+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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)
{
setOptionFrom(copy, option);
return copy;
}
+
public static void setOptionFrom(Option copy, Option option)
{
copy.setName(option.getName());
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());
}
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;
git://source.jalview.org / jalview.git / blobdiff