X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=6e3257d91018a7f32fea9561178338b8f058feb4;hb=8874aa9fd956f7bc248fe15a669a6d8d81d6891b;hp=2fb737a8698d7059b59e4d561a2c2c220a0c87d2;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 2fb737a..6e3257d 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -23,6 +23,7 @@ package jalview.appletgui;
 import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
@@ -50,7 +51,6 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.util.Arrays;
 import java.util.Collections;
-import java.util.Vector;
 
 public class AnnotationLabels extends Panel
         implements ActionListener, MouseListener, MouseMotionListener
@@ -226,7 +226,8 @@ public class AnnotationLabels extends Panel
     ap.annotationPanel.adjustPanelHeight();
     setSize(getSize().width, ap.annotationPanel.getSize().height);
     ap.validate();
-    ap.paintAlignment(true);
+    // TODO: only paint if we needed to
+    ap.paintAlignment(true, true);
   }
 
   boolean editLabelDescription(AlignmentAnnotation annotation)
@@ -548,7 +549,7 @@ public class AnnotationLabels extends Panel
                 {
                   ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
                 }
-                ap.paintAlignment(true);
+                ap.paintAlignment(true, true);
               }
             });
             popup.add(cbmi);
@@ -756,7 +757,7 @@ public class AnnotationLabels extends Panel
                 }
               }
             }
-            ap.paintAlignment(false);
+            ap.paintAlignment(false, false);
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
             ap.av.sendSelection();
           }
@@ -813,7 +814,7 @@ public class AnnotationLabels extends Panel
               sg.addSequence(aa[selectedRow].sequenceRef, false);
             }
             ap.av.setSelectionGroup(sg);
-            ap.paintAlignment(false);
+            ap.paintAlignment(false, false);
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
             ap.av.sendSelection();
           }
@@ -842,8 +843,8 @@ public class AnnotationLabels extends Panel
                     + "\t" + sq.getSequenceAsString() + "\n");
     if (av.hasHiddenColumns())
     {
-      jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector<>(
-              av.getAlignment().getHiddenColumns().getHiddenColumnsCopy());
+      jalview.appletgui.AlignFrame.copiedHiddenColumns = new HiddenColumns(
+              av.getAlignment().getHiddenColumns());
     }
   }