X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;fp=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=1a552d7b1c2498ef54939ae7e4c191b0d2d786a5;hb=7d6575e94bed92bc06043d432576e3a39e8a8e75;hp=2ede9ed477d6b6c0e8cf303a823874e93b8bc085;hpb=792a03fc1994671ae23e7263cefd51c9b0da53cb;p=jalview.git

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 2ede9ed..1a552d7 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -20,14 +20,15 @@
  */
 package jalview.analysis;
 
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
-
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
 
 public class SeqsetUtils
 {
@@ -51,7 +52,7 @@ public class SeqsetUtils
       sqinfo.put("Description", seq.getDescription());
     }
     Vector sfeat = new Vector();
-    jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures();
+    SequenceFeature[] sfarray = seq.getSequenceFeatures();
     if (sfarray != null && sfarray.length > 0)
     {
       for (int i = 0; i < sfarray.length; i++)
@@ -216,8 +217,7 @@ public class SeqsetUtils
   public static boolean deuniquify(Hashtable map, SequenceI[] sequences,
           boolean quiet)
   {
-    jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
-            sequences);
+    SequenceIdMatcher matcher = new SequenceIdMatcher(sequences);
     SequenceI msq = null;
     Enumeration keys = map.keys();
     Vector unmatched = new Vector();
@@ -275,8 +275,7 @@ public class SeqsetUtils
     int msflen = 0;
     for (int i = 0, j = sequences.length; i < j; i++)
     {
-      String tempseq = jalview.analysis.AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars,
+      String tempseq = AlignSeq.extractGaps(Comparison.GapChars,
               sequences[i].getSequenceAsString());
 
       if (tempseq.length() == 0)