X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=3214e70bee4dc267fbb4cd6781dcbf2fb086664e;hb=7335eb77076ba83a2faebeaf45f0aa03407fdcd1;hp=7f2a943d9425ee5a6958b35661f7d314d12844e1;hpb=e83311d25dc8fda9df4ab06f3b1bd53f242a5814;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 7f2a943..3214e70 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -433,6 +433,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     {
       annotationSpaceFillerHolder.setVisible(b);
       annotationPanelHolder.setVisible(b);
+    } else {
+      annotationSpaceFillerHolder.setVisible(false);
+      annotationPanelHolder.setVisible(false);
     }
     validate();
     repaint();
@@ -512,7 +515,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     alabels.setSize(new Dimension(e.width, height));
     annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
     annotationPanelHolder.setSize(new Dimension(d.width, height));
-    seqPanelHolder.setSize(d.width, seqandannot - height);
+    // seqPanelHolder.setSize(d.width, seqandannot - height);
     seqPanel.seqCanvas
             .setSize(d.width, seqPanel.seqCanvas.getSize().height);
     int s = apvscroll.getValue();
@@ -521,8 +524,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       s = 0;
     }
     apvscroll.setValues(s, height, 0, mheight);
-    annotationPanel.setScrollOffset(apvscroll.getValue());
-    alabels.setScrollOffset(apvscroll.getValue());
+    annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+    alabels.setScrollOffset(apvscroll.getValue(), false);
   }
 
   public void setWrapAlignment(boolean wrap)
@@ -544,12 +547,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       annotationPanelHolder.setVisible(true);
       annotationSpaceFillerHolder.setVisible(true);
     }
-
+    
     idSpaceFillerPanel1.setVisible(!wrap);
 
     fontChanged(); // This is so that the scalePanel is resized correctly
 
     validate();
+    sequenceHolderPanel.revalidate();
     repaint();
 
   }
@@ -686,8 +690,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
     if (evt == null || evt.getSource() == apvscroll)
     {
-      annotationPanel.setScrollOffset(apvscroll.getValue());
-      alabels.setScrollOffset(apvscroll.getValue());
+      annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+      alabels.setScrollOffset(apvscroll.getValue(), false);
       // annotationPanel.image=null;
       // alabels.image=null;
       // alabels.repaint();
@@ -817,12 +821,18 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       setScrollValues(av.getStartRes(), av.getStartSeq());
     }
 
-    alabels.repaint();
-
     seqPanel.seqCanvas.repaint();
-    scalePanel.repaint();
-    annotationPanel.repaint();
     idPanel.idCanvas.repaint();
+    if (!av.wrapAlignment) 
+    {
+      if (av.showAnnotation)
+      {
+        alabels.repaint();
+        annotationPanel.repaint();
+      }
+      scalePanel.repaint();
+    }
+    
   }
 
   protected Panel sequenceHolderPanel = new Panel();