X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=e0efa7ca91bc285e1ade8cefe8f3a17ceb141a0f;hb=3ebdd4e28382e38a181aae1eed71549f603f9025;hp=fb2a8ef53d65dab7883bea68b7b3afd4aec2068a;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index fb2a8ef..e0efa7c 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -41,7 +41,10 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+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;
@@ -61,7 +64,6 @@ import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
 
 /**
  * DOCUMENT ME!
@@ -284,28 +286,27 @@ 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)
-    {
-      globalColourScheme = ColourSchemeProperty.getColour(alignment,
-              propertyValue);
+    ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
+            alignment, schemeName);
+    residueShading = new ResidueShader(colourScheme);
 
-      if (globalColourScheme instanceof UserColourScheme)
-      {
-        globalColourScheme = UserDefinedColours.loadDefaultColours();
-        ((UserColourScheme) 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);
     }
   }
 
@@ -383,7 +384,6 @@ public class AlignViewport extends AlignmentViewport implements
     super.setViewStyle(settingsForView);
     setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
             viewStyle.getFontSize()), false);
-
   }
 
   /**
@@ -876,9 +876,9 @@ public class AlignViewport extends AlignmentViewport implements
         MessageManager.getString("label.new_window"), };
     final String question = JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.open_split_window?"));
-    int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
+    int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
             MessageManager.getString("label.open_split_window"),
-            JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null,
+            JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
             options, options[0]);
 
     if (response != 1 && response != 2)