JAL-3899 Update usages of uniquify and deuniquify.

[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 c1ca1b7..d4047d1 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.SeqsetUtils.SequenceInfo;
+import jalview.analysis.TreeModel;
 import jalview.api.FeatureColourI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
@@ -75,7 +77,7 @@ public class JalviewDataset
   /**
    * @return the seqDetails
    */
-  public Hashtable getSeqDetails()
+  public Map<String, SequenceInfo> getSeqDetails()
   {
     return seqDetails;
   }
@@ -151,8 +153,7 @@ public class JalviewDataset
       {
         // the following works because all trees are already had node/SequenceI
         // associations created.
-        jalview.analysis.NJTree njt = new jalview.analysis.NJTree(
-                al.getSequencesArray(), nf);
+        TreeModel njt = new TreeModel(al.getSequencesArray(), null, nf);
         // this just updates the displayed leaf name on the tree according to
         // the SequenceIs.
         njt.renameAssociatedNodes();
@@ -193,7 +194,7 @@ public class JalviewDataset
   /**
    * original identity of each sequence in results
    */
-  Hashtable seqDetails;
+  Map<String, SequenceInfo> seqDetails;
 
   public boolean relaxedIdMatching = false;
 
@@ -211,7 +212,7 @@ public class JalviewDataset
    * @param parentAlignment
    */
   public JalviewDataset(AlignmentI aldataset,
-          Map<String, FeatureColourI> fc, Hashtable seqDets)
+          Map<String, FeatureColourI> fc, Map<String, SequenceInfo> seqDets)
   {
     // TODO not used - remove?
     this(aldataset, fc, seqDets, null);
@@ -233,7 +234,7 @@ public class JalviewDataset
    *          with.
    */
   public JalviewDataset(AlignmentI aldataset,
-          Map<String, FeatureColourI> fc, Hashtable seqDets,
+          Map<String, FeatureColourI> fc, Map<String, SequenceInfo> seqDets,
           AlignmentI parentAlignment)
   {
     this();