length);


        SeekableServiceStream sss = new SeekableServiceStream(new URL(tdfFile));
        sss.seek(position);
        byte[] bytes = new byte[range];
        sss.read(bytes, 0, bytes.length);

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                        // Non-broad URL
                        int l = (int) Math.min(1000, HttpUtils.getInstance().getContentLength(url));
                        if (l > 100) {


                            byte[] firstBytes = new byte[l];
                            str = new IGVSeekableHTTPStream(url);
                            str.readFully(firstBytes);


                            int end = firstBytes.length;
                            int start = end - 100;
                            str.seek(start);

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            testURL = "http://www.broadinstitute.org/igvdata/annotations/seq/hg19/chr12.txt";
        }


        byte[] expectedBytes = {'T', 'C', 'G', 'C', 'T', 'T', 'G', 'A', 'A', 'C', 'C', 'C', 'G', 'G',
                'G', 'A', 'G', 'A', 'G', 'G'};
        IGVSeekableHTTPStream str = null;


        try {
            str = new IGVSeekableHTTPStream(new URL(testURL));


            str.seek(25350000);
            byte[] buffer = new byte[80000];
            str.read(buffer);
            String result = new String(buffer);
            for (int i = 0; i < expectedBytes.length; i++) {
                if (buffer[i] != expectedBytes[i]) {
                    return false;
                }
            }
            return true;
        } finally {
            if (str != null) str.close();
        }
    }

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Related Classes of org.broad.igv.util.stream.IGVSeekableHTTPStream

org.broad.igv.util.HttpUtils

org.broad.igv.util.SeekableServiceStreamTest

java.io.InputStream

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