X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=a331fd04d4f240283971d7206a284c79760253e5;hb=7d6575e94bed92bc06043d432576e3a39e8a8e75;hp=e6d3e83e31517fa891afd499aa729ea14c8f7ea0;hpb=792a03fc1994671ae23e7263cefd51c9b0da53cb;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index e6d3e83..a331fd0 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -20,20 +20,6 @@
  */
 package jalview.analysis;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.TreeMap;
-
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
@@ -52,6 +38,20 @@ import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.TreeMap;
+
 /**
  * grab bag of useful alignment manipulation operations Expect these to be
  * refactored elsewhere at some point.
@@ -149,8 +149,7 @@ public class AlignmentUtils
       s.setStart(s.getStart() - ustream_ds);
       s.setEnd(s_end + downstream.length);
     }
-    AlignmentI newAl = new jalview.datamodel.Alignment(
-            sq.toArray(new SequenceI[0]));
+    AlignmentI newAl = new Alignment(sq.toArray(new SequenceI[0]));
     for (SequenceI s : sq)
     {
       if (s.getAnnotation() != null)
@@ -195,7 +194,7 @@ public class AlignmentUtils
    * name. For use in mapping between different alignment views of the same
    * sequences.
    * 
-   * @see jalview.datamodel.AlignmentI#getSequencesByName()
+   * @see AlignmentI#getSequencesByName()
    */
   public static Map<String, List<SequenceI>> getSequencesByName(
           AlignmentI al)