X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FSeqIdVector.java;h=c77c8da9d90cfb12079c2ea2e453bf1dc1c935c4;hb=a789f790fbb3ab13f1967b42781b837b58bf9bbc;hp=5f7c5519ee72aecdc93a2a3cdd51aac1c34e5500;hpb=231cba7c0cb9097957cd61ef96aab8e32e2d0337;p=jalview.git

diff --git a/src/jalview/ws/rest/params/SeqIdVector.java b/src/jalview/ws/rest/params/SeqIdVector.java
index 5f7c551..c77c8da 100644
--- a/src/jalview/ws/rest/params/SeqIdVector.java
+++ b/src/jalview/ws/rest/params/SeqIdVector.java
@@ -2,6 +2,8 @@ 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;
@@ -10,6 +12,7 @@ import jalview.ws.rest.InputType.molType;
 
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -18,27 +21,33 @@ import org.apache.http.entity.mime.content.ContentBody;
 import org.apache.http.entity.mime.content.StringBody;
 
 /**
- * input a list of sequence IDs separated by some separator 
+ * input a list of sequence IDs separated by some separator
+ * 
  * @author JimP
- *
+ * 
  */
-public class SeqIdVector extends InputType {
+public class SeqIdVector extends InputType
+{
   public SeqIdVector()
   {
-    super(new Class[] { AlignmentI.class} );
+    super(new Class[]
+    { AlignmentI.class });
   }
 
   /**
    * separator for list of sequence IDs - default is ','
    */
-  String sep=",";
+  String sep = ",";
+
   molType type;
+
   @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)
       {
@@ -47,44 +56,66 @@ public class SeqIdVector extends InputType {
       idvector.append(seq.getName());
     }
     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;
   }
+
   @Override
   public String getURLtokenPrefix()
   {
     return "SEQIDS";
   }
+
   @Override
-  public boolean configureProperty(String tok, String val, StringBuffer warnings)
+  public boolean configureProperty(String tok, String val,
+          StringBuffer warnings)
   {
     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");
       }
     }
     return false;
   }
+
+  @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,
+            null));
+    return lst;
+  }
 }