X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FParameterUtils.java;h=1f7646279657e1fdcf3cdb93405efc3b6a2fd77d;hb=a9514dd266ef856c485fd8f9108a3797b87add3f;hp=00878fbb43d70cc33089a155f1176dd231f3e70a;hpb=650159ffaacc133f9d58c604b8010393cdd1f01a;p=jalview.git

diff --git a/src/jalview/ws/jws2/ParameterUtils.java b/src/jalview/ws/jws2/ParameterUtils.java
index 00878fb..1f76462 100644
--- a/src/jalview/ws/jws2/ParameterUtils.java
+++ b/src/jalview/ws/jws2/ParameterUtils.java
@@ -1,11 +1,122 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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.
+ * 
+ * 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/>.
+ */
 package jalview.ws.jws2;
 
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.Reader;
+import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
 
 import compbio.metadata.*;
+
 public class ParameterUtils
 {
+  public static List<String> writeParameterSet(List<Option> optSet,
+          String pseparator)
+  {
+    List<String> pset = new ArrayList<String>();
+    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)
+   * 
+   * @param <T>
+   *          web service type
+   * @param params
+   * @param options
+   * @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)
+   */
+  public static List<Option> processParameters(List<String> params,
+          RunnerConfig options, String pseparator)
+  {
+    List<Option> chosenOptions = new ArrayList<Option>();
+    for (String param : params)
+    {
+      String oname = null;
+      if (isParameter(param, pseparator))
+      {
+        oname = getParamName(param, pseparator);
+      }
+      else
+      {
+        oname = param;
+      }
+      Option o = options.getArgumentByOptionName(oname);
+      if (o == null)
+      {
+        System.out.println("WARN ignoring unsuppoted parameter: " + oname);
+        continue;
+      }
+      if (o instanceof Parameter)
+      {
+        o = copyParameter((Parameter) o);
+      }
+      else
+      {
+        o = copyOption(o);
+      }
+      {
+        try
+        {
+          o.setDefaultValue(isParameter(param, pseparator) ? getParamValue(
+                  param, pseparator) : param);
+        } catch (WrongParameterException e)
+        {
+          System.out.println("Problem setting value for the parameter: "
+                  + param);
+          e.printStackTrace();
+        }
+      }
+      chosenOptions.add(o);
+    }
+    return chosenOptions;
+  }
+
+  static String getParamName(String fullName, String pseparator)
+  {
+    assert isParameter(fullName, pseparator);
+    return fullName.substring(0, fullName.indexOf(pseparator));
+  }
+
+  static String getParamValue(String fullName, String pseparator)
+  {
+    assert isParameter(fullName, pseparator);
+    return fullName.substring(fullName.indexOf(pseparator) + 1);
+  }
+
+  static boolean isParameter(String param, String pseparator)
+  {
+    return param.contains(pseparator);
+  }
 
   public static Option copyOption(Option option)
   {
@@ -13,6 +124,7 @@ public class ParameterUtils
     setOptionFrom(copy, option);
     return copy;
   }
+
   public static void setOptionFrom(Option copy, Option option)
   {
     copy.setName(option.getName());
@@ -20,18 +132,23 @@ public class ParameterUtils
     copy.setFurtherDetails(option.getFurtherDetails());
     copy.setRequired(option.isRequired());
     List<String> names = option.getOptionNames();
-    if (names!=null){
-      if (names.size()==1)
+    if (names != null)
+    {
+      if (names.size() == 1)
       {
         HashSet<String> st = new HashSet();
         st.add(names.get(0));
         copy.setOptionNames(st);
-      } else {
-      copy.addOptionNames(names.toArray(new String[]{}));
+      }
+      else
+      {
+        copy.addOptionNames(names.toArray(new String[]
+        {}));
       }
     }
-    try {
-      if (option.getDefaultValue()!=null)
+    try
+    {
+      if (option.getDefaultValue() != null)
       {
         copy.setDefaultValue(option.getDefaultValue());
       }
@@ -43,34 +160,43 @@ public class ParameterUtils
 
   public static ValueConstrain copyValueConstrain(ValueConstrain vc)
   {
-    try {ValueConstrain copy = new ValueConstrain();
-    if (vc.getMax()!=null) {
-      copy.setMax(vc.getMax().toString());
-    }
-    if (vc.getMin()!=null) {
-      copy.setMin(vc.getMin().toString());
-    }
-    if (vc.getType()!=null) {
-      copy.setType(vc.getType());
-    }
-    return copy;
-    }
-    catch (Exception e)
+    try
+    {
+      ValueConstrain copy = new ValueConstrain();
+      if (vc.getMax() != null)
+      {
+        copy.setMax(vc.getMax().toString());
+      }
+      if (vc.getMin() != null)
+      {
+        copy.setMin(vc.getMin().toString());
+      }
+      if (vc.getType() != null)
+      {
+        copy.setType(vc.getType());
+      }
+      return copy;
+    } catch (Exception e)
     {
       e.printStackTrace();
-      throw new Error("Implementation error: could not copy ValueConstrain!");
+      throw new Error(
+              "Implementation error: could not copy ValueConstrain!");
     }
   }
+
   public static Parameter copyParameter(Parameter parameter)
   {
-    Parameter copy = new Parameter(parameter.getName(), parameter.getDescription());
-    if (parameter.getValidValue()!=null) {
+    Parameter copy = new Parameter(parameter.getName(),
+            parameter.getDescription());
+    if (parameter.getValidValue() != null)
+    {
       copy.setValidValue(copyValueConstrain(parameter.getValidValue()));
     }
     List<String> pv = parameter.getPossibleValues();
-    if (pv!=null)
+    if (pv != null)
     {
-      copy.addPossibleValues(pv.toArray(new String[]{}));
+      copy.addPossibleValues(pv.toArray(new String[]
+      {}));
     }
     setOptionFrom(copy, parameter);
     return copy;