Examples of edu.cornell.med.icb.goby.alignments.AlignmentReaderImpl

Package edu.cornell.med.icb.goby.alignments

Examples of edu.cornell.med.icb.goby.alignments.AlignmentReaderImpl

edu.cornell.med.icb.goby.alignments.AlignmentReaderImpl


    }


    @Test
    public void testOldGobyHybrid() throws IOException {
        AlignmentReader reader = new AlignmentReaderImpl(TestUtils.DATA_DIR + "goby/GDFQPGI-pickrellNA18486_yale-hybrid.entries");
        org.junit.Assert.assertTrue(reader.hasNext());
    }

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    }


    // Test below is disabled, it depends on a resource we don't control
    @Ignore
    public void testOldGobyHybridUrl() throws IOException {
        AlignmentReader reader = new AlignmentReaderImpl("http://gobyweb.apps.campagnelab.org/data/H_T_D/MYHZZJH/MYHZZJH-hybrid-domain.header");
        reader.reposition(10, 1210);
        final Alignments.AlignmentEntry entry = reader.skipTo(10, 1210);
        org.junit.Assert.assertNotNull(entry);
    }

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     * @param filename The filename of any file component for a Goby compact alignment, or the alignment basename.
     * @throws IOException If an error occurs reading the alignment.
     */
    public GobyAlignmentQueryReader(String filename) throws IOException {
        basename = filename;
        reader = new AlignmentReaderImpl(filename);
        reader.readHeader();
        if (!reader.isIndexed()) {
            final String errorMessage = "Goby alignment files must be sorted in order to be loaded in IGV. See the IGV tutorial at http://goby.campagnelab.org/ for details.";
            System.err.println(errorMessage);
            throw new UnsupportedOperationException(errorMessage);

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     */
    private AlignmentReaderImpl getNewLocalReader() {
        if (reader != null) return reader;
        try {


            return new AlignmentReaderImpl(basename);


        } catch (IOException e) {
            throw new RuntimeException(e);
        }
    }

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     */
    private AlignmentReaderImpl getNewLocalReader(int referenceIndex, int start, int end) {
        if (reader != null) return reader;
        try {


            return new AlignmentReaderImpl(basename, referenceIndex, start, referenceIndex, end);


        } catch (IOException e) {
            throw new RuntimeException(e);
        }
    }

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Related Classes of edu.cornell.med.icb.goby.alignments.AlignmentReaderImpl

org.broad.igv.goby.GobyAlignmentQueryReader

org.broad.igv.goby.GobyAlignmentQueryReaderTest

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