Package org.broad.igv.feature

Examples of org.broad.igv.feature.BasicFeature

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        List<Feature> features = getGeneFeatures(filepath, chr, start, end);
        assertEquals(3, features.size());

        for (Feature feat : features) {
            BasicFeature bf = (BasicFeature) feat;
            if (bf.getType().equals("mRNA")) {
                assertEquals(8, bf.getExonCount());
                for (Exon exon : bf.getExons()) {
                    assertEquals(bf.getIdentifier(), exon.getAttributes().get("Parent"));
                    assertWholeExonCoding(exon);
                }
            }
        }
    }
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                features.add(iter.next());
            }

            assertEquals(1, features.size());

            BasicFeature feature = (BasicFeature) features.get(0);
            List<Exon> exons = feature.getExons();
            assertEquals(2, exons.size());

            Exon firstExon = exons.get(0);
            assertTrue(firstExon.isNonCoding());
            assertEquals(11783, firstExon.getStart());
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        AbstractFeatureReader bfr = AbstractFeatureReader.getFeatureReader(bedFile, new IGVBEDCodec());
        Iterator<BasicFeature> iter = bfr.query(chr, start, end);
        int countInterval = 0;
        while (iter.hasNext()) {
            BasicFeature feature = iter.next();
            Assert.assertTrue(feature.getEnd() >= start && feature.getStart() <= end);
            Assert.assertTrue(expectedNames.contains(feature.getName()));
            countInterval++;
        }

        assertEquals(expectedCount, countInterval);
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        AbstractFeatureReader bfr = AbstractFeatureReader.getFeatureReader(bedFile, new IGVBEDCodec());
        Iterator<BasicFeature> iter = bfr.query(chr, start, end);
        int countInterval = 0;
        while (iter.hasNext()) {
            BasicFeature feature = iter.next();
            Assert.assertTrue(feature.getEnd() >= start && feature.getStart() <= end);
            Assert.assertTrue(expectedNames.contains(feature.getName()));
            countInterval++;
        }

        assertEquals(expectedCount, countInterval);
    }
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Related Classes of org.broad.igv.feature.BasicFeature

  • org.broad.igv.cli_plugin.BEDToolsDecoder
  • org.broad.igv.cli_plugin.CufflinksPluginTest
  • org.broad.igv.cursor.CursorIdeogramPanel
  • org.broad.igv.cursor.CursorRegion
  • org.broad.igv.cursor.CursorRegion$FeatureIterator
  • org.broad.igv.cursor.CursorUtils
  • org.broad.igv.dev.db.UCSC_SQL_Test
  • org.broad.igv.feature.genome.GenbankParserTest
  • org.broad.igv.feature.tribble.EMBLTableCodec
  • org.broad.igv.feature.tribble.GFFCodec
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