JAL-2986 failing test added

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 5a14514..67f1081 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -247,7 +247,9 @@ public class SequenceTest
     sq.sequenceChanged();
     assertEquals(6, sq.findIndex(9));
 
-    sq = new Sequence("test/8-13", "-A--B-C-D-E-F--");
+    final String aligned = "-A--B-C-D-E-F--";
+    assertEquals(15, aligned.length());
+    sq = new Sequence("test/8-13", aligned);
     assertEquals(2, sq.findIndex(8));
     sq.sequenceChanged();
     assertEquals(5, sq.findIndex(9));
@@ -263,6 +265,29 @@ public class SequenceTest
     // beyond end returns last residue column
     sq.sequenceChanged();
     assertEquals(13, sq.findIndex(99));
+
+    /*
+     * residue before sequence 'end' but beyond end of sequence returns 
+     * length of sequence (last column) (rightly or wrongly!)
+     */
+    sq = new Sequence("test/8-15", "A-B-C-"); // trailing gap case
+    assertEquals(6, sq.getLength());
+    sq.sequenceChanged();
+    assertEquals(sq.getLength(), sq.findIndex(14));
+    sq = new Sequence("test/8-99", "-A--B-C-D"); // trailing residue case
+    sq.sequenceChanged();
+    assertEquals(sq.getLength(), sq.findIndex(65));
+
+    /*
+     * residue after sequence 'start' but before first residue returns 
+     * zero (before first column) (rightly or wrongly!)
+     */
+    sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case
+    sq.sequenceChanged();
+    assertEquals(0, sq.findIndex(3));
+    sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case
+    sq.sequenceChanged();
+    assertEquals(0, sq.findIndex(2));
   }
 
   /**
@@ -1410,6 +1435,28 @@ public class SequenceTest
 
     // find C given C
     assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, 0)));
+
+    /*
+     * sequence 'end' beyond end of sequence returns length of sequence 
+     *  (for compatibility with pre-cursor code)
+     */
+    sq = new Sequence("test/8-99", "-A--B-C-D-E-F--"); // trailing gap case
+    sq.findIndex(10); // establishes a cursor
+    assertEquals(sq.getLength(), sq.findIndex(65));
+    sq = new Sequence("test/8-99", "-A--B-C-D-E-F"); // trailing residue case
+    sq.findIndex(10); // establishes a cursor
+    assertEquals(sq.getLength(), sq.findIndex(65));
+
+    /*
+     * residue after sequence 'start' but before first residue should return 
+     * zero (for compatibility with pre-cursor code)
+     */
+    sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case
+    sq.findIndex(10); // establishes a cursor
+    assertEquals(0, sq.findIndex(3));
+    sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case
+    sq.findIndex(10); // establishes a cursor
+    assertEquals(0, sq.findIndex(2));
   }
 
   @Test(groups = { "Functional" })