+ // add non-positional feature
+ SequenceFeature sf0 = new SequenceFeature("Cath", "desc", 0, 0, 2f,
+ null);
+ sq.addSequenceFeature(sf0);
+ // add feature on BCD
+ SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 9, 11, 2f,
+ null);
+ sq.addSequenceFeature(sf1);
+ // add feature on DE
+ SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 11, 12, 2f,
+ null);
+ sq.addSequenceFeature(sf2);
+ // add contact feature at [B, H]
+ SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc", 9,
+ 15, 2f,
+ null);
+ sq.addSequenceFeature(sf3);
+ // add contact feature at [F, G]
+ SequenceFeature sf4 = new SequenceFeature("Disulfide Bond", "desc", 13,
+ 14, 2f,
+ null);
+ sq.addSequenceFeature(sf4);
+
+ // no features in columns 1-2 (-A)
+ List<SequenceFeature> found = sq.findFeatures(1, 2);
+ assertTrue(found.isEmpty());
+
+ // columns 1-6 (-ABC--) includes BCD and B/H feature but not DE
+ found = sq.findFeatures(1, 6);
+ assertEquals(2, found.size());
+ assertTrue(found.contains(sf1));
+ assertTrue(found.contains(sf3));
+
+ // columns 5-6 (--) includes (enclosing) BCD but not (contact) B/H feature
+ found = sq.findFeatures(5, 6);
+ assertEquals(1, found.size());
+ assertTrue(found.contains(sf1));
+
+ // columns 7-10 (DEF-) includes BCD, DE, F/G but not B/H feature
+ found = sq.findFeatures(7, 10);
+ assertEquals(3, found.size());
+ assertTrue(found.contains(sf1));
+ assertTrue(found.contains(sf2));
+ assertTrue(found.contains(sf4));