JAL-2371 CollectionColourScheme wraps ColourSchemeI

[jalview.git] / src / jalview / io / AnnotationFile.java

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 2af3fcd..ed70dd4 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1610,8 +1610,7 @@ public class AnnotationFile
     if (sg != null)
     {
       String keyValue, key, value;
-      ColourSchemeI def = sg.cs;
-      sg.cs = null;
+      ColourSchemeI def = sg.getColourScheme();
       while (st.hasMoreTokens())
       {
         keyValue = st.nextToken();
@@ -1624,7 +1623,8 @@ public class AnnotationFile
         }
         else if (key.equalsIgnoreCase("colour"))
         {
-          sg.cs = ColourSchemeProperty.getColourScheme(al, value);
+          sg.cs.setColourScheme(ColourSchemeProperty
+                  .getColourScheme(al, value));
         }
         else if (key.equalsIgnoreCase("pidThreshold"))
         {
@@ -1693,9 +1693,9 @@ public class AnnotationFile
         }
         sg.recalcConservation();
       }
-      if (sg.cs == null)
+      if (sg.getColourScheme() == null)
       {
-        sg.cs = def;
+        sg.setColourScheme(def);
       }
     }
   }