GenotypeIDFilter.java

/*******************************************************************************
 * GenPlay, Einstein Genome Analyzer
 * Copyright (C) 2009, 2014 Albert Einstein College of Medicine
 * 
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 
 * This program 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.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 * Authors: Julien Lajugie <julien.lajugie@einstein.yu.edu>
 *          Nicolas Fourel <nicolas.fourel@einstein.yu.edu>
 *          Eric Bouhassira <eric.bouhassira@einstein.yu.edu>
 * 
 * Website: <http://genplay.einstein.yu.edu>
 ******************************************************************************/
package edu.yu.einstein.genplay.core.multiGenome.filter.VCFID;

import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serializable;
import java.util.List;

import edu.yu.einstein.genplay.core.multiGenome.VCF.VCFLine;
import edu.yu.einstein.genplay.core.multiGenome.VCF.VCFHeaderType.VCFHeaderType;
import edu.yu.einstein.genplay.core.multiGenome.data.display.variant.Variant;
import edu.yu.einstein.genplay.core.multiGenome.filter.utils.FilterUtility;
import edu.yu.einstein.genplay.core.multiGenome.filter.utils.FormatFilterOperatorType;
import edu.yu.einstein.genplay.core.multiGenome.filter.utils.GenotypeUtility;
import edu.yu.einstein.genplay.dataStructure.enums.VCFColumnName;

/**
 * @author Nicolas Fourel
 * @version 0.1
 */
public class GenotypeIDFilter implements IDFilterInterface, Serializable {

	/** Generated default serial ID*/
	private static final long serialVersionUID = -2692600453534744380L;
	private static final int  SAVED_FORMAT_VERSION_NUMBER = 0;			// saved format version

	/** Heterozygote option */
	public static final int  HETEROZYGOTE_OPTION = 0;
	/** Homozygote option */
	public static final int  HOMOZYGOTE_OPTION = 1;


	private FilterUtility				utility;
	private VCFHeaderType 				header;			// ID of the filter
	private int 						filterOption;	// heterozygote or homozygote
	private boolean 					canBePhased;	// true if the genotype can be phased
	private boolean 					canBeUnPhased;	// true if the genotype can be unphased
	private List<String>				genomeNames;	// the list of genomes to apply the filter (if required, null otherwise)
	private FormatFilterOperatorType 	operator;		// the operator to use to filter the genomes (if required, null otherwise)


	/**
	 * Method used for serialization
	 * @param out
	 * @throws IOException
	 */
	private void writeObject(ObjectOutputStream out) throws IOException {
		out.writeInt(SAVED_FORMAT_VERSION_NUMBER);
		out.writeObject(header);
		out.writeInt(filterOption);
		out.writeBoolean(canBePhased);
		out.writeBoolean(canBeUnPhased);
		out.writeObject(genomeNames);
		out.writeObject(operator);
	}


	/**
	 * Method used for unserialization
	 * @param in
	 * @throws IOException
	 * @throws ClassNotFoundException
	 */
	@SuppressWarnings("unchecked")
	private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
		in.readInt();
		header = (VCFHeaderType) in.readObject();
		filterOption = in.readInt();
		canBePhased = in.readBoolean();
		canBeUnPhased = in.readBoolean();
		genomeNames = (List<String>) in.readObject();
		operator = (FormatFilterOperatorType) in.readObject();
		utility = new GenotypeUtility();
	}


	/**
	 * Constructor of {@link GenotypeIDFilter}
	 */
	public GenotypeIDFilter () {
		utility = new GenotypeUtility();
		filterOption = -1;
		canBePhased = true;
		canBeUnPhased = true;
	}


	@Override
	public VCFHeaderType getHeaderType() {
		return header;
	}


	@Override
	public void setHeaderType(VCFHeaderType id) {
		this.header = id;
	}


	/**
	 * @param option the option heterozygote or homozygote
	 */
	public void setOption(int option) {
		this.filterOption = option;
	}


	/**
	 * @return the option heterozygote or homozygote
	 */
	public int getOption() {
		return filterOption;
	}


	/**
	 * @return the canBePhased
	 */
	public boolean canBePhased() {
		return canBePhased;
	}


	/**
	 * @return the canBeUnPhased
	 */
	public boolean canBeUnPhased() {
		return canBeUnPhased;
	}


	/**
	 * @param canBePhased the canBePhased to set
	 */
	public void setCanBePhased(boolean canBePhased) {
		this.canBePhased = canBePhased;
	}


	/**
	 * @param canBeUnPhased the canBeUnPhased to set
	 */
	public void setCanBeUnPhased(boolean canBeUnPhased) {
		this.canBeUnPhased = canBeUnPhased;
	}


	@Override
	public String toStringForDisplay() {
		return utility.toStringForDisplay(this);
	}


	@Override
	public String getErrors() {
		return utility.getErrors(this);
	}


	@Override
	public boolean isValid(VCFLine line) {
		return utility.isValid(this, line);
	}


	@Override
	public boolean isValid(Variant variant) {
		return false;
	}


	@Override
	public boolean equals(Object obj) {
		return utility.equals(this, obj);
	}


	@Override
	public VCFColumnName getColumnName() {
		return header.getColumnCategory();
	}


	@Override
	public void setGenomeNames(List<String> genomeNames) {
		this.genomeNames = genomeNames;
	}


	@Override
	public List<String> getGenomeNames() {
		return genomeNames;
	}


	@Override
	public void setOperator(FormatFilterOperatorType operator) {
		this.operator = operator;
	}


	@Override
	public FormatFilterOperatorType getOperator() {
		return operator;
	}


	@Override
	public IDFilterInterface getDuplicate() {
		IDFilterInterface duplicate = new GenotypeIDFilter();
		duplicate.setHeaderType(getHeaderType());
		((GenotypeIDFilter)duplicate).setOption(getOption());
		((GenotypeIDFilter)duplicate).setCanBePhased(canBePhased);
		((GenotypeIDFilter)duplicate).setCanBeUnPhased(canBeUnPhased);
		duplicate.setGenomeNames(getGenomeNames());
		duplicate.setOperator(getOperator());
		return duplicate;
	}


	@Override
	public String getName() {
		return "GT: Genotype";
	}


	@Override
	public String getDescription() {
		return "Filter for the GT field.";
	}
}