Rank.java

/**
 **                       EnrichmentMap Cytoscape Plugin
 **
 ** Copyright (c) 2008-2009 Bader Lab, Donnelly Centre for Cellular and Biomolecular 
 ** Research, University of Toronto
 **
 ** Contact: http://www.baderlab.org
 **
 ** Code written by: Ruth Isserlin
 ** Authors: Daniele Merico, Ruth Isserlin, Oliver Stueker, Gary D. Bader
 **
 ** This library is free software; you can redistribute it and/or modify it
 ** under the terms of the GNU Lesser General Public License as published
 ** by the Free Software Foundation; either version 2.1 of the License, or
 ** (at your option) any later version.
 **
 ** 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.  The software and
 ** documentation provided hereunder is on an "as is" basis, and
 ** University of Toronto
 ** has no obligations to provide maintenance, support, updates, 
 ** enhancements or modifications.  In no event shall the
 ** University of Toronto
 ** be liable to any party for direct, indirect, special,
 ** incidental or consequential damages, including lost profits, arising
 ** out of the use of this software and its documentation, even if
 ** University of Toronto
 ** has been advised of the possibility of such damage.  
 ** See the GNU Lesser General Public License for more details.
 **
 ** You should have received a copy of the GNU Lesser General Public License
 ** along with this library; if not, write to the Free Software Foundation,
 ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
 **
 **/

// $Id: Ranking.java 393 2009-10-15 20:15:01Z risserlin $
// $LastChangedDate: 2009-10-15 16:15:01 -0400 (Thu, 15 Oct 2009) $
// $LastChangedRevision: 393 $
// $LastChangedBy: risserlin $
// $HeadURL: svn+ssh://server1.baderlab.med.utoronto.ca/svn/EnrichmentMap/trunk/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/Ranking.java $

package org.baderlab.csplugins.enrichmentmap.model;

/**
 * Created by User: risserlin Date: May 1, 2009 Time: 10:42:44 AM
 * <p>
 * Object representing the rank of an individual gene or protein
 */
public class Rank {

	//gene/protein name
	private String Name;

	//score given in the ranking file
	private Double Score;

	//rank computed based on sorting the given scores.  (if the score given are actually ranks then
	//the two will be synonmous)
	private Integer gene_rank;

	/**
	 * Class constructor
	 *
	 * @param name - gene/protein name
	 * @param score - score supplied by user
	 */
	public Rank(String name, Double score) {
		this.Name = name;
		this.Score = score;
	}

	/**
	 * Class constructor
	 *
	 * @param name - gene/protein name
	 * @param score - score supplied by user
	 * @param rank - rank computed based on scores.
	 */
	public Rank(String name, Double score, Integer rank) {
		this.Name = name;
		this.Score = score;
		this.gene_rank = rank;
	}

	/**
	 * Class constructor - for reconstruction from session saved rank files.
	 *
	 * @param tokens - tokenized version of rank file as saved in a session file
	 */
	public Rank(String[] tokens) {

		//make sure that there are 4 tokens (hashkey, name, score, rank)
		if(tokens.length != 4)
			return;

		this.Name = tokens[1];
		this.Score = Double.parseDouble(tokens[2]);
		this.gene_rank = Integer.parseInt(tokens[3]);

	}

	//Getters and Setters

	public String getName() {
		return Name;
	}

	public void setName(String name) {
		Name = name;
	}

	public Double getScore() {
		return Score;
	}

	public void setScore(Double score) {
		Score = score;
	}

	public Integer getRank() {
		return gene_rank;
	}

	public void setRank(Integer rank) {
		this.gene_rank = rank;
	}

	public String toString() {
		return Name + "\t" + Score + "\t" + gene_rank;
	}
}