X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FIdColourScheme.java;h=10d23a2857721e9d1e711c033c54b8f6ecda0361;hb=6d2243ff184e3c1664de42c217bc6ee8b41c9ac5;hp=cd26666e37aca0c8b58ed712aae88a37b0eaec65;hpb=4cb58ab40ed4521e8ac732665098a6c57ad43896;p=jalview.git

diff --git a/src/jalview/schemes/IdColourScheme.java b/src/jalview/schemes/IdColourScheme.java
index cd26666..10d23a2 100644
--- a/src/jalview/schemes/IdColourScheme.java
+++ b/src/jalview/schemes/IdColourScheme.java
@@ -28,23 +28,27 @@ import jalview.datamodel.SequenceI;
 import java.awt.Color;
 import java.util.Map;
 
+/**
+ * shade sequences using the colour shown in the ID panel. Useful to map
+ * sequence groupings onto residue data (eg tree subgroups visualised on
+ * structures or overview window)
+ * 
+ * @author jprocter
+ */
 public class IdColourScheme implements ColourSchemeI
 {
   AlignViewportI view = null;
 
-  AnnotatedCollectionI coll = null;
-
   public IdColourScheme()
   {
 
   }
+
   public IdColourScheme(AlignViewportI view, AnnotatedCollectionI coll)
   {
     this.view = view;
-    this.coll = coll;
   }
 
-
   @Override
   public String getSchemeName()
   {
@@ -57,8 +61,7 @@ public class IdColourScheme implements ColourSchemeI
    */
   @Override
   public ColourSchemeI getInstance(AlignViewportI view,
-          AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+          AnnotatedCollectionI coll)
   {
     return new IdColourScheme(view, coll);
   }
@@ -77,8 +80,12 @@ public class IdColourScheme implements ColourSchemeI
     // ((SequenceGroup)coll).idColour
     // we always return the sequence ID colour, in case the user has customised
     // the displayed Id colour by right-clicking an internal node in the tree.
-    return (view == null) ? Color.WHITE
-            : view.getSequenceColour(seq).darker();
+    if (view == null)
+    {
+      return Color.WHITE;
+    }
+    Color col = view.getSequenceColour(seq);
+    return Color.WHITE.equals(col) ? Color.WHITE : col.darker();
   }
 
   @Override
@@ -96,7 +103,6 @@ public class IdColourScheme implements ColourSchemeI
   @Override
   public boolean isSimple()
   {
-    // this is really a sequence colour
-    return true;
+    return false;
   }
 }