Examples of 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

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

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

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

            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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