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 d41cfc0..67f11c2 100644 (file)
--- a/src/jalview/ws/rest/RestJob.java
+++ b/src/jalview/ws/rest/RestJob.java
@@ -1,30 +1,26 @@
 /*
- * 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.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;
@@ -35,6 +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
 {
 
@@ -50,7 +53,7 @@ public class RestJob extends AWsJob
 
   boolean gotresult;
 
-  Hashtable squniq;
+  Map<String, SequenceInfo> squniq;
 
   /**
    * dataset associated with this input data.
@@ -75,8 +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;
@@ -88,13 +91,15 @@ 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
     ArrayList<InputType> alinp = new ArrayList<InputType>();
     int paramsWithData = 0;
-    // TODO: JAL-715 - generalise the following validation logic for all parameter types
+    // TODO: JAL-715 - generalise the following validation logic for all
+    // parameter types
     // we cheat for moment - since we know a-priori what data is available and
     // what inputs we have implemented so far
     for (Map.Entry<String, InputType> prm : rsd.inputParams.entrySet())
@@ -111,13 +116,15 @@ public class RestJob extends AWsJob
                   && _input.getGroups() != null
                   && _input.getGroups().size() >= -1 + prm.getValue().min)
           {
-            // the test above is not rigorous but fixes JAL-1298, since submission will fail if the partition set doesn't contain at least one partition
+            // the test above is not rigorous but fixes JAL-1298, since
+            // submission will fail if the partition set doesn't contain at
+            // least one partition
             alinp.add(prm.getValue());
           }
           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);
           }
         }
       }