Merge remote-tracking branch 'origin/develop' into imp/JAL-2774

[jalview.git] / test / jalview / datamodel / SequenceTest.java

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 6844072..c0cb09c 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1672,4 +1672,135 @@ public class SequenceTest
     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());
+  }
 }