JAL-4090 release weds 25th Oct 23 - JAL-4308 release notes

[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 9a2316c..a706896 100644 (file)
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -21,7 +21,7 @@
 package jalview.ws.jws2;
 
 import jalview.api.FeatureColourI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceFeature;
@@ -207,11 +207,9 @@ public class AADisorderClient extends JabawsCalcWorker
           scores = scoremanager.getAnnotationForSequence(seqId);
         } catch (Exception q)
         {
-          Cache.log
-                  .info("Couldn't recover disorder prediction for sequence "
-                          + seq.getName() + "(Prediction name was " + seqId
-                          + ")"
-                          + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
+          Console.info("Couldn't recover disorder prediction for sequence "
+                  + seq.getName() + "(Prediction name was " + seqId + ")"
+                  + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
         }
         float last = Float.NaN, val = Float.NaN;
         int lastAnnot = ourAnnot.size();
@@ -239,13 +237,13 @@ 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, methodName);
+                  sf = new SequenceFeature(type[0], type[1], base + rn.from,
+                          base + rn.to, val, methodName);
                 }
                 else
                 {
-                  sf = new SequenceFeature(type[0], type[1],
-                          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))
@@ -344,8 +342,9 @@ public class AADisorderClient extends JabawsCalcWorker
             {
               // set graduated color as fading to white for minimum, and
               // autoscaling to values on alignment
-              FeatureColourI ggc = new FeatureColour(Color.white,
-                      gc.getColour(), Float.MIN_VALUE, Float.MAX_VALUE);
+              FeatureColourI ggc = new FeatureColour(gc.getColour(),
+                      Color.white, gc.getColour(), Color.white,
+                      Float.MIN_VALUE, Float.MAX_VALUE);
               ggc.setAutoScaled(true);
               fr.setColour(ft, ggc);
             }