Examples with ResourceLocator org.broad.igv.util.ResourceLocator used on opensource projects

Example 1 with ResourceLocator

use of org.broad.igv.util.ResourceLocator in project ASCIIGenome by dariober.

the class TrackWiggles method getAttributesFromTDF.

private String getAttributesFromTDF(String attr) {
    String path = this.getWorkFilename();
    try {
        ResourceLocator resourceLocator = new ResourceLocator(path);
        TDFReader reader = new TDFReader(resourceLocator);
        TDFGroup rootGroup = reader.getGroup("/");
        return rootGroup.getAttribute(attr);
    } catch (Exception e) {
        return null;
    }
}

Example 2 with ResourceLocator

use of org.broad.igv.util.ResourceLocator in project ASCIIGenome by dariober.

the class TrackWiggles method getChromosomeNames.

@Override
public List<String> getChromosomeNames() {
    if (this.getTrackFormat().equals(TrackFormat.TDF)) {
        ResourceLocator resourceLocator = new ResourceLocator(this.getWorkFilename());
        TDFReader reader = new TDFReader(resourceLocator);
        List<String> chroms = new ArrayList<String>(reader.getChromosomeNames());
        if (chroms.get(0).equals("All")) {
            chroms.remove(0);
        }
        return chroms;
    // chroms.addAll();
    }
    if (this.getTrackFormat().equals(TrackFormat.BEDGRAPH)) {
        TabixIndex tbi = (TabixIndex) IndexFactory.loadIndex(this.getWorkFilename() + TabixUtils.STANDARD_INDEX_EXTENSION);
        return tbi.getSequenceNames();
    }
    if (this.getTrackFormat().equals(TrackFormat.BIGWIG)) {
        return this.bigWigReader.getChromosomeNames();
    }
    return null;
}