<commit_before>package edu.mssm.pharm.maayanlab.Enrichr;

import java.util.HashSet;

public class EnrichedTerm implements Comparable<EnrichedTerm> {

	private Term associatedTerm;

	private HashSet<String> overlap;
	private int numOfOverlappingGenes;
	
	private double pValue;
	private double adjustedPValue;
	private double zScore;
	private double combinedScore;
	
	public EnrichedTerm(Term associatedTerm, HashSet<String> overlap, double pValue) {
		this.associatedTerm = associatedTerm;
		this.overlap = overlap;
		this.numOfOverlappingGenes = overlap.size();
		this.pValue = (pValue == 0) ? Double.MIN_VALUE : pValue;
	}
	
	public String getName() {
		return associatedTerm.getName();
	}
	
	public double getPValue() {
		return this.pValue;
	}
	
	public double getAdjustedPValue() {
		return this.adjustedPValue;
	}
	
	public double getZScore() {
		return this.zScore;
	}
	
	public double getCombinedScore() {
		return this.combinedScore;
	}
	
	public HashSet<String> getOverlap() {
		return this.overlap;
	}
	
	public void setAdjustedPValue(double adjustedpvalue) {
		this.adjustedPValue = adjustedpvalue;
	}
	
	public void computeScore(int currentRank) {
		double mean = associatedTerm.getMean();
		double standardDeviation = associatedTerm.getStandardDeviation();
		
		if (mean == 0 && standardDeviation == 0)<commit_msg>Abstract HashSet to Set<commit_after>package edu.mssm.pharm.maayanlab.Enrichr;

import java.util.Set;

public class EnrichedTerm implements Comparable<EnrichedTerm> {

	private Term associatedTerm;

	private Set<String> overlap;
	private int numOfOverlappingGenes;
	
	private double pValue;
	private double adjustedPValue;
	private double zScore;
	private double combinedScore;
	
	public EnrichedTerm(Term associatedTerm, Set<String> overlap, double pValue) {
		this.associatedTerm = associatedTerm;
		this.overlap = overlap;
		this.numOfOverlappingGenes = overlap.size();
		this.pValue = (pValue == 0) ? Double.MIN_VALUE : pValue;
	}
	
	public String getName() {
		return associatedTerm.getName();
	}
	
	public double getPValue() {
		return this.pValue;
	}
	
	public double getAdjustedPValue() {
		return this.adjustedPValue;
	}
	
	public double getZScore() {
		return this.zScore;
	}
	
	public double getCombinedScore() {
		return this.combinedScore;
	}
	
	public Set<String> getOverlap() {
		return this.overlap;
	}
	
	public void setAdjustedPValue(double adjustedpvalue) {
		this.adjustedPValue = adjustedpvalue;
	}
	
	public void computeScore(int currentRank) {
		double mean = associatedTerm.getMean();
		double standardDeviation = associatedTerm.getStandardDeviation();
		
		if (mean == 0 && standardDeviation == 0)
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