X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=2398bda010e85fd78177da08ed0d78107c4459a1;hb=refs%2Fheads%2FRelease_2_8_2_Branch;hp=d2670f452a4a14dd9c9a5c56ea44e0899ca9556a;hpb=a3b4ec9805c4cee4c2dbe2a4c98913ee9c189c6b;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index d2670f4..2398bda 100644
--- 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;
@@ -734,8 +735,17 @@ 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)
@@ -1493,11 +1503,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     return av.getAlignment();
   }
 
-  /**
-   * get the name for this view
-   * 
-   * @return
-   */
+
+  @Override
   public String getViewName()
   {
     return av.viewName;