JAL-2437 Fixed reordering of sequences when hiding and revealing

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 33f30cf..db6195a 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -335,24 +335,12 @@ public class Alignment implements AlignmentI
     }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param s
-   *          DOCUMENT ME!
-   */
   @Override
   public void deleteSequence(SequenceI s)
   {
     deleteSequence(findIndex(s));
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param i
-   *          DOCUMENT ME!
-   */
   @Override
   public void deleteSequence(int i)
   {
@@ -366,6 +354,18 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
+  public void deleteHiddenSequence(int i)
+  {
+    if (i > -1 && i < getHeight())
+    {
+      synchronized (sequences)
+      {
+        sequences.remove(i);
+      }
+    }
+  }
+
   /*
    * (non-Javadoc)
    * 

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 1ecff9a..2abb1f8 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -147,7 +147,9 @@ public interface AlignmentI extends AnnotatedCollectionI
   SequenceI replaceSequenceAt(int i, SequenceI seq);
 
   /**
-   * Deletes a sequence from the alignment
+   * Deletes a sequence from the alignment. Updates hidden sequences to account
+   * for the removed sequence. Do NOT use this method to delete sequences which
+   * are just hidden.
    * 
    * @param s
    *          Sequence to be deleted.
@@ -155,7 +157,9 @@ public interface AlignmentI extends AnnotatedCollectionI
   void deleteSequence(SequenceI s);
 
   /**
-   * Deletes a sequence from the alignment.
+   * Deletes a sequence from the alignment. Updates hidden sequences to account
+   * for the removed sequence. Do NOT use this method to delete sequences which
+   * are just hidden.
    * 
    * @param i
    *          Index of sequence to be deleted.
@@ -163,6 +167,14 @@ public interface AlignmentI extends AnnotatedCollectionI
   void deleteSequence(int i);
 
   /**
+   * Deletes a sequence in the alignment which has been hidden.
+   * 
+   * @param i
+   *          Index of sequence to be deleted
+   */
+  void deleteHiddenSequence(int i);
+
+  /**
    * Finds sequence in alignment using sequence name as query.
    * 
    * @param name
@@ -574,4 +586,5 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @return
    */
   public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
+
 }

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 588e5ed..aca0be6 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -154,8 +154,8 @@ public class HiddenSequences
       hiddenSequences = new SequenceI[alignment.getHeight()];
     }
 
-    int alignmentIndex = alignment.findIndex(sequence);
-    alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
+    int absAlignmentIndex = alignment.findIndex(sequence);
+    int alignmentIndex = adjustForHiddenSeqs(absAlignmentIndex);
 
     if (hiddenSequences[alignmentIndex] != null)
     {
@@ -164,7 +164,7 @@ public class HiddenSequences
 
     hiddenSequences[alignmentIndex] = sequence;
 
-    alignment.deleteSequence(sequence);
+    alignment.deleteHiddenSequence(absAlignmentIndex);
   }
 
   public List<SequenceI> showAll(

diff --git a/test/jalview/datamodel/HiddenSequencesTest.java b/test/jalview/datamodel/HiddenSequencesTest.java
index cae3536..b41b98f 100644 (file)
--- a/test/jalview/datamodel/HiddenSequencesTest.java
+++ b/test/jalview/datamodel/HiddenSequencesTest.java
@@ -326,6 +326,53 @@ public class HiddenSequencesTest
     assertEquals(10, al.getHeight());
   }
 
+  /**
+   * Test the method that adds a sequence to the hidden sequences and deletes it
+   * from the alignment, and its converse, where the first hidden sequences are
+   * at the bottom of the alignment (JAL-2437)
+   */
+  @Test(groups = "Functional")
+  public void testHideShowLastSequences()
+  {
+    AlignmentI al = new Alignment(seqs);
+    assertTrue(al.getSequences().contains(seqs[1]));
+    HiddenSequences hs = al.getHiddenSequences();
+    assertEquals(0, hs.getSize());
+    assertEquals(10, al.getHeight());
+
+    /*
+     * hide the last sequence in the alignment
+     */
+    hs.hideSequence(seqs[9]);
+    assertFalse(hs.isHidden(seqs[8]));
+    assertTrue(hs.isHidden(seqs[9]));
+    assertFalse(al.getSequences().contains(seqs[9]));
+    assertEquals(1, hs.getSize());
+    assertEquals(9, al.getHeight());
+
+    /*
+     * hide the third last sequence in the alignment
+     */
+    hs.hideSequence(seqs[7]);
+    assertFalse(hs.isHidden(seqs[8]));
+    assertTrue(hs.isHidden(seqs[7]));
+    assertFalse(al.getSequences().contains(seqs[7]));
+    assertEquals(2, hs.getSize());
+    assertEquals(8, al.getHeight());
+
+    /*
+     * reveal all the sequences, which should be reinstated in the same order as they started in
+     */
+    hs.showAll(null);
+    assertFalse(hs.isHidden(seqs[7]));
+    assertFalse(hs.isHidden(seqs[9]));
+    assertEquals(seqs[7], al.getSequences().get(7));
+    assertEquals(seqs[8], al.getSequences().get(8));
+    assertEquals(seqs[9], al.getSequences().get(9));
+    assertEquals(0, hs.getSize());
+    assertEquals(10, al.getHeight());
+  }
+
   @Test(groups = "Functional")
   public void testIsHidden()
   {