JAL-860 fixed grammar for one structure vs many structures associated with selection

[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 9a98f3e..040e000 100644 (file)
--- a/src/jalview/ws/rest/params/SeqVector.java
+++ b/src/jalview/ws/rest/params/SeqVector.java
@@ -2,22 +2,29 @@ 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;
+import org.jmol.util.ArrayUtil;
 
 /**
  * input a list of sequences separated by some separator 
  * @author JimP
  *
  */
-class SeqVector extends InputType {
+public class SeqVector extends InputType {
   String sep;
   molType type;
   public SeqVector()
@@ -40,4 +47,65 @@ 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+"'");
+    if (type!=null)
+    {
+      prms.add("type='"+type+"'");
+    }
+    return prms;
+  }
+
+  @Override
+  public String getURLtokenPrefix()
+  {
+    return "SEQS";
+  }
+
+  @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,
+            molType.MIX));
+    
+    return lst;
+  }
+
 }
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