X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=09e65623657ae2695be83dd2428db6ca36e15f1a;hb=f3392c352962c6827674ada5948500725e4eed1e;hp=d7ec681351bec6e9bef8e1bc1e2563a117613577;hpb=2e2e6d269fbaa505151fe777374f41111f2910d5;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index d7ec681..09e6562 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -20,12 +20,9 @@
  */
 package jalview.appletgui;
 
-import java.awt.Font;
-
 import jalview.analysis.NJTree;
-import jalview.api.AlignExportSettingI;
 import jalview.api.AlignViewportI;
-import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsModelI;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignmentI;
@@ -42,6 +39,8 @@ import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.Font;
+
 public class AlignViewport extends AlignmentViewport implements
         SelectionSource, VamsasSource, CommandListener
 {
@@ -59,10 +58,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
-  private FeatureRenderer featureRenderer;
-
-  private AlignExportSettingI exportSettings;
-
+  @Override
   public void finalize()
   {
     applet = null;
@@ -193,8 +189,13 @@ public class AlignViewport extends AlignmentViewport implements
 
     if (applet != null)
     {
-      String colour = applet.getParameter("defaultColour");
-
+      String colour = al.isNucleotide() ? applet
+              .getParameter("defaultColourNuc") : applet
+              .getParameter("defaultColourProt");
+      if (colour == null)
+      {
+        colour = applet.getParameter("defaultColour");
+      }
       if (colour == null)
       {
         colour = applet.getParameter("userDefinedColour");
@@ -293,7 +294,6 @@ public class AlignViewport extends AlignmentViewport implements
     return font;
   }
 
-
   public void resetSeqLimits(int height)
   {
     setEndSeq(height / getCharHeight());
@@ -309,7 +309,6 @@ public class AlignViewport extends AlignmentViewport implements
     return currentTree;
   }
 
-
   boolean centreColumnLabels;
 
   public boolean getCentreColumnLabels()
@@ -328,11 +327,12 @@ public class AlignViewport extends AlignmentViewport implements
     return followSelection;
   }
 
+  @Override
   public void sendSelection()
   {
     getStructureSelectionManager().sendSelection(
-                    new SequenceGroup(getSelectionGroup()),
-                    new ColumnSelection(getColumnSelection()), this);
+            new SequenceGroup(getSelectionGroup()),
+            new ColumnSelection(getColumnSelection()), this);
   }
 
   /**
@@ -381,6 +381,7 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
+  @Override
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
@@ -395,6 +396,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return true if alignment characters should be displayed
    */
+  @Override
   public boolean isValidCharWidth()
   {
     return validCharWidth;
@@ -473,28 +475,18 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
+  /**
+   * Applies the supplied feature settings descriptor to currently known
+   * features. This supports an 'initial configuration' of feature colouring
+   * based on a preset or user favourite. This may then be modified in the usual
+   * way using the Feature Settings dialogue.
+   * 
+   * @param featureSettings
+   */
   @Override
-  public FeatureRenderer getFeatureRenderer()
-  {
-    return featureRenderer;
-  }
-
-  @Override
-  public void setFeatureRenderer(FeatureRenderer featureRenderer)
+  public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
   {
-    this.featureRenderer = featureRenderer;
-
+    // TODO implement for applet
   }
 
-  public AlignExportSettingI getExportSettings()
-  {
-    return exportSettings;
-  }
-
-  public void setExportSettings(AlignExportSettingI exportSettings)
-  {
-    this.exportSettings = exportSettings;
-  }
-
-
 }