X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=1b3482f89d9ddf28973aa36c2b88b8b8bbb9e893;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=d363764857a9c85e105f3f6f2970993e13d4a921;hpb=1cc81e06ac2faa5ee4b8879e9fa019956e34259f;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index d363764..1b3482f 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -59,13 +59,17 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
     colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
   }
 
-  public ClustalxColourScheme(AnnotatedCollectionI alignment, Map<SequenceI, SequenceCollectionI> hiddenReps)
+  public ClustalxColourScheme(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
-    alignmentChanged(alignment,hiddenReps);
+    alignmentChanged(alignment, hiddenReps);
   }
-  public void alignmentChanged(AnnotatedCollectionI alignment, Map<SequenceI, SequenceCollectionI> hiddenReps) {
-    int maxWidth=alignment.getWidth();
-    List<SequenceI> seqs=alignment.getSequences(hiddenReps);
+
+  public void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+    int maxWidth = alignment.getWidth();
+    List<SequenceI> seqs = alignment.getSequences(hiddenReps);
     cons2 = new int[maxWidth][24];
     includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
     // get the current setting of the
@@ -86,7 +90,7 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
     int j = 0;
     char[] seq;
 
-    for (SequenceI sq: seqs)
+    for (SequenceI sq : seqs)
     {
       seq = sq.getSequence();