X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConsensusThread.java;h=735b97fcb5e6089bd610f1652a227a6c90956d5d;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=b36f36769fb051be5150b9e207f4354f34bfa35c;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index b36f367..735b97f 100644
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -25,6 +25,7 @@ import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 
 import java.util.Hashtable;
@@ -32,6 +33,8 @@ import java.util.Hashtable;
 public class ConsensusThread extends AlignCalcWorker implements
         AlignCalcWorkerI
 {
+  private long nseq=-1;
+
   public ConsensusThread(AlignViewportI alignViewport,
           AlignmentViewPanel alignPanel)
   {
@@ -95,7 +98,9 @@ public class ConsensusThread extends AlignCalcWorker implements
       hconsensus = new Hashtable[aWidth];
       try
       {
-        AAFrequency.calculate(alignment.getSequencesArray(), 0,
+        SequenceI aseqs[] = alignment.getSequencesArray();
+        nseq = aseqs.length;
+        AAFrequency.calculate(aseqs, 0,
                 alignment.getWidth(), hconsensus, true);
       } catch (ArrayIndexOutOfBoundsException x)
       {
@@ -151,7 +156,7 @@ public class ConsensusThread extends AlignCalcWorker implements
     {
       AAFrequency.completeConsensus(consensus, hconsensus, 0,
               hconsensus.length, alignViewport.getIgnoreGapsConsensus(),
-              alignViewport.isShowSequenceLogo());
+              alignViewport.isShowSequenceLogo(), nseq);
     }
   }
 }