Examples of org.broad.igv.feature.tribble.FeatureFileHeader

org.broad.igv.feature.tribble.FeatureFileHeader
Created by IntelliJ IDEA. User: jrobinso Date: May 22, 2010 Time: 7:10:59 PM To change this template use File | Settings | File Templates.

            //t.setRendererClass(BasicTribbleRenderer.class);


            // Set track properties from header
            Object header = tribbleFeatureSource.getHeader();
            if (header != null && header instanceof FeatureFileHeader) {
                FeatureFileHeader ffh = (FeatureFileHeader) header;
                if (ffh.getTrackType() != null) {
                    t.setTrackType(ffh.getTrackType());
                }
                if (ffh.getTrackProperties() != null) {
                    t.setProperties(ffh.getTrackProperties());
                }


                if (ffh.getTrackType() == TrackType.REPMASK) {
                    t.setHeight(15);
                }
            }
            if (locator.getPath().contains(".narrowPeak") || locator.getPath().contains(".broadPeak")) {
                t.setUseScore(true);

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    }




    public static TrackProperties getTrackProperties(Object header) {
        try {
            FeatureFileHeader ffHeader = (FeatureFileHeader) header;
            if (ffHeader != null) {
                return ffHeader.getTrackProperties();
            } else {
                return null;
            }
        } catch (ClassCastException e) {
            return null;

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        FeatureCodec codec1 = CodecFactory.getCodec(bedFile, genome);
        assertTrue(codec1 instanceof IGVBEDCodec);
        IGVBEDCodec codec = (IGVBEDCodec) codec1;


        AbstractFeatureReader bfr = AbstractFeatureReader.getFeatureReader(bedFile, codec, false);
        FeatureFileHeader header = (FeatureFileHeader) bfr.getHeader();
        Assert.assertNotNull(header);
        assertTrue(codec.isGffTags());


        Iterator<BasicFeature> iter = bfr.iterator();
        while (iter.hasNext()) {

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     */
    @Override
    public Object readActualHeader(LineIterator reader) {


        if (header == null) {
            header = new FeatureFileHeader();
            TrackProperties tp = new TrackProperties();
            tp.setDisplayMode(Track.DisplayMode.EXPANDED);
            header.setTrackProperties(tp);
        }
        return header;

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Related Classes of org.broad.igv.feature.tribble.FeatureFileHeader

org.broad.igv.gwas.EQTLCodec

org.broad.igv.tools.parsers.TestBEDCodecs

org.broad.igv.track.TrackLoader

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