/**
 **                       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 java.util.Objects;
import java.util.Set;

/**
 * Created by User: risserlin Date: Jan 9, 2009 Time: 10:49:55 AM
 * <p>
 * Class representing a comparison of two gene sets (represents an edge in the network)
 */
public class GenesetSimilarity {

	private String geneset1Name;
	private String geneset2Name;

	// currently the interaction type is pp which actually means a protein protein interaction
	// but there is no specification of an enrichment interaction in cytoscape.
	private String interactionType;

	// either jaccard or overlap coeffecient, depends on statistic user specified.
	private double similarityCoeffecient;

	// Hypergeometric
	private double hypergeomPValue;
	private int hypergeomU;
	private int hypergeomN;
	private int hypergeomK;
	private int hypergeomM;

	// Mann-Whitney U
	private double mannWhitPValueTwoSided;
	private double mannWhitPValueGreater;
	private double mannWhitPValueLess;

	// flag that indicates if either of the gene sets has no ranks (and therefore we cannot calculated mann-whit
	private boolean mannWhitMissingRanks;

	// set of genes in common to both gene sets.
	private Set<Integer> overlappingGenes;

	private String datasetName;

	/**
	 * @param geneset1Name - gene set 1 name
	 * @param geneset2Name - gene set 2 name
	 * @param similarityCoeffecient - jaccard or overlap coeffecient for geneset 1 and geneset 2
	 * @param overlappingGenes - set of genes in common to gene set 1 and gene set 2
	 * @param enrichment_set - the enrichment set the similarity comes from.
	 */
	public GenesetSimilarity(String geneset1Name, String geneset2Name, double similarityCoeffecient,
			String interactionType, Set<Integer> overlappingGenes, String datasetName) {
		Objects.requireNonNull(interactionType);
		
		this.geneset1Name = geneset1Name;
		this.geneset2Name = geneset2Name;
		this.similarityCoeffecient = similarityCoeffecient;
		this.overlappingGenes = overlappingGenes;
		this.interactionType = interactionType;
		this.datasetName = datasetName;
		this.hypergeomPValue = -1.0;
	}

	/**
	 * @param geneset1Name - gene set 1 name
	 * @param geneset2Name - gene set 2 name
	 * @param similarityCoeffecient - jaccard or overlap coeffecient for geneset 1 and geneset 2
	 * @param overlappingGenes - set of genes in common to gene set 1 and gene set 2
	 */
	public GenesetSimilarity(String geneset1Name, String geneset2Name, double similarityCoeffecient,
			String interactionType, Set<Integer> overlappingGenes) {
		Objects.requireNonNull(interactionType);
		
		this.geneset1Name = geneset1Name;
		this.geneset2Name = geneset2Name;
		this.similarityCoeffecient = similarityCoeffecient;
		this.overlappingGenes = overlappingGenes;
		this.interactionType = interactionType;
		this.datasetName = "Signature";
		this.hypergeomPValue = -1.0;
	}

	public String getGeneset1Name() {
		return geneset1Name;
	}

	public void setGeneset1Name(String geneset1Name) {
		this.geneset1Name = geneset1Name;
	}

	public String getGeneset2Name() {
		return geneset2Name;
	}

	public void setGeneset2Name(String geneset2Name) {
		this.geneset2Name = geneset2Name;
	}

	public String getInteractionType() {
		return interactionType;
	}

	public double getSimilarityCoeffecient() {
		return similarityCoeffecient;
	}

	public void setSimilarityCoeffecient(double value) {
		this.similarityCoeffecient = value;
	}

	public void setHypergeomPValue(double hypergeomPValue) {
		this.hypergeomPValue = hypergeomPValue;
	}

	public double getHypergeomPValue() {
		return hypergeomPValue;
	}

	public Set<Integer> getOverlappingGenes() {
		return overlappingGenes;
	}

	public void setOverlappingGenes(Set<Integer> overlappingGenes) {
		this.overlappingGenes = overlappingGenes;
	}

	public int getSizeOfOverlap() {
		return overlappingGenes.size();
	}

	public String getDataSetName() {
		return datasetName;
	}

	/**
	 * Get the N value used in the Hypergeometric test. 'U' denotes the size of
	 * the universe (i.e. the size of the union of all gene sets)
	 */
	public int getHypergeomU() {
		return hypergeomU;
	}

	/**
	 * Set the N value used in the Hypergeometric test. 'U' denotes the size of
	 * the universe (i.e. the size of the union of all gene sets)
	 */
	public void setHypergeomU(int value) {
		this.hypergeomU = value;
	}

	/**
	 * Get the n value used in the Hypergeometric test. 'n' denotes the size of
	 * the sample being taken from the universe (i.e. the size of the signature gene set)
	 */
	public int getHypergeomN() {
		return hypergeomN;
	}

	/**
	 * Set the n value used in the Hypergeometric test. 'n' denotes the size of
	 * the sample being taken from the universe (i.e. the size of the signature gene set)
	 */
	public void setHypergeomN(int value) {
		this.hypergeomN = value;
	}

	/**
	 * Get the k value used in the Hypergeometric test. 'k' denotes the number of
	 * successes in the sample (i.e. the size of the overlap)
	 */
	public int getHypergeomK() {
		return hypergeomK;
	}

	/**
	 * Set the k value used in the Hypergeometric test. 'k' denotes the number of
	 * successes in the sample (i.e. the size of the overlap)
	 */
	public void setHypergeomK(int value) {
		this.hypergeomK = value;
	}

	/**
	 * Get the m value used in the Hypergeometric test. 'm' denotes the total
	 * number of successes in the universe (i.e. the size of the enriched gene set)
	 */
	public int getHypergeomM() {
		return hypergeomM;
	}

	/**
	 * Set the m value used in the Hypergeometric test. 'm' denotes the total
	 * number of successes in the universe (i.e. the size of the enriched gene set)
	 */
	public void setHypergeomM(int value) {
		this.hypergeomM = value;
	}

	public double getMannWhitPValueTwoSided() {
		return mannWhitPValueTwoSided;
	}

	public void setMannWhitPValueTwoSided(double value) {
		this.mannWhitPValueTwoSided = value;
	}

	public double getMannWhitPValueGreater() {
		return mannWhitPValueGreater;
	}

	public void setMannWhitPValueGreater(double value) {
		this.mannWhitPValueGreater = value;
	}

	public double getMannWhitPValueLess() {
		return mannWhitPValueLess;
	}

	public void setMannWhitPValueLess(double value) {
		this.mannWhitPValueLess = value;
	}

	public boolean isMannWhitMissingRanks() {
		return mannWhitMissingRanks;
	}

	public void setMannWhitMissingRanks(boolean value) {
		this.mannWhitMissingRanks = value;
	}
}