JAL-2068 redundant implements clauses removed

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

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 1122663..3483dac 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,10 +20,7 @@
  */
 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;
@@ -31,8 +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)
@@ -44,7 +42,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
 
   Hashtable[] hStrucConsensus;
 
-  private long nseq=-1;
+  private long nseq = -1;
 
   @Override
   public void run()
@@ -74,6 +72,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
       if (alignViewport.isClosed())
       {
         abortAndDestroy();
+        return;
       }
       AlignmentI alignment = alignViewport.getAlignment();
 
@@ -97,7 +96,7 @@ 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;
@@ -113,11 +112,10 @@ 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);
@@ -126,11 +124,6 @@ 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);
@@ -166,7 +159,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
     {
       StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
               0, hStrucConsensus.length,
-              alignViewport.getIgnoreGapsConsensus(),
+              alignViewport.isIgnoreGapsConsensus(),
               alignViewport.isShowSequenceLogo(), nseq);
     }
   }