JAL-845 further code/tests/refactoring

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index d2670f4..4bf350b 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.analysis.AnnotationSorter;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
@@ -91,9 +92,7 @@ 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)
   {
@@ -649,7 +648,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-
     int oldX = av.getStartRes();
     int oldY = av.getStartSeq();
 
@@ -734,8 +732,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
   }
 
+  /**
+   * Repaint the alignment including the annotations and overview panels (if
+   * shown).
+   */
   public void paintAlignment(boolean updateOverview)
   {
+    final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+            av.isShowAutocalculatedAbove());
+    sorter.sort(getAlignment()
+            .getAlignmentAnnotation(),
+            av.getSortAnnotationsBy());
     repaint();
 
     if (updateOverview)
@@ -1137,8 +1144,7 @@ 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
@@ -1454,6 +1460,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
               .getStructureSelectionManager();
       ssm.removeStructureViewerListener(seqPanel, null);
       ssm.removeSelectionListener(seqPanel);
+      ssm.removeEditListener(av);
       av.setAlignment(null);
       av = null;
     }
@@ -1493,11 +1500,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     return av.getAlignment();
   }
 
-  /**
-   * get the name for this view
-   * 
-   * @return
-   */
+
+  @Override
   public String getViewName()
   {
     return av.viewName;