From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 19 Jun 2012 16:28:50 +0000 (+0100)
Subject: JAL-975 - doh! valid result if width matches *ungapped* input data
X-Git-Tag: Jalview_2_9~448
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e573bf375782b0dbdfacee15f6477d9630a234ee;p=jalview.git

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
--- 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;