+/*
+ * 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.
+ *
+ * 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/>.
+ * 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;
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)
* @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)
{
{
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: "
}
return chosenOptions;
}
-
static String getParamName(String fullName, String pseparator)
{
{
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();