JAL-1620 version bump and release notes

[jalview.git] / src / jalview / ws / rest / params / SeqVector.java

diff --git a/src/jalview/ws/rest/params/SeqVector.java b/src/jalview/ws/rest/params/SeqVector.java
index 3a5b414..d331de4 100644 (file)
--- a/src/jalview/ws/rest/params/SeqVector.java
+++ b/src/jalview/ws/rest/params/SeqVector.java
@@ -1,39 +1,66 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.rest.params;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.simple.Option;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.NoValidInputDataException;
 import jalview.ws.rest.RestJob;
-import jalview.ws.rest.RestServiceDescription;
-import jalview.ws.rest.InputType.molType;
 
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 import org.apache.http.entity.mime.content.ContentBody;
 import org.apache.http.entity.mime.content.StringBody;
 
 /**
- * input a list of sequences separated by some separator 
+ * input a list of sequences separated by some separator
+ * 
  * @author JimP
- *
+ * 
  */
-public class SeqVector extends InputType {
+public class SeqVector extends InputType
+{
   String sep;
+
   molType type;
+
   public SeqVector()
   {
-    super(new Class[] { AlignmentI.class} );
+    super(new Class[]
+    { AlignmentI.class });
   }
 
   @Override
-  public ContentBody formatForInput(RestJob rj) throws UnsupportedEncodingException, NoValidInputDataException
+  public ContentBody formatForInput(RestJob rj)
+          throws UnsupportedEncodingException, NoValidInputDataException
   {
     StringBuffer idvector = new StringBuffer();
-    boolean list=false;
-    for (SequenceI seq:rj.getSequencesForInput(token, type))
+    boolean list = false;
+    for (SequenceI seq : rj.getSequencesForInput(token, type))
     {
       if (list)
       {
@@ -43,13 +70,17 @@ public class SeqVector extends InputType {
     }
     return new StringBody(idvector.toString());
   }
+
   @Override
   public List<String> getURLEncodedParameter()
   {
     ArrayList<String> prms = new ArrayList<String>();
     super.addBaseParams(prms);
-    prms.add("sep='"+ sep+"'");
-    prms.add("type='"+type+"'");
+    prms.add("sep='" + sep + "'");
+    if (type != null)
+    {
+      prms.add("type='" + type + "'");
+    }
     return prms;
   }
 
@@ -66,20 +97,22 @@ public class SeqVector extends InputType {
 
     if (tok.startsWith("sep"))
     {
-      sep=val;
+      sep = val;
       return true;
     }
     if (tok.startsWith("type"))
     {
-      try {
-        type=molType.valueOf(val);
+      try
+      {
+        type = molType.valueOf(val);
         return true;
       } catch (Exception x)
       {
-        warnings.append("Invalid molecule type '"+val+"'. Must be one of (");
-        for (molType v:molType.values())
+        warnings.append("Invalid molecule type '" + val
+                + "'. Must be one of (");
+        for (molType v : molType.values())
         {
-          warnings.append(" "+v);
+          warnings.append(" " + v);
         }
         warnings.append(")\n");
       }
@@ -87,4 +120,18 @@ public class SeqVector extends InputType {
     return false;
   }
 
-}
\ No newline at end of file
+  @Override
+  public List<OptionI> getOptions()
+  {
+    List<OptionI> lst = getBaseOptions();
+    lst.add(new Option("sep",
+            "Separator character between elements of vector", true, ",",
+            sep, Arrays.asList(new String[]
+            { " ", ",", ";", "\t", "|" }), null));
+    lst.add(createMolTypeOption("type", "Sequence type", false, type,
+            molType.MIX));
+
+    return lst;
+  }
+
+}