JAL-3438 spotless for 2.11.2.0

[jalview.git] / src / jalview / schemes / IdColourScheme.java

diff --git a/src/jalview/schemes/IdColourScheme.java b/src/jalview/schemes/IdColourScheme.java
index a96ac0f..10d23a2 100644 (file)
--- a/src/jalview/schemes/IdColourScheme.java
+++ b/src/jalview/schemes/IdColourScheme.java
@@ -23,29 +23,32 @@ package jalview.schemes;
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceGroup;
 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()
   {
@@ -58,8 +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);
   }
@@ -74,10 +76,16 @@ public class IdColourScheme implements ColourSchemeI
   public Color findColour(char symbol, int position, SequenceI seq,
           String consensusResidue, float pid)
   {
-    return (view == null) ? Color.WHITE
-            : ((coll instanceof SequenceGroup)
-                    ? ((SequenceGroup) coll).idColour
-                    : view.getSequenceColour(seq));
+    // rather than testing if coll is a sequence group, and if so looking at
+    // ((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.
+    if (view == null)
+    {
+      return Color.WHITE;
+    }
+    Color col = view.getSequenceColour(seq);
+    return Color.WHITE.equals(col) ? Color.WHITE : col.darker();
   }
 
   @Override
@@ -95,7 +103,6 @@ public class IdColourScheme implements ColourSchemeI
   @Override
   public boolean isSimple()
   {
-    // this is really a sequence colour
-    return true;
+    return false;
   }
 }