JAL-1620 version bump and release notes

[jalview.git] / src / jalview / workers / ConsensusThread.java

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 7dd25f8..a8c33ce 100644 (file)
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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;
@@ -7,45 +27,59 @@ 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)
   {
     super(alignViewport, alignPanel);
   }
 
+  @Override
   public void run()
   {
+    if (calcMan.isPending(this))
+    {
+      return;
+    }
+    calcMan.notifyStart(this);
+    long started = System.currentTimeMillis();
     try
     {
-      AlignmentAnnotation consensus = alignViewport.getAlignmentConsensusAnnotation();
-      if (consensus==null) { return; 
+      AlignmentAnnotation consensus = alignViewport
+              .getAlignmentConsensusAnnotation();
+      if (consensus == null || calcMan.isPending(this))
+      {
+        calcMan.workerComplete(this);
+        return;
       }
-      calcMan.notifyStart(this); 
-      while (!calcMan.notifyWorking(this)) 
+      while (!calcMan.notifyWorking(this))
       {
+        // System.err.println("Thread (Consensus"+Thread.currentThread().getName()+") Waiting around.");
         try
         {
           if (ap != null)
           {
             ap.paintAlignment(false);
           }
-
           Thread.sleep(200);
         } catch (Exception ex)
         {
           ex.printStackTrace();
         }
       }
-      calcMan.notifyWorking(this);
       if (alignViewport.isClosed())
       {
         abortAndDestroy();
+        return;
       }
       AlignmentI alignment = alignViewport.getAlignment();
 
@@ -59,15 +93,27 @@ 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];
-      AAFrequency.calculate(alignment.getSequencesArray(), 0,
-              alignment.getWidth(), hconsensus, true);
+      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.workerComplete(this);
+        return;
+      }
       alignViewport.setSequenceConsensusHash(hconsensus);
       updateResultAnnotation(true);
       ColourSchemeI globalColourScheme = alignViewport
@@ -97,6 +143,7 @@ public class ConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
    * update the consensus annotation from the sequence profile data using
    * current visualization settings.
    */
+  @Override
   public void updateAnnotation()
   {
     updateResultAnnotation(false);
@@ -107,11 +154,12 @@ 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);
     }
   }
 }