X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=11321eba1b1f91c37fa36065fb6add400ec681c2;hb=9201765247470c08d366abef2713c1c736adf2cb;hp=35a87d49da4d4218197641337c0458815977e160;hpb=8e1be43e250107a4d86898bd554cf03098fa5957;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 35a87d4..11321eb 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -41,16 +41,17 @@ 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.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.UserColourScheme;
-import jalview.structure.CommandListener;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 import jalview.ws.params.AutoCalcSetting;
 
 import java.awt.Container;
@@ -71,7 +72,7 @@ import javax.swing.JInternalFrame;
  * @version $Revision: 1.141 $
  */
 public class AlignViewport extends AlignmentViewport implements
-        SelectionSource, CommandListener
+        SelectionSource
 {
   Font font;
 
@@ -237,10 +238,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   void init()
   {
-    this.startRes = 0;
-    this.endRes = alignment.getWidth() - 1;
-    this.startSeq = 0;
-    this.endSeq = alignment.getHeight() - 1;
+    ranges = new ViewportRanges(this.alignment);
     applyViewProperties();
 
     String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
@@ -285,29 +283,27 @@ public class AlignViewport extends AlignmentViewport implements
     initAutoAnnotation();
     String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
             : Preferences.DEFAULT_COLOUR_PROT;
-    String propertyValue = Cache.getProperty(colourProperty);
-    if (propertyValue == null)
+    String schemeName = Cache.getProperty(colourProperty);
+    if (schemeName == null)
     {
-      // fall back on this property for backwards compatibility
-      propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR);
+      // only DEFAULT_COLOUR available in Jalview before 2.9
+      schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
+              ResidueColourScheme.NONE);
     }
-    if (propertyValue != null)
-    {
-      ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
-              alignment, propertyValue);
-      globalColourScheme = new CollectionColourScheme(colourScheme);
+    ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
+            alignment, schemeName);
+    residueShading = new ResidueShader(colourScheme);
 
-      if (colourScheme instanceof UserColourScheme)
-      {
-        globalColourScheme = new CollectionColourScheme(
-                UserDefinedColours.loadDefaultColours());
-        globalColourScheme.setThreshold(0, isIgnoreGapsConsensus());
-      }
+    if (colourScheme instanceof UserColourScheme)
+    {
+      residueShading = new ResidueShader(
+              UserDefinedColours.loadDefaultColours());
+      residueShading.setThreshold(0, isIgnoreGapsConsensus());
+    }
 
-      if (globalColourScheme != null)
-      {
-        globalColourScheme.setConsensus(hconsensus);
-      }
+    if (residueShading != null)
+    {
+      residueShading.setConsensus(hconsensus);
     }
   }
 
@@ -385,7 +381,6 @@ public class AlignViewport extends AlignmentViewport implements
     super.setViewStyle(settingsForView);
     setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
             viewStyle.getFontSize()), false);
-
   }
 
   /**