X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMappingUtils.java;fp=src%2Fjalview%2Futil%2FMappingUtils.java;h=1fe452d410d74c305a82c4da04aea41d0b84df71;hb=853624fb32058cccc544ae7d13af6ad4b0800b6c;hp=da83338d06d8f33bb6ceaccdd7c7ad89f072bff3;hpb=02d6aa2077a261d41db77a0158f2b4b779a36398;p=jalview.git

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index da83338..1fe452d 100644
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -374,7 +374,8 @@ public final class MappingUtils
               /*
                * Found a sequence mapping. Locate the start/end mapped residues.
                */
-              List<AlignedCodonFrame> mapping = Arrays.asList(new AlignedCodonFrame[] { acf });
+              List<AlignedCodonFrame> mapping = Arrays
+                      .asList(new AlignedCodonFrame[] { acf });
               SearchResults sr = buildSearchResults(selected,
                       startResiduePos, mapping);
               for (Match m : sr.getResults())
@@ -555,9 +556,9 @@ public final class MappingUtils
    * @param fromGapChar
    */
   protected static void mapHiddenColumns(int[] hidden,
-          List<AlignedCodonFrame> mappings,
-          ColumnSelection mappedColumns, List<SequenceI> fromSequences,
-          List<SequenceI> toSequences, char fromGapChar)
+          List<AlignedCodonFrame> mappings, ColumnSelection mappedColumns,
+          List<SequenceI> fromSequences, List<SequenceI> toSequences,
+          char fromGapChar)
   {
     for (int col = hidden[0]; col <= hidden[1]; col++)
     {
@@ -589,9 +590,9 @@ public final class MappingUtils
    * @param fromGapChar
    */
   protected static void mapColumn(int col,
-          List<AlignedCodonFrame> mappings,
-          ColumnSelection mappedColumns, List<SequenceI> fromSequences,
-          List<SequenceI> toSequences, char fromGapChar)
+          List<AlignedCodonFrame> mappings, ColumnSelection mappedColumns,
+          List<SequenceI> fromSequences, List<SequenceI> toSequences,
+          char fromGapChar)
   {
     int[] mappedTo = findMappedColumns(col, mappings, fromSequences,
             toSequences, fromGapChar);
@@ -646,8 +647,7 @@ public final class MappingUtils
        * Get the residue position and find the mapped position.
        */
       int residuePos = fromSeq.findPosition(col);
-      SearchResults sr = buildSearchResults(fromSeq, residuePos,
-              mappings);
+      SearchResults sr = buildSearchResults(fromSeq, residuePos, mappings);
       for (Match m : sr.getResults())
       {
         int mappedStartResidue = m.getStart();
@@ -893,7 +893,7 @@ public final class MappingUtils
     {
       return ranges;
     }
-  
+
     int[] copy = Arrays.copyOf(ranges, ranges.length);
     int sxpos = -1;
     int cdspos = 0;
@@ -921,7 +921,7 @@ public final class MappingUtils
         break;
       }
     }
-  
+
     if (sxpos > 0)
     {
       /*