X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=9629a5f237258e2d8453c36f41e6b9154f4a255f;hb=4d0d1076f9334762b2cac00697e6971e75f02aeb;hp=b289be78def6a149bc9ed2d26c8b86bef6c68d52;hpb=61f891719b37bdc88c1c48d85ebf8b656c2bdcd0;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index b289be7..9629a5f 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -20,13 +20,14 @@
  */
 package jalview.appletgui;
 
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureSettingsModelI;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
@@ -41,6 +42,7 @@ import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Font;
+import java.awt.FontMetrics;
 
 public class AlignViewport extends AlignmentViewport implements
         SelectionSource
@@ -51,7 +53,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean validCharWidth = true;
 
-  NJTree currentTree = null;
+  TreeModel currentTree = null;
 
   public jalview.bin.JalviewLite applet;
 
@@ -127,7 +129,7 @@ public class AlignViewport extends AlignmentViewport implements
         }
       }
     }
-    setFont(font);
+    setFont(font, true);
 
     MAC = new jalview.util.Platform().isAMac();
 
@@ -147,6 +149,9 @@ public class AlignViewport extends AlignmentViewport implements
       showConsensus = applet.getDefaultParameter("showConsensus",
               showConsensus);
 
+      showOccupancy = applet.getDefaultParameter("showOccupancy",
+              showOccupancy);
+
       setShowUnconserved(applet.getDefaultParameter("showUnconserved",
               getShowUnconserved()));
 
@@ -267,7 +272,11 @@ public class AlignViewport extends AlignmentViewport implements
 
   private float heightScale = 1, widthScale = 1;
 
-  public void setFont(Font f)
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public void setFont(Font f, boolean setGrid)
   {
     font = f;
     if (nullFrame == null)
@@ -276,14 +285,17 @@ public class AlignViewport extends AlignmentViewport implements
       nullFrame.addNotify();
     }
 
-    java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
-    setCharHeight((int) (heightScale * fm.getHeight()));
-    setCharWidth((int) (widthScale * fm.charWidth('M')));
+    if (setGrid)
+    {
+      FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
+      setCharHeight((int) (heightScale * fm.getHeight()));
+      setCharWidth((int) (widthScale * fm.charWidth('M')));
+    }
 
     if (isUpperCasebold())
     {
       Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
-      fm = nullFrame.getGraphics().getFontMetrics(f2);
+      FontMetrics fm = nullFrame.getGraphics().getFontMetrics(f2);
       setCharWidth((int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
     }
   }
@@ -298,12 +310,12 @@ public class AlignViewport extends AlignmentViewport implements
     ranges.setEndSeq(height / getCharHeight());
   }
 
-  public void setCurrentTree(NJTree tree)
+  public void setCurrentTree(TreeModel tree)
   {
     currentTree = tree;
   }
 
-  public NJTree getCurrentTree()
+  public TreeModel getCurrentTree()
   {
     return currentTree;
   }
@@ -331,7 +343,8 @@ public class AlignViewport extends AlignmentViewport implements
   {
     getStructureSelectionManager().sendSelection(
             new SequenceGroup(getSelectionGroup()),
-            new ColumnSelection(getColumnSelection()), this);
+            new ColumnSelection(getColumnSelection()),
+            new HiddenColumns(getAlignment().getHiddenColumns()), this);
   }
 
   /**