/*******************************************************************************
* GenPlay, Einstein Genome Analyzer
* Copyright (C) 2009, 2014 Albert Einstein College of Medicine
*
* This program 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.
*
* This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
* Authors: Julien Lajugie <julien.lajugie@einstein.yu.edu>
* Nicolas Fourel <nicolas.fourel@einstein.yu.edu>
* Eric Bouhassira <eric.bouhassira@einstein.yu.edu>
*
* Website: <http://genplay.einstein.yu.edu>
******************************************************************************/
package edu.yu.einstein.genplay.core.multiGenome.VCF.VCFHeaderType;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import edu.yu.einstein.genplay.dataStructure.enums.VCFColumnName;
/**
* This class manages the ALT VCF field type information.
* @author Nicolas Fourel
* @version 0.1
*/
public class VCFHeaderAltType implements VCFHeaderType {
private static final long serialVersionUID = 7171924074043506204L; // generated ID
private static final int SAVED_FORMAT_VERSION_NUMBER = 0; // saved format version
private String id; // information ID
private String description; // field description
@Override
public String getAsOriginalLine() {
String line = "";
line += "##ALT=<ID=";
line += id;
line += ",Description=\"";
line += description;
line += "\">";
return line;
}
@Override
public VCFColumnName getColumnCategory() {
return VCFColumnName.ALT;
}
@Override
public String getDescription() {
return description;
}
@Override
public String getId() {
return id;
}
/**
* Method used for unserialization
* @param in
* @throws IOException
* @throws ClassNotFoundException
*/
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
in.readInt();
id = (String) in.readObject();
description = (String) in.readObject();
}
@Override
public void setColumnCategory(VCFColumnName columnCategory) {}
@Override
public void setDescription(String description) {
this.description = description;
}
@Override
public void setId(String id) {
this.id = id;
}
@Override
public String toString () {
return getColumnCategory() + " - " + id + ": " + description;
}
/**
* Method used for serialization
* @param out
* @throws IOException
*/
private void writeObject(ObjectOutputStream out) throws IOException {
out.writeInt(SAVED_FORMAT_VERSION_NUMBER);
out.writeObject(id);
out.writeObject(description);
}
}