X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2Fjabaws2%2FAAConClient.java;fp=src%2Fjalview%2Fws%2Fjws2%2Fjabaws2%2FAAConClient.java;h=18b6ce18360b32eebddc9fcca31dd3a99acd44f0;hb=a1df6edfaf77aefab83a34bfd1331bc679a86142;hp=f0a4b67248981b81e4779a924e62de653ba2bf20;hpb=b55dff11e4b566dcaa3a219c463f09afb65cf92d;p=jalview.git

diff --git a/src/jalview/ws/jws2/jabaws2/AAConClient.java b/src/jalview/ws/jws2/jabaws2/AAConClient.java
index f0a4b67..18b6ce1 100644
--- a/src/jalview/ws/jws2/jabaws2/AAConClient.java
+++ b/src/jalview/ws/jws2/jabaws2/AAConClient.java
@@ -20,10 +20,11 @@
  */
 package jalview.ws.jws2.jabaws2;
 
-import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.util.MessageManager;
-import jalview.ws.gui.AnnotationWsJob;
 import jalview.ws.uimodel.AlignAnalysisUIText;
 
 import java.util.ArrayList;
@@ -64,13 +65,17 @@ public class AAConClient extends JabawsAnnotationInstance
   }
 
   @Override
-  List<AlignmentAnnotation> annotationFromScoreManager(
-          AnnotationWsJob running, AlignViewportI alignViewport,
-          boolean[] gapMap)
+  List<AlignmentAnnotation> annotationFromScoreManager(AlignmentI seqs,
+          Map<String, FeatureColourI> featureColours,
+          Map<String, FeatureMatcherSetI> featureFilters)
   {
+    return aacons_annotation(seqs.getWidth(), seqs, null);
+  }
 
+  private List<AlignmentAnnotation> aacons_annotation(int alWidth,
+          AlignmentI alignViewport, boolean[] gapMap)
+  {
     Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
-    int alWidth = alignViewport.getAlignment().getWidth();
     ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<>();
     for (String score : scoremap.keySet())
     {
@@ -91,8 +96,9 @@ public class AAConClient extends JabawsAnnotationInstance
         }
         else
         {
-          createAnnotationRowsForScores(alignViewport, gapMap, ourAnnot,
-                  getCalcId(), alWidth, scr);
+          createAnnotationRowsForScores(alignViewport, null, ourAnnot,
+                  getCalcId(),
+                  scr.getScores().size(), scr);
         }
       }
     }