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/* Copyright (c) 2009 Peter Troshin
*
* JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
*
* This library is free software; you can redistribute it and/or modify it under the terms of the
* Apache License version 2 as published by the Apache Software Foundation
*
* This library 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 Apache
* License for more details.
*
* A copy of the license is in apache_license.txt. It is also available here:
* @see: http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Any republication or derived work distributed in source code form
* must include this copyright and license notice.
*/
package compbio.metadata;
import java.util.ArrayList;
import java.util.List;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlElementWrapper;
import javax.xml.bind.annotation.XmlTransient;
import compbio.util.SysPrefs;
/**
* Collection of Options and Parameters with their values
*
* @see Option
* @see Parameter
*
* @author pvtroshin
*
* @version 1.0 December 2009
* @param <T>
* executable type
*/
@XmlAccessorType(XmlAccessType.FIELD)
public class Preset<T> {
@XmlTransient
private static final String SPACE = " ";
@XmlElement(required = true, nillable = false)
// @XmlID - ? require no spaces (!)
String name;
String description;
@XmlElement(required = true, nillable = false)
@XmlElementWrapper(name = "optlist")
List<String> option;
public void setOptions(List<String> option) {
this.option = option;
}
public void setName(String name) {
this.name = name;
}
public void setDescription(String description) {
this.description = description;
}
/**
* @return a List of Options as a String
*/
public List<String> getOptions() {
return new ArrayList<String>(option);
}
/**
*
* @return - name of the Preset
*/
public String getName() {
return name;
}
/**
*
* @return - a long description of the Preset
*/
public String getDescription() {
return description;
}
/**
* Converts list of options as String to type Option
*
* @param rconfig
* @return List of Options
* @throws WrongParameterException
* if the value of the parameter is invalid @see
* {@link Parameter}
*/
public List<Option<T>> getArguments(RunnerConfig<T> rconfig)
throws WrongParameterException {
List<Option<T>> options = new ArrayList<Option<T>>();
for (String optionName : option) {
optionName = optionName.trim();
String oname = getName(optionName);
Option<T> option = rconfig.getArgumentByOptionName(oname);
if (option != null) {
// Set default value to the preset value
if (containValue(optionName)) {
// extract and set value to the parameter
option.setDefaultValue(getValue(optionName));
} else {
// set value to the option as default, as this could be a
// multi-option value
option.setDefaultValue(oname);
}
options.add(option);
}
}
return options;
}
boolean containValue(String option) {
if (option.trim().contains(SPACE)) {
return true;
}
return false;
}
String getName(String option) {
option = option.trim();
if (containValue(option)) {
return option.substring(0, option.indexOf(SPACE)).trim();
}
return option;
}
String getValue(String option) {
assert containValue(option);
option = option.trim();
return option.substring(option.indexOf(SPACE) + 1).trim();
}
@Override
public String toString() {
String value = "Preset name: '" + name + "'" + SysPrefs.newlinechar;
value += "Description: " + description + SysPrefs.newlinechar;
value += "Options: " + SysPrefs.newlinechar;
for (String oname : this.option) {
value += oname + SysPrefs.newlinechar;
}
value += SysPrefs.newlinechar;
return value;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result
+ ((description == null) ? 0 : description.hashCode());
result = prime * result + ((name == null) ? 0 : name.hashCode());
result = prime * result + ((option == null) ? 0 : option.hashCode());
return result;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
Preset other = (Preset) obj;
if (description == null) {
if (other.description != null)
return false;
} else if (!description.equals(other.description))
return false;
if (name == null) {
if (other.name != null)
return false;
} else if (!name.equals(other.name))
return false;
if (option == null) {
if (other.option != null)
return false;
} else if (!option.equals(other.option))
return false;
return true;
}
}
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