X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2FRestJob.java;h=d41cfc00e20052d5a54863707c294344ed81c729;hb=84684213f7f7c7b31d3c33dc49ca3b377a295438;hp=695c4cb1bc94947054e5e4f715f955b6a42bcdbc;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/ws/rest/RestJob.java b/src/jalview/ws/rest/RestJob.java
index 695c4cb..d41cfc0 100644
--- 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)
- * 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 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,31 +14,23 @@
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.rest;
 
-import java.io.IOException;
-import java.sql.ResultSet;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Hashtable;
-import java.util.List;
 import java.util.Map;
-import java.util.Map.Entry;
 import java.util.Set;
 import java.util.Vector;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
-import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.io.packed.DataProvider;
 import jalview.io.packed.JalviewDataset;
-import jalview.io.packed.ParsePackedSet;
-import jalview.io.packed.SimpleDataProvider;
-import jalview.io.packed.DataProvider.JvDataType;
 import jalview.ws.AWsJob;
 import jalview.ws.rest.params.Alignment;
 import jalview.ws.rest.params.SeqGroupIndexVector;
@@ -96,12 +88,13 @@ 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);
     // 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())
@@ -114,11 +107,11 @@ 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