javatidy

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

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 69236d8..ea900dc 100644 (file)
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -11,16 +11,20 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 
-public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
+public class StrucConsensusThread extends AlignCalcWorker implements
+        AlignCalcWorkerI
 {
   public StrucConsensusThread(AlignViewportI alignViewport,
           AlignmentViewPanel alignPanel)
   {
     super(alignViewport, alignPanel);
   }
+
   AlignmentAnnotation strucConsensus;
+
   Hashtable[] hStrucConsensus;
 
+  @Override
   public void run()
   {
     try
@@ -54,8 +58,8 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
         calcMan.workerComplete(this);
         return;
       }
-      strucConsensus=alignViewport.getAlignmentStrucConsensusAnnotation();
-      hStrucConsensus=alignViewport.getRnaStructureConsensusHash();
+      strucConsensus = alignViewport.getAlignmentStrucConsensusAnnotation();
+      hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
       strucConsensus.annotations = null;
       strucConsensus.annotations = new Annotation[aWidth];
 
@@ -74,19 +78,20 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
         }
       }
       // check to see if its valid
-      
-      if (rnaStruc==null || !rnaStruc.isValidStruc())
+
+      if (rnaStruc == null || !rnaStruc.isValidStruc())
       {
         calcMan.workerComplete(this);
         return;
       }
-      
-      jalview.analysis.StructureFrequency.calculate(alignment.getSequencesArray(), 0,
-              alignment.getWidth(), hStrucConsensus, true, rnaStruc);
+
+      jalview.analysis.StructureFrequency.calculate(
+              alignment.getSequencesArray(), 0, alignment.getWidth(),
+              hStrucConsensus, true, rnaStruc);
       alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
       // TODO AlignmentAnnotation rnaStruc!!!
       updateResultAnnotation(true);
-      if (alignViewport.getGlobalColourScheme()!= null)
+      if (alignViewport.getGlobalColourScheme() != null)
       {
         alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
       }
@@ -107,10 +112,12 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
     }
 
   }
+
   /**
    * update the consensus annotation from the sequence profile data using
    * current visualization settings.
    */
+  @Override
   public void updateAnnotation()
   {
     updateResultAnnotation(false);
@@ -118,12 +125,13 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
 
   public void updateResultAnnotation(boolean immediate)
   {
-    if (immediate || !calcMan.isWorking(this) && strucConsensus!=null && hStrucConsensus!=null)
+    if (immediate || !calcMan.isWorking(this) && strucConsensus != null
+            && hStrucConsensus != null)
     {
-      StructureFrequency.completeConsensus(strucConsensus,
-              hStrucConsensus, 0, hStrucConsensus.length,
+      StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
+              0, hStrucConsensus.length,
               alignViewport.getIgnoreGapsConsensus(),
-            alignViewport.isShowSequenceLogo());
+              alignViewport.isShowSequenceLogo());
     }
   }