JAL-975 - doh! valid result if width matches *ungapped* input data

diff --git a/src/jalview/ws/jws2/AAConsClient.java b/src/jalview/ws/jws2/AAConsClient.java
index c76ea1c..f6c3fcf 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;