Examples of IGVFeature

Examples of org.broad.igv.feature.IGVFeature

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        assertEquals("notmeaningful", track.getName());

        List<Feature> features = track.getFeatures("chr1", 0, Integer.MAX_VALUE);
        assertEquals(2, features.size());

        IGVFeature feat0 = (IGVFeature) features.get(0);
        IGVFeature feat1 = (IGVFeature) features.get(1);

        assertEquals(707 - 1, feat0.getStart());
        assertEquals(943, feat0.getEnd());
        assertEquals(7563 - 1, feat1.getStart());
        assertEquals(7938, feat1.getEnd());
    }
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Examples of org.broad.igv.feature.IGVFeature

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            return nextFeat != null;
        }

        @Override
        public IGVFeature next() {
            IGVFeature nF = nextFeat;
            findNext();
            return nF;
        }
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Examples of org.broad.igv.feature.IGVFeature

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            List<Feature> features = getFeatures(chr);
            if (features != null) {
                long offset = genome.getCumulativeOffset(chr);
                for (Feature feature : features) {
                    if (feature instanceof IGVFeature) {
                        IGVFeature f = (IGVFeature) feature;
                        int genStart = (int) ((offset + f.getStart()) / 1000);
                        int genEnd = (int) ((offset + f.getEnd()) / 1000);
                        if (genEnd > lastFeaturePosition + sampleLength) {
                            BasicFeature f2 = new BasicFeature(Globals.CHR_ALL, genStart, genEnd);
                            if (f instanceof BasicFeature) {
                                BasicFeature bf = (BasicFeature) f;
                                f2.setThickEnd((int) ((offset + bf.getThickEnd()) / 1000));
                                f2.setThickStart((int) ((offset + bf.getThickStart()) / 1000));
                                f2.setName(f.getName());
                            }
                            chrAllFeatures.add(f2);

                            lastFeaturePosition = genEnd;
                        }
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