X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=f927e638c2d175394f06716bdfd85be15627e36a;hb=571d15a897c11bdc2dda76ce03686604596f220d;hp=2e76e1aece976095f614ed165759c257d98c1240;hpb=8e1be43e250107a4d86898bd554cf03098fa5957;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 2e76e1a..f927e63 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -32,10 +32,9 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.CollectionColourScheme;
+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;
@@ -44,7 +43,7 @@ import jalview.viewmodel.AlignmentViewport;
 import java.awt.Font;
 
 public class AlignViewport extends AlignmentViewport implements
-        SelectionSource, VamsasSource, CommandListener
+        SelectionSource
 {
   boolean cursorMode = false;
 
@@ -77,10 +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
@@ -209,17 +208,17 @@ public class AlignViewport extends AlignmentViewport implements
 
       if (colour != null)
       {
-        globalColourScheme = new CollectionColourScheme(
+        residueShading = new ResidueShader(
                 ColourSchemeProperty.getColourScheme(alignment, colour));
-        if (globalColourScheme != null)
+        if (residueShading != null)
         {
-          globalColourScheme.setConsensus(hconsensus);
+          residueShading.setConsensus(hconsensus);
         }
       }
 
       if (applet.getParameter("userDefinedColour") != null)
       {
-        globalColourScheme = new CollectionColourScheme(
+        residueShading = new ResidueShader(
                 new UserColourScheme(
                         applet.getParameter("userDefinedColour")));
       }