X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FComplementConsensusThread.java;h=aca8ed0354492fc3fdcbe5ad080b74506c4e49a3;hb=aa96618cbd41b40e2377f3f1f105aea90a5a86e0;hp=71bfb40c2ff1e91f36b9db47514a9b2d369fd86e;hpb=b6acaa87c22c1d31deb3f9b87a143def43ae34b7;p=jalview.git

diff --git a/src/jalview/workers/ComplementConsensusThread.java b/src/jalview/workers/ComplementConsensusThread.java
index 71bfb40..aca8ed0 100644
--- a/src/jalview/workers/ComplementConsensusThread.java
+++ b/src/jalview/workers/ComplementConsensusThread.java
@@ -1,14 +1,33 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 java.util.ConcurrentModificationException;
-import java.util.Hashtable;
-
 import jalview.analysis.AAFrequency;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
+
+import java.util.ConcurrentModificationException;
+import java.util.Hashtable;
 
 /**
  * A thread to recompute the consensus of the cDNA complement for a linked
@@ -33,7 +52,7 @@ public class ComplementConsensusThread extends ConsensusThread
   }
 
   @Override
-  protected Hashtable[] getViewportConsensus()
+  protected Hashtable<String, Object>[] getViewportConsensus()
   {
     return alignViewport.getComplementConsensusHash();
   }
@@ -44,9 +63,11 @@ public class ComplementConsensusThread extends ConsensusThread
   @Override
   protected void computeConsensus(AlignmentI alignment)
   {
-    Hashtable[] hconsensus = new Hashtable[alignment.getWidth()];
+    @SuppressWarnings("unchecked")
+    Hashtable<String, Object>[] hconsensus = new Hashtable[alignment
+            .getWidth()];
 
-    SequenceI[] aseqs = getSequences();
+    // SequenceI[] aseqs = getSequences();
 
     /*
      * Allow 3 tries at this, since this thread can start up while we are still
@@ -76,12 +97,23 @@ public class ComplementConsensusThread extends ConsensusThread
    * @param consensusData
    *          the computed consensus data
    */
-  @Override
   protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
-          Hashtable[] consensusData)
+          Hashtable<String, Object>[] consensusData)
   {
     AAFrequency.completeCdnaConsensus(consensusAnnotation, consensusData,
             alignViewport.isShowSequenceLogo(), getSequences().length);
   }
 
+  @Override
+  public void updateResultAnnotation(boolean immediate)
+  {
+    AlignmentAnnotation consensus = getConsensusAnnotation();
+    Hashtable<String, Object>[] hconsensus = getViewportConsensus();
+    if (immediate || !calcMan.isWorking(this) && consensus != null
+            && hconsensus != null)
+    {
+      deriveConsensus(consensus, hconsensus);
+    }
+  }
+
 }