/*******************************************************************************
* 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.dataStructure.genome;
import java.io.Serializable;
import java.util.HashMap;
import java.util.Map;
/**
* This class contains genome information
* @author Nicolas Fourel
*/
public class Genome implements Serializable {
private static final long serialVersionUID = 6313753019744936641L; // generated ID
private Map<String, Assembly> assemblyList; // List of assembly
private final String name; // Name of the Genome
/**
* Constructor of {@link Genome}
* @param name name of the genome
*/
public Genome (String name) {
assemblyList = new HashMap<String, Assembly>();
this.name = name;
}
/**
* Add an assembly to the genome if the assembly is not already existing.
* @param assembly genome to add
*/
protected void addAssembly (Assembly assembly) {
if (!assemblyList.containsKey(assembly.getIndexName())){
assemblyList.put(assembly.getIndexName(), assembly);
}
}
/**
* @return the genome name
*/
public String getName() {
return name;
}
/**
* @return the assembly list
*/
public Map<String, Assembly> getAssemblyList() {
return assemblyList;
}
/**
* @param assemblyList the new assembly list
*/
protected void setAssemblyList(Map<String, Assembly> assemblyList) {
this.assemblyList = assemblyList;
}
@Override
public String toString() {
return getName();
}
}