X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2FRestJob.java;h=67f11c269ea760dd5e18d8a9a0e8cd11b528b52b;hb=ca9ab48d85c35112da4d9bf6273a41e734d0872b;hp=72dbb64fd001e79634781a40fb1f5122d41a5ca5;hpb=381ab4041500f6b7f07c84b87f0fa1adf71013ae;p=jalview.git

diff --git a/src/jalview/ws/rest/RestJob.java b/src/jalview/ws/rest/RestJob.java
index 72dbb64..67f11c2 100644
--- a/src/jalview/ws/rest/RestJob.java
+++ b/src/jalview/ws/rest/RestJob.java
@@ -1,29 +1,26 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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;
@@ -34,6 +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
 {
 
@@ -49,7 +53,7 @@ public class RestJob extends AWsJob
 
   boolean gotresult;
 
-  Hashtable squniq;
+  Map<String, SequenceInfo> squniq;
 
   /**
    * dataset associated with this input data.
@@ -74,8 +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;
@@ -87,12 +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
     // 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())
@@ -105,17 +112,19 @@ public class RestJob extends AWsJob
         }
         else
         {
-          // TODO: move validation of input data to SeqGroupIndexVector
-          if ((prm.getValue() instanceof SeqGroupIndexVector)
-                  && (_input.getGroups() != null && _input.getGroups()
-                          .size() >= prm.getValue().min))
+          if (prm.getValue() instanceof SeqGroupIndexVector
+                  && _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
             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);
           }
         }
       }