/*******************************************************************************
* 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.StringUtility;
import edu.yu.einstein.genplay.dataStructure.enums.VCFColumnName;
/**
* @author Nicolas Fourel
* @version 0.1
*/
public class StringIDFilter implements StringIDFilterInterface, Serializable {
/** Generated default serial ID*/
private static final long serialVersionUID = -4601435986037527188L;
private static final int SAVED_FORMAT_VERSION_NUMBER = 0; // saved format version
private FilterUtility utility;
private VCFHeaderType header; // ID of the filter
private String value; // value of the filter
private boolean required; // true if the value is required to pass the the filter
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);
if (header != null) {
out.writeObject(header);
}
out.writeObject(value);
out.writeBoolean(required);
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();
try {
header = (VCFHeaderType) in.readObject();
} catch (Exception e) {
header = null;
}
value = (String) in.readObject();
required = in.readBoolean();
genomeNames = (List<String>) in.readObject();
operator = (FormatFilterOperatorType) in.readObject();
utility = new StringUtility();
}
/**
* Constructor of {@link StringIDFilter}
*/
public StringIDFilter () {
utility = new StringUtility();
}
@Override
public VCFHeaderType getHeaderType() {
return header;
}
@Override
public void setHeaderType(VCFHeaderType id) {
this.header = id;
}
@Override
public String getValue() {
return value;
}
@Override
public void setValue(String value) {
this.value = value;
}
@Override
public boolean isRequired() {
return required;
}
@Override
public void setRequired(boolean required) {
this.required = required;
}
@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() {
StringIDFilterInterface duplicate = new StringIDFilter();
duplicate.setHeaderType(getHeaderType());
duplicate.setValue(getValue());
duplicate.setRequired(isRequired());
duplicate.setGenomeNames(getGenomeNames());
duplicate.setOperator(getOperator());
return duplicate;
}
@Override
public String getName() {
return "String filter";
}
@Override
public String getDescription() {
return "Filter for strings.";
}
}