JAL-1683 replace year/version strings with tokens in source

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

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index ea900dc..02d584a 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 ($$Version-Rel$$)
+ * 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.Hashtable;
-
-import jalview.analysis.AAFrequency;
 import jalview.analysis.StructureFrequency;
 import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignViewportI;
@@ -10,6 +27,9 @@ import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+
+import java.util.Hashtable;
 
 public class StrucConsensusThread extends AlignCalcWorker implements
         AlignCalcWorkerI
@@ -24,11 +44,17 @@ public class StrucConsensusThread extends AlignCalcWorker implements
 
   Hashtable[] hStrucConsensus;
 
+  private long nseq = -1;
+
   @Override
   public void run()
   {
     try
     {
+      if (calcMan.isPending(this))
+      {
+        return;
+      }
       calcMan.notifyStart(this);
       while (!calcMan.notifyWorking(this))
       {
@@ -36,7 +62,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
         {
           if (ap != null)
           {
-            ap.paintAlignment(false);
+            // ap.paintAlignment(false);
           }
 
           Thread.sleep(200);
@@ -48,6 +74,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
       if (alignViewport.isClosed())
       {
         abortAndDestroy();
+        return;
       }
       AlignmentI alignment = alignViewport.getAlignment();
 
@@ -85,9 +112,17 @@ public class StrucConsensusThread extends AlignCalcWorker implements
         return;
       }
 
-      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);
+        return;
+      }
       alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
       // TODO AlignmentAnnotation rnaStruc!!!
       updateResultAnnotation(true);
@@ -103,12 +138,13 @@ public class StrucConsensusThread extends AlignCalcWorker implements
       // 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);
+      }
     }
 
   }
@@ -131,8 +167,8 @@ 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
+}