X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FStrucConsensusThread.java;h=25e5cde1c50152d718ff739248272ffc7362a1dd;hb=6fb502e4a8749d1d98f5442c3b8156ab47996b77;hp=a7f919b9661f7cc0da0688f8b545a124df566051;hpb=f61b2748a32ef03e687abc37b97640873c2e44aa;p=jalview.git

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index a7f919b..25e5cde 100644
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -1,3 +1,20 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
 package jalview.workers;
 
 import java.util.Hashtable;
@@ -9,6 +26,7 @@ import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
 
 public class StrucConsensusThread extends AlignCalcWorker implements
         AlignCalcWorkerI
@@ -23,6 +41,8 @@ public class StrucConsensusThread extends AlignCalcWorker implements
 
   Hashtable[] hStrucConsensus;
 
+  private long nseq=-1;
+
   @Override
   public void run()
   {
@@ -88,10 +108,13 @@ public class StrucConsensusThread extends AlignCalcWorker implements
         return;
       }
 
-      try {
-              jalview.analysis.StructureFrequency.calculate(
-              alignment.getSequencesArray(), 0, alignment.getWidth(),
-              hStrucConsensus, true, rnaStruc);
+      try
+      {
+        final SequenceI[] arr=
+                alignment.getSequencesArray();
+        nseq = arr.length;
+        jalview.analysis.StructureFrequency.calculate(arr, 0, alignment.getWidth(),
+                hStrucConsensus, true, rnaStruc);
       } catch (ArrayIndexOutOfBoundsException x)
       {
         calcMan.workerComplete(this);
@@ -141,8 +164,8 @@ public class StrucConsensusThread extends AlignCalcWorker implements
       StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
               0, hStrucConsensus.length,
               alignViewport.getIgnoreGapsConsensus(),
-              alignViewport.isShowSequenceLogo());
+              alignViewport.isShowSequenceLogo(), nseq);
     }
   }
 
-}
\ No newline at end of file
+}