/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
import java.net.MalformedURLException;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import compbio.metadata.*;
public class ParameterUtils
{
public static List writeParameterSet(List optSet,
String pseparator)
{
List pset = new ArrayList();
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
* web service type
* @param params
* @param options
* @return List of Options of type T
*
*/
/*
* @SuppressWarnings(value = { "true" }) public static List>
* processParameters(List params, RunnerConfig options, String
* pseparator)
*/
public static List processParameters(List params,
RunnerConfig options, String pseparator)
{
List chosenOptions = new ArrayList ();
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)
{
Option copy = new Option(option.getName(), option.getDescription());
setOptionFrom(copy, option);
return copy;
}
public static void setOptionFrom(Option copy, Option option)
{
copy.setName(option.getName());
copy.setDescription(option.getDescription());
copy.setBasicURL(option.getBasicURL());
copy.setFurtherDetails(option.getFurtherDetails());
copy.setRequired(option.isRequired());
List names = option.getOptionNames();
if (names != null)
{
if (names.size() == 1)
{
HashSet st = new HashSet();
st.add(names.get(0));
copy.setOptionNames(st);
}
else
{
copy.addOptionNames(names.toArray(new String[]
{}));
}
}
try
{
if (option.getDefaultValue() != null)
{
copy.setDefaultValue(option.getDefaultValue());
}
} catch (Exception ex)
{
ex.printStackTrace();
}
}
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)
{
e.printStackTrace();
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)
{
copy.setValidValue(copyValueConstrain(parameter.getValidValue()));
}
List pv = parameter.getPossibleValues();
if (pv != null)
{
copy.addPossibleValues(pv.toArray(new String[]
{}));
}
setOptionFrom(copy, parameter);
return copy;
}
}