JAL-2089 patch broken merge to master for Release 2.10.0b1

[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 40c80a6..c1ca1b7 100644 (file)
--- a/src/jalview/io/packed/JalviewDataset.java
+++ b/src/jalview/io/packed/JalviewDataset.java
@@ -1,30 +1,35 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io.packed;
 
+import jalview.api.FeatureColourI;
 import jalview.datamodel.AlignmentI;
 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
 {
@@ -53,7 +58,7 @@ public class JalviewDataset
   /**
    * @return the featureColours
    */
-  public Hashtable getFeatureColours()
+  public Map<String, FeatureColourI> getFeatureColours()
   {
     return featureColours;
   }
@@ -62,7 +67,7 @@ public class JalviewDataset
    * @param featureColours
    *          the featureColours to set
    */
-  public void setFeatureColours(Hashtable featureColours)
+  public void setFeatureColours(Map<String, FeatureColourI> featureColours)
   {
     this.featureColours = featureColours;
   }
@@ -183,7 +188,7 @@ public class JalviewDataset
   /**
    * current set of feature colours
    */
-  Hashtable featureColours;
+  Map<String, FeatureColourI> featureColours;
 
   /**
    * original identity of each sequence in results
@@ -197,7 +202,7 @@ public class JalviewDataset
     seqDetails = new Hashtable();
     al = new ArrayList<AlignmentSet>();
     parentDataset = null;
-    featureColours = new Hashtable();
+    featureColours = new HashMap<String, FeatureColourI>();
   }
 
   /**
@@ -205,9 +210,10 @@ public class JalviewDataset
    * 
    * @param parentAlignment
    */
-  public JalviewDataset(AlignmentI aldataset, Hashtable fc,
-          Hashtable seqDets)
+  public JalviewDataset(AlignmentI aldataset,
+          Map<String, FeatureColourI> fc, Hashtable seqDets)
   {
+    // TODO not used - remove?
     this(aldataset, fc, seqDets, null);
   }
 
@@ -226,8 +232,9 @@ public class JalviewDataset
    *          (may be null) alignment to associate new annotation and trees
    *          with.
    */
-  public JalviewDataset(AlignmentI aldataset, Hashtable fc,
-          Hashtable seqDets, AlignmentI parentAlignment)
+  public JalviewDataset(AlignmentI aldataset,
+          Map<String, FeatureColourI> fc, Hashtable seqDets,
+          AlignmentI parentAlignment)
   {
     this();
     parentDataset = aldataset;