GenericResult.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.
 **
 **/

// $Id$
// $LastChangedDate$
// $LastChangedRevision$
// $LastChangedBy$
// $HeadURL$

package org.baderlab.csplugins.enrichmentmap.model;

import org.baderlab.csplugins.enrichmentmap.model.EnrichmentResultFilterParams.NESFilter;

/**
 * Created by User: risserlin Date: Jan 28, 2009 Time: 3:25:51 PM
 * <p>
 * Class representing a generic enrichment result.
 */
public class GenericResult extends EnrichmentResult {

	//optional parameters
	private final double fdrqvalue;

	//make the generic file synonamous with gsea result file
	//the phenotype is deduced from the sign of the ES score so create a variable to store
	//the phenotype.
	private final double NES;
	
	
	/**
	 * Class constructor
	 * @param tokens - string tokenized line from a generic result file as stored in the session file
	 * @deprecated Parsing of tokens should be done by calling code.
	 */
	@Deprecated
	public GenericResult(String[] tokens) {
		//ignore the first token as it is from the hash
		super(tokens[1], tokens[2], Double.parseDouble(tokens[3]), Integer.parseInt(tokens[4]));
		this.fdrqvalue = Double.parseDouble(tokens[5]);
		this.NES = Double.parseDouble(tokens[6]);
	}

	/**
	 * Class constructor - minimal requirements
	 *
	 * @param name - gene set name (enrichment result)
	 * @param description - gene set description
	 * @param pvalue - enrichment p-value
	 * @param gssize - gene set size
	 */
	public GenericResult(String name, String description, double pvalue, int gssize) {
		super(name, description, pvalue, gssize);
		this.fdrqvalue = 1.0;
		this.NES = 1.0;
	}

	/**
	 * Class constructor - minimal requirement with addition of fdr qvalue
	 *
	 * @param name - gene set name (enrichment result)
	 * @param description - gene set description
	 * @param pvalue - enrichment p-value
	 * @param gssize - gene set size
	 * @param fdrqvalue - enrichment fdr q-value
	 */
	public GenericResult(String name, String description, double pvalue, int gssize, double fdrqvalue) {
		super(name, description, pvalue, gssize);
		this.fdrqvalue = fdrqvalue;
		this.NES = 1.0;
	}

	/**
	 * Class constructor - minimal requirements with addition of fdr qvalue and phenotype
	 *
	 * @param name  - gene set name (enrichment result)
	 * @param description  - gene set description
	 * @param pvalue - enrichment p-value
	 * @param gssize - gene set size
	 * @param fdrqvalue - enrichment fdr q-value
	 * @param phenotype - which phenotype or class is this enrichment results associated with
	 */
	public GenericResult(String name, String description, double pvalue, int gssize, double fdrqvalue, double phenotype) {
		super(name, description, pvalue, gssize);
		this.fdrqvalue = fdrqvalue;
		this.NES = phenotype;
	}

	/**
	 * Is this a gene set of interest, does its enrichment score pass the
	 * p-value threshold (and optionallly does it also pass the fdr 1-value
	 * threshold)
	 *
	 * @param pvalue - pvalue of current gene set enrichment
	 * @param fdrqvalue - fdr q-value of current gene set enrichment
	 * @param useFDR  - is there a fdr q-value threshold set
	 * @return whether these p-value and fdr q-value for the specified gene set
	 *         enrichment fall into our gene sets of interest category (i.e. do
	 *         these values pass the specified thresholds)
	 */
	@Override
	public boolean geneSetOfInterest(EnrichmentResultFilterParams params) {
		if(params.getNESFilter() == NESFilter.POSITIVE && getNES() <= 0)
			return false;
		if(params.getNESFilter() == NESFilter.NEGATIVE && getNES() >= 0)
			return false;
		
		double pvalue = params.getPvalue();
		double fdrqvalue = params.getQvalue();
		boolean useFDR = params.isFDR();
		
		if(useFDR)
			return (getPvalue() <= pvalue) && (this.fdrqvalue <= fdrqvalue);
		else
			return (getPvalue() <= pvalue);
	}

	//Getters and Setters
	public double getFdrqvalue() {
		return fdrqvalue;
	}


	/**
	 * @return 1.0 for Phenotype A or -1.0 for Phenotype B
	 */
	public double getNES() {
		return NES;
	}


	public String toString() {
		return getName() + "\t" + getDescription() + "\t" + getPvalue() + "\t" + getGsSize() + "\t" + fdrqvalue + "\t" + NES;
	}

}