JAL-3899 Update usages of uniquify and deuniquify.

[jalview.git] / src / jalview / ws / rest / RestJob.java

diff --git a/src/jalview/ws/rest/RestJob.java b/src/jalview/ws/rest/RestJob.java
index f080127..67f11c2 100644 (file)
--- a/src/jalview/ws/rest/RestJob.java
+++ b/src/jalview/ws/rest/RestJob.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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.
  * 
@@ -20,13 +20,7 @@
  */
 package jalview.ws.rest;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Hashtable;
-import java.util.Map;
-import java.util.Set;
-import java.util.Vector;
-
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
@@ -37,6 +31,13 @@ import jalview.ws.AWsJob;
 import jalview.ws.rest.params.Alignment;
 import jalview.ws.rest.params.SeqGroupIndexVector;
 
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
+
 public class RestJob extends AWsJob
 {
 
@@ -52,7 +53,7 @@ public class RestJob extends AWsJob
 
   boolean gotresult;
 
-  Hashtable squniq;
+  Map<String, SequenceInfo> squniq;
 
   /**
    * dataset associated with this input data.
@@ -77,8 +78,8 @@ public class RestJob extends AWsJob
    * @param viscontigs
    *          visible contigs of an alignment view from which _input was derived
    */
-  public RestJob(int jobNum, RestJobThread restJobThread,
-          AlignmentI _input, int[] viscontigs)
+  public RestJob(int jobNum, RestJobThread restJobThread, AlignmentI _input,
+          int[] viscontigs)
   {
     rsd = restJobThread.restClient.service;
     jobnum = jobNum;
@@ -90,8 +91,8 @@ public class RestJob extends AWsJob
     // get sequences for the alignmentI
     // get groups trimmed to alignment columns
     // get any annotation trimmed to start/end columns, too.
-    squniq = jalview.analysis.SeqsetUtils.uniquify(
-            _input.getSequencesArray(), true);
+    squniq = jalview.analysis.SeqsetUtils
+            .uniquify(_input.getSequencesArray(), true);
     // prepare input
     // form alignment+groups+annotation,preprocess and then record references
     // for formatters
@@ -122,8 +123,8 @@ public class RestJob extends AWsJob
           }
           else
           {
-            statMessage = ("Not enough groups defined on the alignment - need at least " + prm
-                    .getValue().min);
+            statMessage = ("Not enough groups defined on the alignment - need at least "
+                    + prm.getValue().min);
           }
         }
       }