mungo merge

[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..817ba9c 100644 (file)
--- a/src/jalview/io/packed/JalviewDataset.java
+++ b/src/jalview/io/packed/JalviewDataset.java
@@ -25,8 +25,10 @@ import jalview.datamodel.SequenceI;
 import jalview.io.NewickFile;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 
 public class JalviewDataset
 {
@@ -55,7 +57,7 @@ public class JalviewDataset
   /**
    * @return the featureColours
    */
-  public Hashtable getFeatureColours()
+  public Map<String, Object> getFeatureColours()
   {
     return featureColours;
   }
@@ -64,7 +66,7 @@ public class JalviewDataset
    * @param featureColours
    *          the featureColours to set
    */
-  public void setFeatureColours(Hashtable featureColours)
+  public void setFeatureColours(Map<String, Object> featureColours)
   {
     this.featureColours = featureColours;
   }
@@ -185,7 +187,7 @@ public class JalviewDataset
   /**
    * current set of feature colours
    */
-  Hashtable featureColours;
+  Map<String, Object> featureColours;
 
   /**
    * original identity of each sequence in results
@@ -199,7 +201,7 @@ public class JalviewDataset
     seqDetails = new Hashtable();
     al = new ArrayList<AlignmentSet>();
     parentDataset = null;
-    featureColours = new Hashtable();
+    featureColours = new HashMap<String, Object>();
   }
 
   /**
@@ -207,9 +209,10 @@ public class JalviewDataset
    * 
    * @param parentAlignment
    */
-  public JalviewDataset(AlignmentI aldataset, Hashtable fc,
+  public JalviewDataset(AlignmentI aldataset, Map<String, Object> fc,
           Hashtable seqDets)
   {
+    // TODO not used - remove?
     this(aldataset, fc, seqDets, null);
   }
 
@@ -228,7 +231,7 @@ public class JalviewDataset
    *          (may be null) alignment to associate new annotation and trees
    *          with.
    */
-  public JalviewDataset(AlignmentI aldataset, Hashtable fc,
+  public JalviewDataset(AlignmentI aldataset, Map<String, Object> fc,
           Hashtable seqDets, AlignmentI parentAlignment)
   {
     this();