Merge branch 'kjvdh/features/testing' into spikes/koen

[jalview.git] / src / jalview / controller / AlignViewController.java

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index dd05843..460c2b3 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -52,14 +52,6 @@ public class AlignViewController implements AlignViewControllerI
    */
   private AlignViewControllerGuiI avcg;
 
-  @Override
-  protected void finalize() throws Throwable
-  {
-    viewport = null;
-    alignPanel = null;
-    avcg = null;
-  };
-
   public AlignViewController(AlignViewControllerGuiI alignFrame,
           AlignViewportI viewport, AlignmentViewPanel alignPanel)
   {
@@ -190,7 +182,7 @@ public class AlignViewController implements AlignViewControllerI
       if (changed)
       {
         viewport.setColumnSelection(cs);
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(false, false);
         int columnCount = invert
                 ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
                         - bs.cardinality()
@@ -215,7 +207,7 @@ public class AlignViewController implements AlignViewControllerI
       if (!extendCurrent)
       {
         cs.clear();
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(false, false);
       }
     }
     return false;
@@ -337,7 +329,7 @@ public class AlignViewController implements AlignViewControllerI
     AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
     avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
             viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
 
   }
 
@@ -375,7 +367,7 @@ public class AlignViewController implements AlignViewControllerI
       {
         avcg.getFeatureSettingsUI().discoverAllFeatureData();
       }
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
     }
 
     return featuresFile;
@@ -414,7 +406,7 @@ public class AlignViewController implements AlignViewControllerI
       if (changed)
       {
         viewport.setColumnSelection(cs);
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(false, false);
         int columnCount = invert
                 ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
                         - bs.cardinality()
@@ -438,7 +430,7 @@ public class AlignViewController implements AlignViewControllerI
       if (!extendCurrent)
       {
         cs.clear();
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(false, false);
       }
     }
     return false;