JAL-345 invert logic is not quite right - REVISE THIS!

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 01ec8b1..ea6c6f8 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -2786,7 +2786,7 @@ public abstract class AlignmentViewport
     int lastSeq = alignment.getHeight() - 1;
     List<AlignedCodonFrame> seqMappings = null;
     for (int seqNo = ranges
-            .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+            .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
       if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
@@ -2954,4 +2954,25 @@ public abstract class AlignmentViewport
   {
     return currentTree;
   }
+
+  List<SequenceI> highlightedSeqs = null;
+
+  /**
+   * Highlight the IDs for the given sequences call alignPanel.repaint() to
+   * update view after setting.
+   * 
+   * @param list
+   *          List<SequenceI>
+   */
+  @Override
+  public void setHighlightedSeqs(List<SequenceI> list)
+  {
+    highlightedSeqs = list;
+  }
+
+  @Override
+  public List<SequenceI> getHighlightedSeqs()
+  {
+    return highlightedSeqs;
+  }
 }