JAL-919, JAL-715 - prototype service editing dialog using jalview parameter model...

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

diff --git a/src/jalview/ws/rest/params/SeqIdVector.java b/src/jalview/ws/rest/params/SeqIdVector.java
index 9bdaed1..c77c8da 100644 (file)
--- a/src/jalview/ws/rest/params/SeqIdVector.java
+++ b/src/jalview/ws/rest/params/SeqIdVector.java
@@ -2,38 +2,52 @@ 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 java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 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
- *
+ * 
  */
-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)
       {
@@ -43,4 +57,65 @@ class SeqIdVector extends InputType {
     }
     return new StringBody(idvector.toString());
   }
-}
\ No newline at end of file
+
+  @Override
+  public List<String> getURLEncodedParameter()
+  {
+    ArrayList<String> prms = new ArrayList<String>();
+    super.addBaseParams(prms);
+    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)
+  {
+    if (tok.startsWith("sep"))
+    {
+      sep = val;
+      return true;
+    }
+    if (tok.startsWith("type"))
+    {
+      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(" " + 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;
+  }
+}