X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=6f713fcd0f5bac377c71d0ba7ff1701d43821b9c;hb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;hp=eedc8637a906cbebedf5954e85bad31a334e463f;hpb=b76d0ffcb6effa94954f75e030d1d67c890134eb;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index eedc863..6f713fc 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -552,8 +552,8 @@ public class AlignViewport implements SelectionSource
         consensus.annotations = new Annotation[aWidth];
 
         hconsensus = new Hashtable[aWidth];
-        AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
-                .getWidth(), hconsensus, true);
+        AAFrequency.calculate(alignment.getSequencesArray(), 0,
+                alignment.getWidth(), hconsensus, true);
         updateAnnotation(true);
 
         if (globalColourScheme != null)
@@ -589,7 +589,8 @@ public class AlignViewport implements SelectionSource
 
     protected void updateAnnotation(boolean immediate)
     {
-      // TODO: make calls thread-safe, so if another thread calls this method, it will either return or wait until one calculation is finished.
+      // TODO: make calls thread-safe, so if another thread calls this method,
+      // it will either return or wait until one calculation is finished.
       if (immediate
               || (!updatingConsensus && consensus != null && hconsensus != null))
       {
@@ -1852,8 +1853,8 @@ public class AlignViewport implements SelectionSource
       {
         Alignment al = (Alignment) alignment;
         Conservation c = new Conservation("All",
-                ResidueProperties.propHash, 3, al.getSequences(), 0, al
-                        .getWidth() - 1);
+                ResidueProperties.propHash, 3, al.getSequences(), 0,
+                al.getWidth() - 1);
         c.calculate();
         c.verdict(false, ConsPercGaps);
 
@@ -1867,8 +1868,8 @@ public class AlignViewport implements SelectionSource
       SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
       if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
       {
-        ((ClustalxColourScheme) sg.cs).resetClustalX(sg
-                .getSequences(hiddenRepSequences), sg.getWidth());
+        ((ClustalxColourScheme) sg.cs).resetClustalX(
+                sg.getSequences(hiddenRepSequences), sg.getWidth());
       }
       sg.recalcConservation();
     }