X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=afe57e0dd9c4581486bd8db99d502c3c180b5663;hb=0288494d034d48dd8ce0c5a8654ac2ee695b4573;hp=9e82ae5cffaebe5f5e2c7a26d3af828ec30d5c4d;hpb=a09d6f5c16b0e222806e035cd38bfb4c4eb92c75;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 9e82ae5..afe57e0 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;
@@ -32,18 +32,19 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShader;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.UserColourScheme;
-import jalview.structure.CommandListener;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Font;
 
 public class AlignViewport extends AlignmentViewport implements
-        SelectionSource, VamsasSource, CommandListener
+        SelectionSource
 {
   boolean cursorMode = false;
 
@@ -51,7 +52,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean validCharWidth = true;
 
-  NJTree currentTree = null;
+  TreeModel currentTree = null;
 
   public jalview.bin.JalviewLite applet;
 
@@ -74,12 +75,10 @@ public class AlignViewport extends AlignmentViewport implements
     calculator = new jalview.workers.AlignCalcManager();
     this.applet = applet;
     alignment = al;
+    ranges = new ViewportRanges(this.alignment);
     // we always pad gaps
     this.setPadGaps(true);
-    this.startRes = 0;
-    this.endRes = al.getWidth() - 1;
-    this.startSeq = 0;
-    this.endSeq = al.getHeight() - 1;
+
     if (applet != null)
     {
       // get the width and height scaling factors if they were specified
@@ -150,6 +149,9 @@ public class AlignViewport extends AlignmentViewport implements
       showConsensus = applet.getDefaultParameter("showConsensus",
               showConsensus);
 
+      showOccupancy = applet.getDefaultParameter("showOccupancy",
+              showOccupancy);
+
       setShowUnconserved(applet.getDefaultParameter("showUnconserved",
               getShowUnconserved()));
 
@@ -208,18 +210,19 @@ public class AlignViewport extends AlignmentViewport implements
 
       if (colour != null)
       {
-        globalColourScheme = ColourSchemeProperty.getColourScheme(
-                alignment, colour);
-        if (globalColourScheme != null)
+        residueShading = new ResidueShader(
+                ColourSchemeProperty.getColourScheme(alignment, colour));
+        if (residueShading != null)
         {
-          globalColourScheme.setConsensus(hconsensus);
+          residueShading.setConsensus(hconsensus);
         }
       }
 
       if (applet.getParameter("userDefinedColour") != null)
       {
-        globalColourScheme = new UserColourScheme(
-                applet.getParameter("userDefinedColour"));
+        residueShading = new ResidueShader(
+                new UserColourScheme(
+                        applet.getParameter("userDefinedColour")));
       }
     }
     initAutoAnnotation();
@@ -297,15 +300,15 @@ public class AlignViewport extends AlignmentViewport implements
 
   public void resetSeqLimits(int height)
   {
-    setEndSeq(height / getCharHeight());
+    ranges.setEndSeq(height / getCharHeight());
   }
 
-  public void setCurrentTree(NJTree tree)
+  public void setCurrentTree(TreeModel tree)
   {
     currentTree = tree;
   }
 
-  public NJTree getCurrentTree()
+  public TreeModel getCurrentTree()
   {
     return currentTree;
   }