X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FParameterUtils.java;h=e2bfbbd6682e7b923edd7df44dd980e92b376d95;hb=8d0d8f010041eb2089bfe0bf7e5ad481ceae56d5;hp=f66027d5fbdd22cd13a1abe10074daaf51771460;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/ws/jws2/ParameterUtils.java b/src/jalview/ws/jws2/ParameterUtils.java
index f66027d..e2bfbbd 100644
--- a/src/jalview/ws/jws2/ParameterUtils.java
+++ b/src/jalview/ws/jws2/ParameterUtils.java
@@ -1,25 +1,26 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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.
- * 
+ * 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/>.
+ * 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.jws2;
 
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.Reader;
+import java.net.MalformedURLException;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
@@ -28,15 +29,17 @@ import compbio.metadata.*;
 
 public class ParameterUtils
 {
-  public static List<String> writeParameterSet(List<Option> optSet, String pseparator)
+  public static List<String> writeParameterSet(List<Option> optSet,
+          String pseparator)
   {
     List<String> pset = new ArrayList<String>();
-    for (Option o:optSet)
+    for (Option o : optSet)
     {
       pset.add(o.toCommand(pseparator));
     }
     return pset;
   }
+
   /**
    * Converts options supplied via parameters file into {@code Option} objects
    * (Refactored from compbio.ws.client.Jws2Client)
@@ -48,11 +51,11 @@ public class ParameterUtils
    * @return List of Options of type T
    * 
    */
-/*  @SuppressWarnings(value =
-  { "true" })
-  public static <T> List<Option<T>> processParameters(List<String> params,
-          RunnerConfig<T> options, String pseparator)
-  */
+  /*
+   * @SuppressWarnings(value = { "true" }) public static <T> List<Option<T>>
+   * processParameters(List<String> params, RunnerConfig<T> options, String
+   * pseparator)
+   */
   public static List<Option> processParameters(List<String> params,
           RunnerConfig options, String pseparator)
   {
@@ -85,7 +88,8 @@ public class ParameterUtils
       {
         try
         {
-          o.setDefaultValue(isParameter(param, pseparator) ? getParamValue(param, pseparator) : param);
+          o.setDefaultValue(isParameter(param, pseparator) ? getParamValue(
+                  param, pseparator) : param);
         } catch (WrongParameterException e)
         {
           System.out.println("Problem setting value for the parameter: "
@@ -97,7 +101,6 @@ public class ParameterUtils
     }
     return chosenOptions;
   }
-  
 
   static String getParamName(String fullName, String pseparator)
   {
@@ -127,6 +130,7 @@ public class ParameterUtils
   {
     copy.setName(option.getName());
     copy.setDescription(option.getDescription());
+    copy.setBasicURL(option.getBasicURL());
     copy.setFurtherDetails(option.getFurtherDetails());
     copy.setRequired(option.isRequired());
     List<String> names = option.getOptionNames();