assertSame(newseqs.get(0), mapping.getAaSeqs()[0]);
assertEquals(1, mapping.getdnaToProt().length);
assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
- assertArrayEquals(new int[] { 12923, 13060 }, mapping.getdnaToProt()[0]
- .getFromRanges().get(0));
+ assertArrayEquals(new int[] { 12923, 13060 },
+ mapping.getdnaToProt()[0].getFromRanges().get(0));
assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
- assertArrayEquals(new int[] { 1, 138 }, mapping.getdnaToProt()[0]
- .getToRanges().get(0));
+ assertArrayEquals(new int[] { 1, 138 },
+ mapping.getdnaToProt()[0].getToRanges().get(0));
}
/**
assertSame(newseqs.get(0), mapping.getAaSeqs()[0]);
assertEquals(1, mapping.getdnaToProt().length);
assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
- assertArrayEquals(new int[] { 12923, 13060 }, mapping.getdnaToProt()[0]
- .getFromRanges().get(0));
+ assertArrayEquals(new int[] { 12923, 13060 },
+ mapping.getdnaToProt()[0].getFromRanges().get(0));
assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
- assertArrayEquals(new int[] { 138, 1 }, mapping.getdnaToProt()[0]
- .getToRanges().get(0));
+ assertArrayEquals(new int[] { 138, 1 },
+ mapping.getdnaToProt()[0].getToRanges().get(0));
}
/**
assertEquals(1, mapping.getdnaToProt().length);
assertEquals(2, mapping.getdnaToProt()[0].getFromRanges().size());
// the two spliced dna ranges are combined in one MapList
- assertArrayEquals(new int[] { 12923, 13060 }, mapping.getdnaToProt()[0]
- .getFromRanges().get(0));
- assertArrayEquals(new int[] { 13411, 13550 }, mapping.getdnaToProt()[0]
- .getFromRanges().get(1));
+ assertArrayEquals(new int[] { 12923, 13060 },
+ mapping.getdnaToProt()[0].getFromRanges().get(0));
+ assertArrayEquals(new int[] { 13411, 13550 },
+ mapping.getdnaToProt()[0].getFromRanges().get(1));
assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
// the two cdna ranges are merged into one contiguous region
- assertArrayEquals(new int[] { 1, 278 }, mapping.getdnaToProt()[0]
- .getToRanges().get(0));
+ assertArrayEquals(new int[] { 1, 278 },
+ mapping.getdnaToProt()[0].getToRanges().get(0));
}
@Test(groups = "Functional")
// Ensembl variant feature - extract "alleles" value
// may be sequence_variant or a sub-type in the sequence ontology
- sf = new SequenceFeature("feature_variant", "desc", 10, 20, 3f, "group");
+ sf = new SequenceFeature("feature_variant", "desc", 10, 20, 3f,
+ "group");
List<String> atts = new ArrayList<String>();
atts.add("A");
atts.add("C");