JAL-845 SplitFrame for "show product" and after aligning from SplitFrame

[jalview.git] / src / jalview / gui / AlignmentPanel.java

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index f493fcf..ccbc031 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -95,9 +95,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * Creates a new AlignmentPanel object.
    * 
    * @param af
-   *          DOCUMENT ME!
    * @param av
-   *          DOCUMENT ME!
    */
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
@@ -672,7 +670,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-
     int oldX = av.getStartRes();
     int oldY = av.getStartSeq();
 
@@ -1170,8 +1167,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (alignFrame != null && !headless)
     {
       alignFrame.setProgressBar(MessageManager.formatMessage(
-              "status.saving_file",
-              new String[]
+              "status.saving_file", new Object[]
               { type.getLabel() }), progress);
     }
     try
@@ -1332,24 +1328,24 @@ public class AlignmentPanel extends GAlignmentPanel implements
           for (res = 0; res < alwidth; res++)
           {
             text = new StringBuffer();
-            Object obj = null;
+            String triplet = null;
             if (av.getAlignment().isNucleotide())
             {
-              obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)
+              triplet = ResidueProperties.nucleotideName.get(seq
+                      .getCharAt(res)
                       + "");
             }
             else
             {
-              obj = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+              triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
                       + "");
             }
 
-            if (obj == null)
+            if (triplet == null)
             {
               continue;
             }
 
-            String triplet = obj.toString();
             int alIndex = seq.findPosition(res);
             gSize = groups.length;
             for (g = 0; g < gSize; g++)
@@ -1497,6 +1493,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
               .getStructureSelectionManager();
       ssm.removeStructureViewerListener(getSeqPanel(), null);
       ssm.removeSelectionListener(getSeqPanel());
+      ssm.removeCommandListener(av);
+      ssm.removeStructureViewerListener(getSeqPanel(), null);
+      ssm.removeSelectionListener(getSeqPanel());
       av.setAlignment(null);
       av = null;
     }