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Variant annotation and effect prediction package.

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package org.snpeff.reactome.events;

import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;

import org.snpeff.reactome.Entity;

/**
 * A Reactome pathway
 * 
 * @author pcingola
 *
 */
public class Pathway extends Reaction implements Iterable {

	HashMap events; // Count number of events

	public Pathway(int id, String name) {
		super(id, name);
		events = new HashMap();
	}

	public void add(Event e) {
		if (e == null) return;

		if (!events.containsKey(e)) events.put(e, 1);
		events.put(e, events.get(e) + 1);
	}

	public boolean contains(Object o) {
		return events.containsKey(o);
	}

	public boolean isEmpty() {
		return events.isEmpty();
	}

	@Override
	public Iterator iterator() {
		return events.keySet().iterator();
	}

	public int size() {
		return events.size();
	}

	@Override
	public String toString() {
		return toString(0, new HashSet());
	}

	@Override
	public String toString(int tabs, HashSet done) {
		done.add(this);

		StringBuilder sb = new StringBuilder();
		sb.append(super.toString(tabs, done));

		for (Event e : this)
			sb.append(e.toString(tabs + 1, done) + "\n");

		return sb.toString();
	}

}