X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=e4c6c5c473298006b3a2e09b3674348e040e38e6;hb=c68ebaddf1925d9458aab5f2fea6e6f3240b3b99;hp=09dccfec441f4478df02a8c32f56a41a4265d4c9;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 09dccfe..e4c6c5c 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -105,13 +105,47 @@ 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;
+      renderOrder = null;
+      featureGroups = new Hashtable();
+      featureColours = new Hashtable();
+      featureOrder = new Hashtable();
+      if (fr.renderOrder != null)
+      {
+        this.renderOrder = new String[fr.renderOrder.length];
+        System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
+                renderOrder.length);
+      }
+      if (fr.featureGroups != null)
+      {
+        this.featureGroups = new Hashtable(fr.featureGroups);
+      }
+      if (fr.featureColours != null)
+      {
+        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;
+      if (fr.featureOrder != null)
+      {
+        this.featureOrder = new Hashtable(fr.featureOrder);
+      }
     }
   }
 
@@ -1329,7 +1363,7 @@ 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)