SetOfGeneSets.java

package org.baderlab.csplugins.enrichmentmap.model;

import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;

/**
 * Class represents a set of genesets.  In GSEA the set of genesets is contained in a gmt file.
 */
public class SetOfGeneSets {

	//name of results (ie. Dataset1 or name specified by user)
	private String name;

	/** 
	 * The set of genesets
	 * Hash Key = name of gene set
	 * Hash Value = Gene set
	 * 
	 * Note: Must declare the type as HashMap because it forces GSON to deserialize using 
	 * an actual HashMap, otherwise it wants to use a LinkedTreeMap which uses much more memory.
	 */
	private HashMap<String, GeneSet> geneSets;

	//filename
	private String filename;
	
	public SetOfGeneSets(String name) {
		this.name = name;
		filename = "";
		geneSets = new HashMap<>();
	}
	
	public SetOfGeneSets() {
		this("");
	}

	/**
	 * Create a set of Genesets on re-load Given - the dataset these genesets
	 * are associated with and the loaded in EM property file
	 */
	public SetOfGeneSets(String ds, HashMap<String, String> props) {
		if (props.containsKey(ds + "%" + this.getClass().getSimpleName() + "%name"))
			this.name = props.get(ds + "%" + this.getClass().getSimpleName() + "%name");
		
		if (props.containsKey(ds + "%" + this.getClass().getSimpleName() + "%filename"))
			this.filename = props.get(ds + "%" + this.getClass().getSimpleName() + "%filename");
	}

	/**
	 * FilterGenesets - restrict the genes contained in each gene set to only
	 * the genes found in the expression file.
	 */
	public void filterGeneSets(Set<Integer> datasetGenes) {
		HashMap<String, GeneSet> filteredGenesets = new HashMap<>();

		//iterate through each geneset and filter each one
		for (String geneSetName : geneSets.keySet()) {
			GeneSet geneSet = geneSets.get(geneSetName);
			Set<Integer> genesetGenes = geneSet.getGenes();
			
			Set<Integer> intersection = new HashSet<>(genesetGenes);
			intersection.retainAll(datasetGenes);
			
			GeneSet newGeneSet = new GeneSet(geneSetName, geneSet.getDescription(), intersection);
			filteredGenesets.put(geneSetName, newGeneSet);
		}
		
		geneSets = filteredGenesets;
	}
	
	public String getName() {
		return name;
	}

	public void setName(String name) {
		this.name = name;
	}

	public Map<String, GeneSet> getGeneSets() {
		return geneSets;
	}

	public void setGeneSets(HashMap<String, GeneSet> geneSets) {
		this.geneSets = geneSets;
	}

	public void addGeneSet(String key, GeneSet geneSet) {
		synchronized (geneSet) {
			geneSets.put(key, geneSet);
		}
	}
	
	public String getFilename() {
		return filename;
	}

	public void setFilename(String filename) {
		this.filename = filename;
	}

	public GeneSet getGeneSetByName(String name) {
		if (geneSets != null) {
			if (geneSets.containsKey(name))
				return geneSets.get(name);
		}
		
		return null;
	}
	
	/**
	 * @return The number of gene sets in this set
	 */
	public int size() {
		return geneSets.size();
	}

	public void clear() {
		geneSets.clear();
	}
}