From 05a1420df55d0f180ce3c0337133e9be98a643b7 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 9 Jun 2010 14:06:03 +0000
Subject: [PATCH] patch for JAL-545 - make deep copy of feature settings

---
 src/jalview/gui/FeatureRenderer.java |   28 +++++++++++++++++++++++-----
 1 file changed, 23 insertions(+), 5 deletions(-)

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 09dccfe..b822bc5 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -105,13 +105,31 @@ public class FeatureRenderer
       this.featureOrder = featureOrder;
     }
 
+    /**
+     * create an independent instance of the feature renderer settings
+     * 
+     * @param fr
+     */
     public FeatureRendererSettings(FeatureRenderer fr)
     {
-      this.renderOrder = fr.renderOrder;
-      this.featureGroups = fr.featureGroups;
-      this.featureColours = fr.featureColours;
+      this.renderOrder = new String[fr.renderOrder.length];
+      System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
+              renderOrder.length);
+      this.featureGroups = new Hashtable(fr.featureGroups);
+      this.featureColours = new Hashtable(fr.featureColours);
+      Enumeration en = fr.featureColours.keys();
+      while (en.hasMoreElements())
+      {
+        Object next = en.nextElement();
+        Object val = featureColours.get(next);
+        if (val instanceof GraduatedColor)
+        {
+          featureColours
+                  .put(next, new GraduatedColor((GraduatedColor) val));
+        }
+      }
       this.transparency = fr.transparency;
-      this.featureOrder = fr.featureOrder;
+      this.featureOrder = new Hashtable(fr.featureOrder);
     }
   }
 
@@ -1329,7 +1347,7 @@ public class FeatureRenderer
       {
         String type = data[i][0].toString();
         setColour(type, data[i][1]); // todo : typesafety - feature color
-                                     // interface object
+        // interface object
         if (((Boolean) data[i][2]).booleanValue())
         {
           av.featuresDisplayed.put(type, new Integer(getColour(type)
-- 
1.7.10.2