Merge branch 'develop' into features/mchmmer

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 9464c74..7972626 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -825,7 +825,7 @@ public class Sequence extends ASequence implements SequenceI
    * @param curs
    * @return
    */
-  protected int findIndex(int pos, SequenceCursor curs)
+  protected int findIndex(final int pos, SequenceCursor curs)
   {
     if (!isValidCursor(curs))
     {
@@ -851,10 +851,15 @@ public class Sequence extends ASequence implements SequenceI
     while (newPos != pos)
     {
       col += delta; // shift one column left or right
-      if (col < 0 || col == sequence.length)
+      if (col < 0)
       {
         break;
       }
+      if (col == sequence.length)
+      {
+        col--; // return last column if we failed to reach pos
+        break;
+      }
       if (!Comparison.isGap(sequence[col]))
       {
         newPos += delta;
@@ -862,7 +867,14 @@ public class Sequence extends ASequence implements SequenceI
     }
 
     col++; // convert back to base 1
-    updateCursor(pos, col, curs.firstColumnPosition);
+
+    /*
+     * only update cursor if we found the target position
+     */
+    if (newPos == pos)
+    {
+      updateCursor(pos, col, curs.firstColumnPosition);
+    }
 
     return col;
   }

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 5a14514..79bb2bb 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));
   }
 
   /**
@@ -1402,14 +1427,61 @@ public class SequenceTest
   {
     Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
 
-    // find F given A
+    // find F given A, check cursor is now at the found position
     assertEquals(10, sq.findIndex(13, new SequenceCursor(sq, 8, 2, 0)));
+    SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertEquals(13, cursor.residuePosition);
+    assertEquals(10, cursor.columnPosition);
 
     // find A given F
     assertEquals(2, sq.findIndex(8, new SequenceCursor(sq, 13, 10, 0)));
+    cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertEquals(8, cursor.residuePosition);
+    assertEquals(2, cursor.columnPosition);
 
-    // find C given C
+    // find C given C (no cursor update is done for this case)
     assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, 0)));
+    SequenceCursor cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertSame(cursor2, cursor);
+
+    /*
+     * sequence 'end' beyond end of sequence returns length of sequence 
+     *  (for compatibility with pre-cursor code)
+     *  - also verify the cursor is left in a valid state
+     */
+    sq = new Sequence("test/8-99", "-A--B-C-D-E-F--"); // trailing gap case
+    assertEquals(7, sq.findIndex(10)); // establishes a cursor
+    cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertEquals(10, cursor.residuePosition);
+    assertEquals(7, cursor.columnPosition);
+    assertEquals(sq.getLength(), sq.findIndex(65));
+    cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertSame(cursor, cursor2); // not updated for this case!
+
+    sq = new Sequence("test/8-99", "-A--B-C-D-E-F"); // trailing residue case
+    sq.findIndex(10); // establishes a cursor
+    cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertEquals(sq.getLength(), sq.findIndex(65));
+    cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertSame(cursor, cursor2); // not updated for this case!
+
+    /*
+     * 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
+    cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertEquals(0, sq.findIndex(3));
+    cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertSame(cursor, cursor2); // not updated for this case!
+
+    sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case
+    sq.findIndex(10); // establishes a cursor
+    cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertEquals(0, sq.findIndex(2));
+    cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertSame(cursor, cursor2); // not updated for this case!
   }
 
   @Test(groups = { "Functional" })