From b71733cda46c5a88cb65417501727f2e4b4cf135 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 19 Nov 2018 18:06:31 +0000
Subject: [PATCH] =?utf8?q?JAL-3127=20javadoc,=20don=E2=80=99t=20darken=20whi?=
 =?utf8?q?te=20when=20shading=20residues,=20and=20don=E2=80=99t=20need=20to=20?=
 =?utf8?q?hold=20reference=20to=20group?=
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---
 src/jalview/schemes/IdColourScheme.java |   21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/src/jalview/schemes/IdColourScheme.java b/src/jalview/schemes/IdColourScheme.java
index 65dbcc9..5add470 100644
--- a/src/jalview/schemes/IdColourScheme.java
+++ b/src/jalview/schemes/IdColourScheme.java
@@ -28,12 +28,17 @@ 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()
   {
 
@@ -41,7 +46,6 @@ public class IdColourScheme implements ColourSchemeI
   public IdColourScheme(AlignViewportI view, AnnotatedCollectionI coll)
   {
     this.view = view;
-    this.coll = coll;
   }
 
 
@@ -76,8 +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
@@ -95,7 +103,6 @@ public class IdColourScheme implements ColourSchemeI
   @Override
   public boolean isSimple()
   {
-    // this is really a sequence colour
-    return true;
+    return false;
   }
 }
-- 
1.7.10.2