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 f4b1c31..b877d20 100644 (file)
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -20,14 +20,15 @@
  */
 package jalview.ws.jws2;
 
+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.UserColourScheme;
+import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 
@@ -236,14 +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))
@@ -306,8 +307,8 @@ public class AADisorderClient extends JabawsCalcWorker
                 annot.description += "<br/>" + threshNote;
               }
               annot.description += "</html>";
-              Color col = new UserColourScheme(typeName)
-                      .createColourFromName(typeName + scr.getMethod());
+              Color col = ColorUtils.createColourFromName(typeName
+                      + scr.getMethod());
               for (int p = 0, ps = annot.annotations.length; p < ps; p++)
               {
                 if (annot.annotations[p] != null)
@@ -335,13 +336,13 @@ public class AADisorderClient extends JabawsCalcWorker
                   .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);
             }