From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 19 Nov 2018 18:06:31 +0000 (+0000)
Subject: JAL-3127 javadoc, don’t darken white when shading residues, and don’t need to hold... 
X-Git-Tag: Release_2_11_0~17^2~46^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b71733cda46c5a88cb65417501727f2e4b4cf135;p=jalview.git

JAL-3127 javadoc, don’t darken white when shading residues, and don’t need to hold reference to group
---

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;
   }
 }