JAL-2446 merged to spike branch

[jalview.git] / src / jalview / ws / jws2 / AADisorderClient.java

diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index 0cf76e0..b877d20 100644 (file)
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -20,7 +20,6 @@
  */
 package jalview.ws.jws2;
 
-import jalview.api.AlignCalcWorkerI;
 import jalview.api.FeatureColourI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
@@ -29,7 +28,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.schemes.FeatureColour;
-import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 
@@ -238,14 +237,14 @@ public class AADisorderClient extends JabawsCalcWorker
                 }
                 if (vals.hasNext())
                 {
+                  val = vals.next().floatValue();
                   sf = new SequenceFeature(type[0], type[1],
-                          base + rn.from, base + rn.to, val = vals.next()
-                                  .floatValue(), methodName);
+                          base + rn.from, base + rn.to, val, methodName);
                 }
                 else
                 {
-                  sf = new SequenceFeature(type[0], type[1], null, base
-                          + rn.from, base + rn.to, methodName);
+                  sf = new SequenceFeature(type[0], type[1],
+                          base + rn.from, base + rn.to, methodName);
                 }
                 dseq.addSequenceFeature(sf);
                 if (last != val && !Float.isNaN(last))
@@ -308,7 +307,7 @@ public class AADisorderClient extends JabawsCalcWorker
                 annot.description += "<br/>" + threshNote;
               }
               annot.description += "</html>";
-              Color col = UserColourScheme.createColourFromName(typeName
+              Color col = ColorUtils.createColourFromName(typeName
                       + scr.getMethod());
               for (int p = 0, ps = annot.annotations.length; p < ps; p++)
               {