X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2FRestJob.java;h=bb8fb72ae88abeb4206bbbb2f83dcae8829b19e1;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=d2a0a05fab238431b9f47da71b538b059e6afca9;hpb=ad20cd92225f2ee8c251d39b00b90555d382a616;p=jalview.git
diff --git a/src/jalview/ws/rest/RestJob.java b/src/jalview/ws/rest/RestJob.java
index d2a0a05..bb8fb72 100644
--- a/src/jalview/ws/rest/RestJob.java
+++ b/src/jalview/ws/rest/RestJob.java
@@ -1,29 +1,25 @@
/*
- * 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 2.9.0b1)
+ * Copyright (C) 2015 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
@@ -34,6 +30,13 @@ 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
{
@@ -87,12 +90,15 @@ 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);
// prepare input
// form alignment+groups+annotation,preprocess and then record references
// for formatters
ArrayList alinp = new ArrayList();
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 prm : rsd.inputParams.entrySet())
@@ -105,11 +111,13 @@ 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