X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=f927e638c2d175394f06716bdfd85be15627e36a;hb=571d15a897c11bdc2dda76ce03686604596f220d;hp=b025f648d0b6905051174fa506e2bf00e8ec612a;hpb=320c96aed11f5c396a9efd9ea83b0e35f05e21e4;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index b025f64..f927e63 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -32,9 +32,9 @@ 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;
@@ -43,7 +43,7 @@ import jalview.viewmodel.AlignmentViewport;
 import java.awt.Font;
 
 public class AlignViewport extends AlignmentViewport implements
-        SelectionSource, VamsasSource, CommandListener
+        SelectionSource
 {
   boolean cursorMode = false;
 
@@ -76,10 +76,10 @@ public class AlignViewport extends AlignmentViewport implements
     alignment = al;
     // we always pad gaps
     this.setPadGaps(true);
-    this.startRes = 0;
-    this.endRes = al.getWidth() - 1;
-    this.startSeq = 0;
-    this.endSeq = al.getHeight() - 1;
+    this.setStartRes(0);
+    this.setEndRes(al.getWidth() - 1);
+    this.setStartSeq(0);
+    this.setEndSeq(al.getHeight() - 1);
     if (applet != null)
     {
       // get the width and height scaling factors if they were specified
@@ -208,18 +208,19 @@ 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)
       {
-        ((UserColourScheme) globalColourScheme).parseAppletParameter(applet
-                .getParameter("userDefinedColour"));
+        residueShading = new ResidueShader(
+                new UserColourScheme(
+                        applet.getParameter("userDefinedColour")));
       }
     }
     initAutoAnnotation();