JAL-1432 updated copyright notices

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

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 69236d8..9496506 100644 (file)
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -1,8 +1,25 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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 java.util.Hashtable;
 
-import jalview.analysis.AAFrequency;
 import jalview.analysis.StructureFrequency;
 import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignViewportI;
@@ -11,20 +28,28 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 
-public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
+public class StrucConsensusThread extends AlignCalcWorker implements
+        AlignCalcWorkerI
 {
   public StrucConsensusThread(AlignViewportI alignViewport,
           AlignmentViewPanel alignPanel)
   {
     super(alignViewport, alignPanel);
   }
+
   AlignmentAnnotation strucConsensus;
+
   Hashtable[] hStrucConsensus;
 
+  @Override
   public void run()
   {
     try
     {
+      if (calcMan.isPending(this))
+      {
+        return;
+      }
       calcMan.notifyStart(this);
       while (!calcMan.notifyWorking(this))
       {
@@ -32,7 +57,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
         {
           if (ap != null)
           {
-            ap.paintAlignment(false);
+            // ap.paintAlignment(false);
           }
 
           Thread.sleep(200);
@@ -54,8 +79,8 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
         calcMan.workerComplete(this);
         return;
       }
-      strucConsensus=alignViewport.getAlignmentStrucConsensusAnnotation();
-      hStrucConsensus=alignViewport.getRnaStructureConsensusHash();
+      strucConsensus = alignViewport.getAlignmentStrucConsensusAnnotation();
+      hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
       strucConsensus.annotations = null;
       strucConsensus.annotations = new Annotation[aWidth];
 
@@ -74,19 +99,27 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
         }
       }
       // check to see if its valid
-      
-      if (rnaStruc==null || !rnaStruc.isValidStruc())
+
+      if (rnaStruc == null || !rnaStruc.isValidStruc())
+      {
+        calcMan.workerComplete(this);
+        return;
+      }
+
+      try
+      {
+        jalview.analysis.StructureFrequency.calculate(
+                alignment.getSequencesArray(), 0, alignment.getWidth(),
+                hStrucConsensus, true, rnaStruc);
+      } catch (ArrayIndexOutOfBoundsException x)
       {
         calcMan.workerComplete(this);
         return;
       }
-      
-      jalview.analysis.StructureFrequency.calculate(alignment.getSequencesArray(), 0,
-              alignment.getWidth(), hStrucConsensus, true, rnaStruc);
       alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
       // TODO AlignmentAnnotation rnaStruc!!!
       updateResultAnnotation(true);
-      if (alignViewport.getGlobalColourScheme()!= null)
+      if (alignViewport.getGlobalColourScheme() != null)
       {
         alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
       }
@@ -98,19 +131,22 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
       // consensus = null;
       // hconsensus = null;
       ap.raiseOOMWarning("calculating RNA structure consensus", error);
-    }
-
-    calcMan.workerComplete(this);
-    if (ap != null)
+    } finally
     {
-      ap.paintAlignment(true);
+      calcMan.workerComplete(this);
+      if (ap != null)
+      {
+        ap.paintAlignment(true);
+      }
     }
 
   }
+
   /**
    * update the consensus annotation from the sequence profile data using
    * current visualization settings.
    */
+  @Override
   public void updateAnnotation()
   {
     updateResultAnnotation(false);
@@ -118,13 +154,14 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
 
   public void updateResultAnnotation(boolean immediate)
   {
-    if (immediate || !calcMan.isWorking(this) && strucConsensus!=null && hStrucConsensus!=null)
+    if (immediate || !calcMan.isWorking(this) && strucConsensus != null
+            && hStrucConsensus != null)
     {
-      StructureFrequency.completeConsensus(strucConsensus,
-              hStrucConsensus, 0, hStrucConsensus.length,
+      StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
+              0, hStrucConsensus.length,
               alignViewport.getIgnoreGapsConsensus(),
-            alignViewport.isShowSequenceLogo());
+              alignViewport.isShowSequenceLogo());
     }
   }
 
-}
\ No newline at end of file
+}