X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMappingUtils.java;h=adfd39744b15680e469497c3c6002a9dde688904;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=f2213adcdcffa65363e887cf4b6cad441f17a4ec;hpb=619cc880371f3228e6a1fb33c6bfb6e7a7e2622c;p=jalview.git

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index f2213ad..adfd397 100644
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -1,13 +1,5 @@
 package jalview.util;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
 import jalview.analysis.AlignmentSorter;
 import jalview.api.AlignViewportI;
 import jalview.commands.CommandI;
@@ -25,6 +17,14 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
 /**
  * Helper methods for manipulations involving sequence mappings.
  * 
@@ -200,8 +200,8 @@ public final class MappingUtils
              */
             int mappedEditPos = action == Action.DELETE_GAP ? match[0]
                     - mappedCount : match[0];
-            Edit e = result.new Edit(action, new SequenceI[]
-            { targetSeq }, mappedEditPos, mappedCount, gapChar);
+            Edit e = result.new Edit(action, new SequenceI[] { targetSeq },
+                    mappedEditPos, mappedCount, gapChar);
             result.addEdit(e);
 
             /*
@@ -339,7 +339,7 @@ public final class MappingUtils
        */
       int startResiduePos = selected.findPosition(firstUngappedPos);
       int endResiduePos = selected.findPosition(lastUngappedPos);
-      
+
       for (AlignedCodonFrame acf : codonFrames)
       {
         SequenceI mappedSequence = targetIsNucleotide ? acf
@@ -424,7 +424,8 @@ public final class MappingUtils
     {
       for (AlignedCodonFrame acf : mappings)
       {
-        SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq) : acf.getAaForDnaSeq(seq);
+        SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq)
+                : acf.getAaForDnaSeq(seq);
         if (mappedSeq != null)
         {
           for (SequenceI seq2 : mapTo.getSequences())
@@ -645,8 +646,10 @@ public final class MappingUtils
     {
       return result;
     }
-    for (AlignedCodonFrame mapping : mappings) {
-      if (mapping.involvesSequence(sequence)) {
+    for (AlignedCodonFrame mapping : mappings)
+    {
+      if (mapping.involvesSequence(sequence))
+      {
         result.add(mapping);
       }
     }