X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConsensusThread.java;h=735b97fcb5e6089bd610f1652a227a6c90956d5d;hb=e716284ee3824cfc190e43eaa4f9335e3ac75637;hp=9bdd714739bf2841be55a499f1f74cfb967f1ea3;hpb=f61b2748a32ef03e687abc37b97640873c2e44aa;p=jalview.git

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 9bdd714..735b97f 100644
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.workers;
 
 import jalview.analysis.AAFrequency;
@@ -7,12 +25,16 @@ 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;
 
-public class ConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
+public class ConsensusThread extends AlignCalcWorker implements
+        AlignCalcWorkerI
 {
+  private long nseq=-1;
+
   public ConsensusThread(AlignViewportI alignViewport,
           AlignmentViewPanel alignPanel)
   {
@@ -27,11 +49,13 @@ public class ConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
       return;
     }
     calcMan.notifyStart(this);
-    long started=System.currentTimeMillis();
+    long started = System.currentTimeMillis();
     try
     {
-      AlignmentAnnotation consensus = alignViewport.getAlignmentConsensusAnnotation();
-      if (consensus==null || calcMan.isPending(this))  {
+      AlignmentAnnotation consensus = alignViewport
+              .getAlignmentConsensusAnnotation();
+      if (consensus == null || calcMan.isPending(this))
+      {
         calcMan.workerComplete(this);
         return;
       }
@@ -42,7 +66,7 @@ public class ConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
         {
           if (ap != null)
           {
-           ap.paintAlignment(false);
+            ap.paintAlignment(false);
           }
           Thread.sleep(200);
         } catch (Exception ex)
@@ -66,21 +90,24 @@ public class ConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
 
         return;
       }
-      consensus = alignViewport
-              .getAlignmentConsensusAnnotation();
+      consensus = alignViewport.getAlignmentConsensusAnnotation();
 
       consensus.annotations = null;
       consensus.annotations = new Annotation[aWidth];
       Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
       hconsensus = new Hashtable[aWidth];
-      try {
-       AAFrequency.calculate(alignment.getSequencesArray(), 0,
-              alignment.getWidth(), hconsensus, true);
-      } catch (ArrayIndexOutOfBoundsException x){
+      try
+      {
+        SequenceI aseqs[] = alignment.getSequencesArray();
+        nseq = aseqs.length;
+        AAFrequency.calculate(aseqs, 0,
+                alignment.getWidth(), hconsensus, true);
+      } catch (ArrayIndexOutOfBoundsException x)
+      {
         // this happens due to a race condition -
         // alignment was edited at same time as calculation was running
         //
-//        calcMan.workerCannotRun(this);
+        // calcMan.workerCannotRun(this);
         calcMan.workerComplete(this);
         return;
       }
@@ -124,11 +151,12 @@ public class ConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
     AlignmentAnnotation consensus = alignViewport
             .getAlignmentConsensusAnnotation();
     Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
-    if (immediate || !calcMan.isWorking(this) && consensus!=null && hconsensus!=null)
+    if (immediate || !calcMan.isWorking(this) && consensus != null
+            && hconsensus != null)
     {
       AAFrequency.completeConsensus(consensus, hconsensus, 0,
-            hconsensus.length, alignViewport.getIgnoreGapsConsensus(),
-            alignViewport.isShowSequenceLogo());
+              hconsensus.length, alignViewport.getIgnoreGapsConsensus(),
+              alignViewport.isShowSequenceLogo(), nseq);
     }
   }
 }