X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=73cd9e9027ea4a817ecbbec74a0a5989c33dd4ac;hb=c2e5d3d1ebe3b283bdde15637c590721cd6c5637;hp=61621aedddf419e727c737bf92244d5a138adabb;hpb=e5b2edf3955c50cfd61799ad12cdc9016603ee1c;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 61621ae..73cd9e9 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -20,7 +20,7 @@
  */
 package jalview.appletgui;
 
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureSettingsModelI;
 import jalview.bin.JalviewLite;
@@ -40,9 +40,9 @@ import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Font;
+import java.awt.FontMetrics;
 
 public class AlignViewport extends AlignmentViewport implements
         SelectionSource
@@ -53,7 +53,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean validCharWidth = true;
 
-  NJTree currentTree = null;
+  TreeModel currentTree = null;
 
   public jalview.bin.JalviewLite applet;
 
@@ -72,11 +72,10 @@ public class AlignViewport extends AlignmentViewport implements
 
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
-    super();
+    super(al);
     calculator = new jalview.workers.AlignCalcManager();
     this.applet = applet;
-    alignment = al;
-    ranges = new ViewportRanges(this.alignment);
+
     // we always pad gaps
     this.setPadGaps(true);
 
@@ -130,7 +129,7 @@ public class AlignViewport extends AlignmentViewport implements
         }
       }
     }
-    setFont(font);
+    setFont(font, true);
 
     MAC = new jalview.util.Platform().isAMac();
 
@@ -273,7 +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)
@@ -282,14 +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)));
     }
   }
@@ -304,12 +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;
   }
@@ -443,8 +449,9 @@ public class AlignViewport extends AlignmentViewport implements
     int seqOffset = findComplementScrollTarget(sr);
     if (!sr.isEmpty())
     {
-      complementPanel.setFollowingComplementScroll(true);
+      complementPanel.setToScrollComplementPanel(false);
       complementPanel.scrollToCentre(sr, seqOffset);
+      complementPanel.setToScrollComplementPanel(true);
     }
   }