X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConservationThread.java;h=021e6e2cfb63d928755823bb3759a15230b2c92c;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=194c389cef1d8df1f043a2c13bc5a2a3b4a81f4a;hpb=1cc81e06ac2faa5ee4b8879e9fa019956e34259f;p=jalview.git

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 194c389..021e6e2 100644
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -27,20 +27,26 @@ import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 
-public class ConservationThread extends AlignCalcWorker implements AlignCalcWorkerI
+public class ConservationThread extends AlignCalcWorker implements
+        AlignCalcWorkerI
 {
 
-  private int ConsPercGaps = 25; // JBPNote : This should be a configurable property!
+  private int ConsPercGaps = 25; // JBPNote : This should be a configurable
+                                 // property!
 
-  public ConservationThread(AlignViewportI alignViewport, AlignmentViewPanel alignPanel)
+  public ConservationThread(AlignViewportI alignViewport,
+          AlignmentViewPanel alignPanel)
   {
     super(alignViewport, alignPanel);
     ConsPercGaps = alignViewport.getConsPercGaps();
   }
 
   private Conservation cons;
-  AlignmentAnnotation conservation,quality;
+
+  AlignmentAnnotation conservation, quality;
+
   int alWidth;
+
   @Override
   public void run()
   {
@@ -62,31 +68,34 @@ public class ConservationThread extends AlignCalcWorker implements AlignCalcWork
           ex.printStackTrace();
         }
       }
-      if (alignViewport.isClosed()) {
+      if (alignViewport.isClosed())
+      {
         abortAndDestroy();
       }
-      List<AlignmentAnnotation>ourAnnot = new ArrayList<AlignmentAnnotation>();
-      AlignmentI alignment=alignViewport.getAlignment();
-      conservation=alignViewport.getAlignmentConservationAnnotation();
-      quality=alignViewport.getAlignmentQualityAnnot();
+      List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
+      AlignmentI alignment = alignViewport.getAlignment();
+      conservation = alignViewport.getAlignmentConservationAnnotation();
+      quality = alignViewport.getAlignmentQualityAnnot();
       ourAnnot.add(conservation);
       ourAnnot.add(quality);
       ourAnnots = ourAnnot;
 
       // AlignViewport.UPDATING_CONSERVATION = true;
 
-      if (alignment==null || (alWidth=alignment.getWidth())< 0)
+      if (alignment == null || (alWidth = alignment.getWidth()) < 0)
       {
         calcMan.workerComplete(this);
-        //.updatingConservation = false;
-        //AlignViewport.UPDATING_CONSERVATION = false;
+        // .updatingConservation = false;
+        // AlignViewport.UPDATING_CONSERVATION = false;
 
         return;
       }
-      try {
-      cons = Conservation.calculateConservation("All",
-              jalview.schemes.ResidueProperties.propHash, 3,
-              alignment.getSequences(), 0, alWidth - 1, false, ConsPercGaps, quality!=null);
+      try
+      {
+        cons = Conservation.calculateConservation("All",
+                jalview.schemes.ResidueProperties.propHash, 3,
+                alignment.getSequences(), 0, alWidth - 1, false,
+                ConsPercGaps, quality != null);
       } catch (IndexOutOfBoundsException x)
       {
         // probable race condition. just finish and return without any fuss.
@@ -113,10 +122,11 @@ public class ConservationThread extends AlignCalcWorker implements AlignCalcWork
 
   private void updateResultAnnotation(boolean b)
   {
-    if (b || !calcMan.isWorking(this) && cons!=null && conservation!=null && quality!=null)
-    cons.completeAnnotations(conservation,
-            quality, 0, alWidth);
+    if (b || !calcMan.isWorking(this) && cons != null
+            && conservation != null && quality != null)
+      cons.completeAnnotations(conservation, quality, 0, alWidth);
   }
+
   @Override
   public void updateAnnotation()
   {