/*
* get features by type
*/
- assertTrue(store.getPositionalFeatures(null).isEmpty());
+ assertTrue(store.getPositionalFeatures((String) null).isEmpty());
assertTrue(store.getPositionalFeatures("Cath").isEmpty());
assertTrue(store.getPositionalFeatures("METAL").isEmpty());
/*
* get contact features by type
*/
- assertTrue(store.getContactFeatures(null).isEmpty());
+ assertTrue(store.getContactFeatures((String) null).isEmpty());
assertTrue(store.getContactFeatures("Cath").isEmpty());
assertTrue(store.getContactFeatures("Pfam").isEmpty());
assertTrue(store.getContactFeatures("DISULPHIDE BOND").isEmpty());
/*
* get non-positional features by type
*/
- assertTrue(store.getNonPositionalFeatures(null).isEmpty());
+ assertTrue(store.getNonPositionalFeatures((String) null).isEmpty());
assertTrue(store.getNonPositionalFeatures("Cath").isEmpty());
assertTrue(store.getNonPositionalFeatures("PFAM").isEmpty());
// null type is weird but possible:
SequenceFeature sf13 = addFeature(sf, null, 5, 12);
- List<SequenceFeature> overlaps = sf.findFeatures("Pfam", 200, 200);
+ List<SequenceFeature> overlaps = sf.findFeatures(200, 200, "Pfam");
assertTrue(overlaps.isEmpty());
- overlaps = sf.findFeatures("Pfam", 1, 9);
+ overlaps = sf.findFeatures( 1, 9, "Pfam");
assertEquals(overlaps.size(), 1);
assertTrue(overlaps.contains(sf2));
- overlaps = sf.findFeatures("Pfam", 5, 18);
+ overlaps = sf.findFeatures( 5, 18, "Pfam");
assertEquals(overlaps.size(), 2);
assertTrue(overlaps.contains(sf1));
assertTrue(overlaps.contains(sf2));
- overlaps = sf.findFeatures("Pfam", 30, 40);
+ overlaps = sf.findFeatures(30, 40, "Pfam");
assertEquals(overlaps.size(), 3);
assertTrue(overlaps.contains(sf1));
assertTrue(overlaps.contains(sf3));
assertTrue(overlaps.contains(sf4));
- overlaps = sf.findFeatures("Pfam", 80, 90);
+ overlaps = sf.findFeatures( 80, 90, "Pfam");
assertEquals(overlaps.size(), 2);
assertTrue(overlaps.contains(sf4));
assertTrue(overlaps.contains(sf5));
- overlaps = sf.findFeatures("Pfam", 68, 70);
+ overlaps = sf.findFeatures( 68, 70, "Pfam");
assertEquals(overlaps.size(), 3);
assertTrue(overlaps.contains(sf4));
assertTrue(overlaps.contains(sf5));
assertTrue(overlaps.contains(sf6));
- overlaps = sf.findFeatures("Cath", 16, 69);
+ overlaps = sf.findFeatures(16, 69, "Cath");
assertEquals(overlaps.size(), 4);
assertTrue(overlaps.contains(sf7));
assertFalse(overlaps.contains(sf8));
assertTrue(overlaps.contains(sf11));
assertFalse(overlaps.contains(sf12));
- assertTrue(sf.findFeatures("Metal", 0, 1000).isEmpty());
+ assertTrue(sf.findFeatures(0, 1000, "Metal").isEmpty());
- overlaps = sf.findFeatures(null, 7, 7);
+ overlaps = sf.findFeatures(7, 7, (String) null);
assertEquals(overlaps.size(), 1);
assertTrue(overlaps.contains(sf13));
}