X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FStrucConsensusThread.java;h=9694b3759eea8b5d013fd7f07bb0b7bec8e7cad6;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=ea900dc7cacf814d7e83b6c74a87a77783e4f406;hpb=d668b0fe1a9eefb95c935bc6c71a88e67642e712;p=jalview.git

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index ea900dc..9694b37 100644
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -1,8 +1,25 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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();
 
@@ -71,7 +98,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
       // select rna struct to use for calculation
       for (int i = 0; i < aa.length; i++)
       {
-        if (aa[i].getRNAStruc() != null && aa[i].isValidStruc())
+        if (aa[i].visible && aa[i].isRNA() && aa[i].isValidStruc())
         {
           rnaStruc = aa[i];
           break;
@@ -85,17 +112,20 @@ 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);
-      if (alignViewport.getGlobalColourScheme() != null)
-      {
-        alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
-      }
-
     } catch (OutOfMemoryError error)
     {
       calcMan.workerCannotRun(this);
@@ -103,12 +133,13 @@ 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);
+      }
     }
 
   }
@@ -130,9 +161,9 @@ public class StrucConsensusThread extends AlignCalcWorker implements
     {
       StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
               0, hStrucConsensus.length,
-              alignViewport.getIgnoreGapsConsensus(),
-              alignViewport.isShowSequenceLogo());
+              alignViewport.isIgnoreGapsConsensus(),
+              alignViewport.isShowSequenceLogo(), nseq);
     }
   }
 
-}
\ No newline at end of file
+}