JAL-2829 unit tests for failing cases

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index c0cb09c..f470d45 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1803,4 +1803,54 @@ public class SequenceTest
     sq.checkValidRange();
     assertEquals(22, sq.getEnd());
   }
+
+  @Test(groups = { "Functional" })
+  public void testDeleteChars_withGaps()
+  {
+    /*
+     * delete gaps only
+     */
+    SequenceI sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
+    sq.deleteChars(1, 2); // delete first gap
+    assertEquals("AB-C", sq.getSequenceAsString());
+    assertEquals(8, sq.getStart());
+    assertEquals(10, sq.getEnd());
+    assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
+
+    /*
+     * delete gaps and residues at start (no new dataset sequence)
+     */
+    sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    sq.deleteChars(0, 3); // delete A-B
+    assertEquals("-C", sq.getSequenceAsString());
+    assertEquals(10, sq.getStart());
+    assertEquals(10, sq.getEnd());
+    assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
+
+    /*
+     * delete gaps and residues at end (no new dataset sequence)
+     */
+    sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    sq.deleteChars(2, 5); // delete B-C
+    assertEquals("A-", sq.getSequenceAsString());
+    assertEquals(8, sq.getStart());
+    assertEquals(8, sq.getEnd());
+    assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
+
+    /*
+     * delete gaps and residues internally (new dataset sequence)
+     */
+    sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    sq.deleteChars(1, 3); // delete -B
+    assertEquals("A-C", sq.getSequenceAsString());
+    assertEquals(8, sq.getStart());
+    assertEquals(9, sq.getEnd());
+    assertEquals("ACDEF", sq.getDatasetSequence().getSequenceAsString());
+    assertEquals(8, sq.getDatasetSequence().getStart());
+  }
 }