JAL-2738 update spike branch with latest

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

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index dd05843..69e31cf 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -190,7 +190,7 @@ 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 +215,7 @@ public class AlignViewController implements AlignViewControllerI
       if (!extendCurrent)
       {
         cs.clear();
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(false, false);
       }
     }
     return false;
@@ -337,7 +337,7 @@ 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 +375,7 @@ public class AlignViewController implements AlignViewControllerI
       {
         avcg.getFeatureSettingsUI().discoverAllFeatureData();
       }
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
     }
 
     return featuresFile;
@@ -414,7 +414,7 @@ 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 +438,7 @@ public class AlignViewController implements AlignViewControllerI
       if (!extendCurrent)
       {
         cs.clear();
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(false, false);
       }
     }
     return false;