X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAADisorderClient.java;h=7d1c5142e904a3dcf0adfb2a72d51551651b82a8;hb=d9c7868a610eff29a8eddb160b6dc78a94a72470;hp=65620cc88e583496e390193d4d454cc77c5efe62;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index 65620cc..7d1c514 100644
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
  * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -21,13 +21,14 @@
 package jalview.ws.jws2;
 
 import jalview.api.AlignCalcWorkerI;
+import jalview.api.FeatureColourI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
 import jalview.schemes.UserColourScheme;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
@@ -46,8 +47,7 @@ import compbio.data.sequence.Score;
 import compbio.data.sequence.ScoreManager.ScoreHolder;
 import compbio.metadata.Argument;
 
-public class AADisorderClient extends JabawsCalcWorker implements
-        AlignCalcWorkerI
+public class AADisorderClient extends JabawsCalcWorker
 {
 
   private static final String THRESHOLD = "THRESHOLD";
@@ -308,8 +308,8 @@ public class AADisorderClient extends JabawsCalcWorker implements
                 annot.description += "<br/>" + threshNote;
               }
               annot.description += "</html>";
-              Color col = new UserColourScheme(typeName)
-                      .createColourFromName(typeName + scr.getMethod());
+              Color col = UserColourScheme.createColourFromName(typeName
+                      + scr.getMethod());
               for (int p = 0, ps = annot.annotations.length; p < ps; p++)
               {
                 if (annot.annotations[p] != null)
@@ -337,13 +337,13 @@ public class AADisorderClient extends JabawsCalcWorker implements
                   .cloneFeatureRenderer();
           for (String ft : fc.keySet())
           {
-            Object gc = fr.getFeatureStyle(ft);
-            if (gc instanceof Color)
+            FeatureColourI gc = fr.getFeatureStyle(ft);
+            if (gc.isSimpleColour())
             {
               // set graduated color as fading to white for minimum, and
               // autoscaling to values on alignment
-              GraduatedColor ggc = new GraduatedColor(Color.white,
-                      (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
+              FeatureColourI ggc = new FeatureColour(Color.white,
+                      gc.getColour(), Float.MIN_VALUE, Float.MAX_VALUE);
               ggc.setAutoScaled(true);
               fr.setColour(ft, ggc);
             }