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JAL-2674 Changed CigarArray constructor to use HiddenColumns iterator
[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
f66027d
..
c7fad05
100644
(file)
--- a/
src/jalview/ws/jws2/ParameterUtils.java
+++ b/
src/jalview/ws/jws2/ParameterUtils.java
@@
-1,42
+1,50
@@
/*
/*
- * 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
*
* 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.
*
* 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;
*/
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 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
{
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>();
{
List<String> pset = new ArrayList<String>();
- for (Option o:optSet)
+ for (Option o : optSet)
{
pset.add(o.toCommand(pseparator));
}
return pset;
}
{
pset.add(o.toCommand(pseparator));
}
return pset;
}
+
/**
* Converts options supplied via parameters file into {@code Option} objects
* (Refactored from compbio.ws.client.Jws2Client)
/**
* Converts options supplied via parameters file into {@code Option} objects
* (Refactored from compbio.ws.client.Jws2Client)
@@
-48,11
+56,11
@@
public class ParameterUtils
* @return List of Options of type T
*
*/
* @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)
{
public static List<Option> processParameters(List<String> params,
RunnerConfig options, String pseparator)
{
@@
-85,11
+93,13
@@
public class ParameterUtils
{
try
{
{
try
{
- o.setDefaultValue(isParameter(param, pseparator) ? getParamValue(param, pseparator) : param);
+ o.setDefaultValue(isParameter(param, pseparator)
+ ? getParamValue(param, pseparator)
+ : param);
} catch (WrongParameterException e)
{
} catch (WrongParameterException e)
{
- System.out.println("Problem setting value for the parameter: "
- + param);
+ System.out.println(
+ "Problem setting value for the parameter: " + param);
e.printStackTrace();
}
}
e.printStackTrace();
}
}
@@
-97,7
+107,6
@@
public class ParameterUtils
}
return chosenOptions;
}
}
return chosenOptions;
}
-
static String getParamName(String fullName, String pseparator)
{
static String getParamName(String fullName, String pseparator)
{
@@
-127,6
+136,7
@@
public class ParameterUtils
{
copy.setName(option.getName());
copy.setDescription(option.getDescription());
{
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();
copy.setFurtherDetails(option.getFurtherDetails());
copy.setRequired(option.isRequired());
List<String> names = option.getOptionNames();
@@
-140,8
+150,7
@@
public class ParameterUtils
}
else
{
}
else
{
- copy.addOptionNames(names.toArray(new String[]
- {}));
+ copy.addOptionNames(names.toArray(new String[] {}));
}
}
try
}
}
try
@@
-177,8
+186,8
@@
public class ParameterUtils
} catch (Exception e)
{
e.printStackTrace();
} 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"));
}
}
}
}
@@
-193,8
+202,7
@@
public class ParameterUtils
List<String> pv = parameter.getPossibleValues();
if (pv != null)
{
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;
}
setOptionFrom(copy, parameter);
return copy;