null);
sq.addSequenceFeature(sf0);
// add feature on BCD
- SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 9, 11, 2f,
+ SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 9, 11, 2f,
null);
- sq.addSequenceFeature(sf1);
+ sq.addSequenceFeature(sfBCD);
// add feature on DE
- SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 11, 12, 2f,
+ SequenceFeature sfDE = new SequenceFeature("Cath", "desc", 11, 12, 2f,
null);
- sq.addSequenceFeature(sf2);
+ sq.addSequenceFeature(sfDE);
// add contact feature at [B, H]
- SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc", 9,
- 15, 2f,
- null);
- sq.addSequenceFeature(sf3);
+ SequenceFeature sfContactBH = new SequenceFeature("Disulphide bond",
+ "desc", 9, 15, 2f, null);
+ sq.addSequenceFeature(sfContactBH);
// add contact feature at [F, G]
- SequenceFeature sf4 = new SequenceFeature("Disulfide Bond", "desc", 13,
- 14, 2f,
- null);
- sq.addSequenceFeature(sf4);
+ SequenceFeature sfContactFG = new SequenceFeature("Disulfide Bond",
+ "desc", 13, 14, 2f, null);
+ sq.addSequenceFeature(sfContactFG);
+ // add single position feature at [I]
+ SequenceFeature sfI = new SequenceFeature("Disulfide Bond",
+ "desc", 16, 16, null);
+ sq.addSequenceFeature(sfI);
// no features in columns 1-2 (-A)
List<SequenceFeature> found = sq.findFeatures(1, 2);
// 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));
+ assertTrue(found.contains(sfBCD));
+ assertTrue(found.contains(sfContactBH));
// 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));
+ assertTrue(found.contains(sfBCD));
// 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));
+ assertTrue(found.contains(sfBCD));
+ assertTrue(found.contains(sfDE));
+ assertTrue(found.contains(sfContactFG));
+
+ // columns 10-11 (--) should find nothing
+ found = sq.findFeatures(10, 11);
+ assertEquals(0, found.size());
+
+ // columns 14-14 (I) should find variant feature
+ found = sq.findFeatures(14, 14);
+ assertEquals(1, found.size());
+ assertTrue(found.contains(sfI));
}
@Test(groups = { "Functional" })
assertEquals(new Range(8, 13), sq.findPositions(1, 13)); // the lot
assertEquals(new Range(8, 13), sq.findPositions(1, 99));
}
+
+ @Test(groups = { "Functional" })
+ public void testFindFeatures_largeEndPos()
+ {
+ /*
+ * imitate a PDB sequence where end is larger than end position
+ */
+ SequenceI sq = new Sequence("test", "-ABC--DEF--", 1, 20);
+ sq.createDatasetSequence();
+
+ assertTrue(sq.findFeatures(1, 9).isEmpty());
+ // should be no array bounds exception - JAL-2772
+ assertTrue(sq.findFeatures(1, 15).isEmpty());
+
+ // add feature on BCD
+ SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 2, 4, 2f,
+ null);
+ sq.addSequenceFeature(sfBCD);
+
+ // no features in columns 1-2 (-A)
+ List<SequenceFeature> found = sq.findFeatures(1, 2);
+ assertTrue(found.isEmpty());
+
+ // columns 1-6 (-ABC--) includes BCD
+ found = sq.findFeatures(1, 6);
+ assertEquals(1, found.size());
+ assertTrue(found.contains(sfBCD));
+
+ // columns 10-11 (--) should find nothing
+ found = sq.findFeatures(10, 11);
+ assertEquals(0, found.size());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSetName()
+ {
+ SequenceI sq = new Sequence("test", "-ABC---DE-F--");
+ assertEquals("test", sq.getName());
+ assertEquals(1, sq.getStart());
+ assertEquals(6, sq.getEnd());
+
+ sq.setName("testing");
+ assertEquals("testing", sq.getName());
+
+ sq.setName("test/8-10");
+ assertEquals("test", sq.getName());
+ assertEquals(8, sq.getStart());
+ assertEquals(13, sq.getEnd()); // note end is recomputed
+
+ sq.setName("testing/7-99");
+ assertEquals("testing", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd()); // end may be beyond physical end
+
+ sq.setName("/2-3");
+ assertEquals("", sq.getName());
+ assertEquals(2, sq.getStart());
+ assertEquals(7, sq.getEnd());
+
+ sq.setName("test/"); // invalid
+ assertEquals("test/", sq.getName());
+ assertEquals(2, sq.getStart());
+ assertEquals(7, sq.getEnd());
+
+ sq.setName("test/6-13/7-99");
+ assertEquals("test/6-13", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+
+ sq.setName("test/0-5"); // 0 is invalid - ignored
+ assertEquals("test/0-5", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+
+ sq.setName("test/a-5"); // a is invalid - ignored
+ assertEquals("test/a-5", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+
+ sq.setName("test/6-5"); // start > end is invalid - ignored
+ assertEquals("test/6-5", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+
+ sq.setName("test/5"); // invalid - ignored
+ assertEquals("test/5", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+
+ sq.setName("test/-5"); // invalid - ignored
+ assertEquals("test/-5", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+
+ sq.setName("test/5-"); // invalid - ignored
+ assertEquals("test/5-", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+
+ sq.setName("test/5-6-7"); // invalid - ignored
+ assertEquals("test/5-6-7", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+
+ sq.setName(null); // invalid, gets converted to space
+ assertEquals("", sq.getName());
+ assertEquals(7, sq.getStart());
+ assertEquals(99, sq.getEnd());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testCheckValidRange()
+ {
+ Sequence sq = new Sequence("test/7-12", "-ABC---DE-F--");
+ assertEquals(7, sq.getStart());
+ assertEquals(12, sq.getEnd());
+
+ /*
+ * checkValidRange ensures end is at least the last residue position
+ */
+ PA.setValue(sq, "end", 2);
+ sq.checkValidRange();
+ assertEquals(12, sq.getEnd());
+
+ /*
+ * end may be beyond the last residue position
+ */
+ PA.setValue(sq, "end", 22);
+ sq.checkValidRange();
+ assertEquals(22, sq.getEnd());
+ }
}