JAL-975 JAL-1119 - prototype adjustable AACons parameters for the currrent alignment...

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

diff --git a/src/jalview/ws/jws2/AAConsClient.java b/src/jalview/ws/jws2/AAConsClient.java
index c76ea1c..58d0fa9 100644 (file)
--- a/src/jalview/ws/jws2/AAConsClient.java
+++ b/src/jalview/ws/jws2/AAConsClient.java
@@ -75,7 +75,7 @@ public class AAConsClient extends JabawsAlignCalcWorker
             // simple annotation row
             annotation = alignViewport.getAlignment().findOrCreateAnnotation(scr.getMethod(), true, null, null);
             Annotation[] elm = new Annotation[alWidth];
-            if (alWidth == scr.getScores().size())
+            if (alWidth == gapMap.length) // scr.getScores().size())
             {
               Iterator<Float> vals = scr.getScores().iterator();
               float m = 0f, x = 0f;
@@ -156,4 +156,11 @@ public class AAConsClient extends JabawsAlignCalcWorker
     }
   }
 
+  public static void removeAAConsAnnotation(AlignmentPanel alignPanel)
+  {
+    // List<AlignmentAnnotation>
+    // ourannots=alignPanel.getAlignment().findAnnotation(Screen3D.)
+    // TODO Auto-generated method stub
+
+  }
 }