JAL-1807 explicit imports (jalview.io.*)

[jalview.git] / src / jalview / io / packed / JalviewDataset.java

diff --git a/src/jalview/io/packed/JalviewDataset.java b/src/jalview/io/packed/JalviewDataset.java
index d613796..76c9b18 100644 (file)
--- a/src/jalview/io/packed/JalviewDataset.java
+++ b/src/jalview/io/packed/JalviewDataset.java
@@ -20,6 +20,8 @@
  */
 package jalview.io.packed;
 
+import jalview.analysis.NJTree;
+import jalview.analysis.SeqsetUtils;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.io.NewickFile;
@@ -103,12 +105,12 @@ public class JalviewDataset
   {
     public AlignmentI al;
 
-    public List<jalview.io.NewickFile> trees;
+    public List<NewickFile> trees;
 
     AlignmentSet(AlignmentI a)
     {
       al = a;
-      trees = new ArrayList<jalview.io.NewickFile>();
+      trees = new ArrayList<NewickFile>();
     }
 
     /**
@@ -141,15 +143,13 @@ public class JalviewDataset
       // jalview.analysis.SeqsetUtils.deuniquifyAndMerge(parentDataset,
       // seqDetails, al,true);
 
-      jalview.analysis.SeqsetUtils.deuniquify(seqDetails,
-              al.getSequencesArray(), true);
+      SeqsetUtils.deuniquify(seqDetails, al.getSequencesArray(), true);
       // 2. Update names of associated nodes in any trees
       for (NewickFile nf : trees)
       {
         // the following works because all trees are already had node/SequenceI
         // associations created.
-        jalview.analysis.NJTree njt = new jalview.analysis.NJTree(
-                al.getSequencesArray(), nf);
+        NJTree njt = new NJTree(al.getSequencesArray(), nf);
         // this just updates the displayed leaf name on the tree according to
         // the SequenceIs.
         njt.renameAssociatedNodes();