JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console...

[jalview.git] / src / jalview / ws / jws2 / ParameterUtils.java

diff --git a/src/jalview/ws/jws2/ParameterUtils.java b/src/jalview/ws/jws2/ParameterUtils.java
index 1f76462..0fb36ad 100644 (file)
--- a/src/jalview/ws/jws2/ParameterUtils.java
+++ b/src/jalview/ws/jws2/ParameterUtils.java
@@ -1,30 +1,36 @@
 /*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 jalview.util.MessageManager;
+
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
 
-import compbio.metadata.*;
+import compbio.metadata.Option;
+import compbio.metadata.Parameter;
+import compbio.metadata.RunnerConfig;
+import compbio.metadata.ValueConstrain;
+import compbio.metadata.WrongParameterException;
 
 public class ParameterUtils
 {
@@ -73,7 +79,7 @@ public class ParameterUtils
       Option o = options.getArgumentByOptionName(oname);
       if (o == null)
       {
-        System.out.println("WARN ignoring unsuppoted parameter: " + oname);
+        jalview.bin.Console.outPrintln("WARN ignoring unsuppoted parameter: " + oname);
         continue;
       }
       if (o instanceof Parameter)
@@ -87,12 +93,13 @@ 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: "
-                  + param);
+          jalview.bin.Console.outPrintln(
+                  "Problem setting value for the parameter: " + param);
           e.printStackTrace();
         }
       }
@@ -129,6 +136,7 @@ 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();
@@ -142,8 +150,7 @@ public class ParameterUtils
       }
       else
       {
-        copy.addOptionNames(names.toArray(new String[]
-        {}));
+        copy.addOptionNames(names.toArray(new String[] {}));
       }
     }
     try
@@ -179,8 +186,8 @@ public class ParameterUtils
     } catch (Exception e)
     {
       e.printStackTrace();
-      throw new Error(
-              "Implementation error: could not copy ValueConstrain!");
+      throw new Error(MessageManager.getString(
+              "error.implementation_error_couldnt_copy_value_constraint"));
     }
   }
 
@@ -195,8 +202,7 @@ public class ParameterUtils
     List<String> pv = parameter.getPossibleValues();
     if (pv != null)
     {
-      copy.addPossibleValues(pv.toArray(new String[]
-      {}));
+      copy.addPossibleValues(pv.toArray(new String[] {}));
     }
     setOptionFrom(copy, parameter);
     return copy;