JAL-1925 update source version in license

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

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 72d26ff..9694b37 100644 (file)
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -1,6 +1,6 @@
 /*
- * 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 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,8 +20,6 @@
  */
 package jalview.workers;
 
-import java.util.Hashtable;
-
 import jalview.analysis.StructureFrequency;
 import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignViewportI;
@@ -31,6 +29,8 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceI;
 
+import java.util.Hashtable;
+
 public class StrucConsensusThread extends AlignCalcWorker implements
         AlignCalcWorkerI
 {
@@ -74,6 +74,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
       if (alignViewport.isClosed())
       {
         abortAndDestroy();
+        return;
       }
       AlignmentI alignment = alignViewport.getAlignment();
 
@@ -97,7 +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;
@@ -125,11 +126,6 @@ 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);
@@ -165,7 +161,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
     {
       StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
               0, hStrucConsensus.length,
-              alignViewport.getIgnoreGapsConsensus(),
+              alignViewport.isIgnoreGapsConsensus(),
               alignViewport.isShowSequenceLogo(), nseq);
     }
   }