Merge branch 'develop' into feature/JAL-3551Pymol

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

diff --git a/src/jalview/workers/ComplementConsensusThread.java b/src/jalview/workers/ComplementConsensusThread.java
index 431fbec..aca8ed0 100644 (file)
--- a/src/jalview/workers/ComplementConsensusThread.java
+++ b/src/jalview/workers/ComplementConsensusThread.java
@@ -25,7 +25,6 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
 
 import java.util.ConcurrentModificationException;
 import java.util.Hashtable;
@@ -53,7 +52,7 @@ public class ComplementConsensusThread extends ConsensusThread
   }
 
   @Override
-  protected Hashtable[] getViewportConsensus()
+  protected Hashtable<String, Object>[] getViewportConsensus()
   {
     return alignViewport.getComplementConsensusHash();
   }
@@ -64,9 +63,11 @@ public class ComplementConsensusThread extends ConsensusThread
   @Override
   protected void computeConsensus(AlignmentI alignment)
   {
-    Hashtable[] hconsensus = new Hashtable[alignment.getWidth()];
+    @SuppressWarnings("unchecked")
+    Hashtable<String, Object>[] hconsensus = new Hashtable[alignment
+            .getWidth()];
 
-    SequenceI[] aseqs = getSequences();
+    // SequenceI[] aseqs = getSequences();
 
     /*
      * Allow 3 tries at this, since this thread can start up while we are still
@@ -97,7 +98,7 @@ public class ComplementConsensusThread extends ConsensusThread
    *          the computed consensus data
    */
   protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
-          Hashtable[] consensusData)
+          Hashtable<String, Object>[] consensusData)
   {
     AAFrequency.completeCdnaConsensus(consensusAnnotation, consensusData,
             alignViewport.isShowSequenceLogo(), getSequences().length);
@@ -107,7 +108,7 @@ public class ComplementConsensusThread extends ConsensusThread
   public void updateResultAnnotation(boolean immediate)
   {
     AlignmentAnnotation consensus = getConsensusAnnotation();
-    Hashtable[] hconsensus = getViewportConsensus();
+    Hashtable<String, Object>[] hconsensus = getViewportConsensus();
     if (immediate || !calcMan.isWorking(this) && consensus != null
             && hconsensus != null)
     {