JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 3d0526a..5ed2885 100644 (file)
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -1,27 +1,26 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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/>.
+ * 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.StructureFrequency;
-import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
@@ -29,8 +28,9 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceI;
 
-public class StrucConsensusThread extends AlignCalcWorker implements
-        AlignCalcWorkerI
+import java.util.Hashtable;
+
+public class StrucConsensusThread extends AlignCalcWorker
 {
   public StrucConsensusThread(AlignViewportI alignViewport,
           AlignmentViewPanel alignPanel)
@@ -42,7 +42,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
 
   Hashtable[] hStrucConsensus;
 
-  private long nseq=-1;
+  private long nseq = -1;
 
   @Override
   public void run()
@@ -72,6 +72,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
       if (alignViewport.isClosed())
       {
         abortAndDestroy();
+        return;
       }
       AlignmentI alignment = alignViewport.getAlignment();
 
@@ -93,12 +94,15 @@ public class StrucConsensusThread extends AlignCalcWorker implements
               .getAlignmentAnnotation();
       AlignmentAnnotation rnaStruc = null;
       // select rna struct to use for calculation
-      for (int i = 0; i < aa.length; i++)
+      if (aa != null)
       {
-        if (aa[i].getRNAStruc() != null && aa[i].isValidStruc())
+        for (int i = 0; i < aa.length; i++)
         {
-          rnaStruc = aa[i];
-          break;
+          if (aa[i].visible && aa[i].isRNA() && aa[i].isValidStruc())
+          {
+            rnaStruc = aa[i];
+            break;
+          }
         }
       }
       // check to see if its valid
@@ -111,11 +115,10 @@ public class StrucConsensusThread extends AlignCalcWorker implements
 
       try
       {
-        final SequenceI[] arr=
-                alignment.getSequencesArray();
+        final SequenceI[] arr = alignment.getSequencesArray();
         nseq = arr.length;
-        jalview.analysis.StructureFrequency.calculate(arr, 0, alignment.getWidth(),
-                hStrucConsensus, true, rnaStruc);
+        jalview.analysis.StructureFrequency.calculate(arr, 0,
+                alignment.getWidth(), hStrucConsensus, true, rnaStruc);
       } catch (ArrayIndexOutOfBoundsException x)
       {
         calcMan.workerComplete(this);
@@ -124,14 +127,9 @@ public class StrucConsensusThread extends AlignCalcWorker implements
       alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
       // TODO AlignmentAnnotation rnaStruc!!!
       updateResultAnnotation(true);
-      if (alignViewport.getGlobalColourScheme() != null)
-      {
-        alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
-      }
-
     } catch (OutOfMemoryError error)
     {
-      calcMan.workerCannotRun(this);
+      calcMan.disableWorker(this);
 
       // consensus = null;
       // hconsensus = null;
@@ -164,7 +162,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
     {
       StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
               0, hStrucConsensus.length,
-              alignViewport.getIgnoreGapsConsensus(),
+              alignViewport.isIgnoreGapsConsensus(),
               alignViewport.isShowSequenceLogo(), nseq);
     }
   }