X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=201f88b251154217f055ef5c23181c1ad4457591;hb=4b7d3640209c4434d569c746672cf9eed4250ace;hp=0906872507a184e146456f5891062aa2e0c66076;hpb=b3fb6325a8bc315c5c938faf10ffd2e73d965f16;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 0906872..201f88b 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -184,10 +184,10 @@ public class AlignmentUtils
       // TODO use Character.toLowerCase to avoid creating String objects?
       char[] upstream = new String(ds
               .getSequence(s.getStart() - 1 - ustream_ds, s.getStart() - 1))
-              .toLowerCase(Locale.ROOT).toCharArray();
+                      .toLowerCase(Locale.ROOT).toCharArray();
       char[] downstream = new String(
               ds.getSequence(s_end - 1, s_end + dstream_ds))
-              .toLowerCase(Locale.ROOT).toCharArray();
+                      .toLowerCase(Locale.ROOT).toCharArray();
       char[] coreseq = s.getSequence();
       char[] nseq = new char[offset + upstream.length + downstream.length
               + coreseq.length];
@@ -1471,19 +1471,20 @@ public class AlignmentUtils
          */
         final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
                 .findAnnotations(seq, dsann.getCalcId(), dsann.label);
-        boolean found=false;
+        boolean found = false;
         if (matchedAlignmentAnnotations != null)
         {
-          for (AlignmentAnnotation matched:matchedAlignmentAnnotations)
+          for (AlignmentAnnotation matched : matchedAlignmentAnnotations)
           {
             if (dsann.description.equals(matched.description))
             {
-              found=true;
+              found = true;
               break;
             }
           }
         }
-        if (!found) {
+        if (!found)
+        {
           result.add(dsann);
           if (labelForCalcId != null)
           {