/*******************************************************************************
* 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.data.display.variant;
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.manager.project.ProjectManager;
import edu.yu.einstein.genplay.core.multiGenome.VCF.VCFLine;
import edu.yu.einstein.genplay.core.multiGenome.VCF.VCFFile.VCFFile;
import edu.yu.einstein.genplay.core.multiGenome.data.display.content.MGChromosomeContent;
import edu.yu.einstein.genplay.dataStructure.chromosome.Chromosome;
import edu.yu.einstein.genplay.dataStructure.enums.AlleleType;
import edu.yu.einstein.genplay.dataStructure.enums.VariantType;
import edu.yu.einstein.genplay.exception.ExceptionManager;
/**
* @author Nicolas Fourel
* @version 0.1
*/
public abstract class Variant implements Serializable {
/** Default serial version ID */
private static final long serialVersionUID = 7940616840753151748L;
private static final int SAVED_FORMAT_VERSION_NUMBER = 0; // saved format version
protected MGChromosomeContent chromosomeContent;
protected int referencePositionIndex;
protected int start;
/**
* Constructor of {@link Variant}
* @param chromosomeContent the {@link MGChromosomeContent}
* @param referencePositionIndex the index position on the reference genome
*/
public Variant (MGChromosomeContent chromosomeContent, int referencePositionIndex) {
this(chromosomeContent, referencePositionIndex, -1);
}
/**
* Constructor of {@link Variant}
* @param chromosomeContent the {@link MGChromosomeContent}
* @param referencePositionIndex the index position on the reference genome
* @param start start position
*/
public Variant (MGChromosomeContent chromosomeContent, int referencePositionIndex, int start) {
this.chromosomeContent = chromosomeContent;
this.referencePositionIndex = referencePositionIndex;
this.start = start;
}
/**
* @return the chromosomeContent
*/
public MGChromosomeContent getChromosomeContent() {
return chromosomeContent;
}
/**
* @return a description of the {@link Variant}
*/
public String getDescription () {
String description = "";
description += "INDEX: " + referencePositionIndex + "; ";
description += "REF: " + chromosomeContent.getPositions().get(referencePositionIndex) + "; ";
description += "START: " + start + ";";
return description;
}
/**
* @return the length of the variant
*/
public int getLength() {
return getStop() - getStart();
}
/**
* @return the reference genome position
*/
public int getReferenceGenomePosition() {
return chromosomeContent.getPositions().get(referencePositionIndex);
}
/**
* @return the referencePositionIndex
*/
public int getReferencePositionIndex() {
return referencePositionIndex;
}
/**
* @return the score of the {@link Variant}
*/
public float getScore () {
return chromosomeContent.getScore(referencePositionIndex);
}
/**
* @return the start position on the meta genome
*/
public int getStart () {
return start;
}
/**
* @return the stop position on the meta genome
*/
public abstract int getStop ();
/**
* @return the {@link VariantType} of the {@link Variant}
*/
public abstract VariantType getType ();
/**
* @return the sequence of nucleotide for the variant
*/
public String getVariantSequence() {
return "-";
}
/**
* This method makes sense only for {@link InsertionVariant} and {@link SNPVariant}.
* Otherwise, it returns the result of the regular method and parameters will not be used at all.
* @param genomeName the name of the genome
* @param alleType the {@link AlleleType}
* @return the sequence of nucleotide for a {@link InsertionVariant} and {@link SNPVariant}
*/
public String getVariantSequence(String genomeName, AlleleType alleType) {
return getVariantSequence();
}
/**
* @return the {@link VCFLine} of the variant, null if not found or for special {@link Variant} such as {@link MixVariant}
*/
public VCFLine getVCFLine() {
if (chromosomeContent == null) {
return null;
}
Chromosome chromosome = chromosomeContent.getChromosome();
int referencePosition = getReferenceGenomePosition();
VCFFile file = ProjectManager.getInstance().getMultiGenomeProject().getFileContentManager().getFile(chromosome, chromosomeContent);
List<String> results = null;
try {
int start = referencePosition - 1;
int stop = referencePosition;
if (start < 0) {
start = 0;
stop = 1;
}
results = file.getReader().query(chromosome.getName(), start, stop);
} catch (IOException e) {
ExceptionManager.getInstance().caughtException(e);
}
if ((results != null) && (results.size() > 0)) {
if ((results.size() == 1) || isReference()) {
return new VCFLine(results.get(0), file.getHeader());
} else {
for (String currentLine: results) {
// if there is more than one line at the variant position we search
// for a line with at least one variant type corresponding to this variant's type
VCFLine line = new VCFLine(currentLine, file.getHeader());
line.processForAnalyse();
for (VariantType currentType: line.getAlternativesTypes()) {
if (currentType == getType()) {
return line;
}
}
}
}
}
return null;
}
/**
* @return true if the {@link Variant} is an alternative, false otherwise
*/
public boolean isAlternative () {
return (this instanceof InsertionVariant) || (this instanceof DeletionVariant) || (this instanceof SNPVariant);
}
/**
* A variant is dominant according to the following order of importance:
* - is an alternative
* - is a reference
* - is a no call
* - is a mix of variants
*
* If the given variant is null, the current variant is dominant.
* If both, current and given, variants are not at the same position, none of them is dominant.
* If both, current and given, variants have the same type, both of them are dominants.
*
* @param variant the variant to compare
* @return true if the current variant is dominant compare to the given variant, false otherwise
*/
public boolean isDominant (Variant variant) {
Boolean result = false;
if (variant == null) {
result = true;
} else if (getStart() == variant.getStart()) {
if ( (isAlternative() && variant.isAlternative()) ||
(isReference() && variant.isReference()) ||
(isNoCall() && variant.isNoCall()) ||
(isMix() && variant.isMix())){
result = true;
} else if (isAlternative() && (variant.isMix() || variant.isReference() || variant.isNoCall())) {
result = true;
} else if (isReference() && (variant.isNoCall() || variant.isMix())) {
result = true;
} else if (isNoCall() && variant.isMix()) {
result = true;
}
}
return result;
}
/**
* @return true if the {@link Variant} is a {@link MixVariant}, false otherwise
*/
public boolean isMix () {
return (this instanceof MixVariant);
}
/**
* @return true if the {@link Variant} is a {@link NoCallVariant}, false otherwise
*/
public boolean isNoCall () {
return (this instanceof NoCallVariant);
}
/**
* @return true if the {@link Variant} is a {@link ReferenceVariant}, false otherwise
*/
public boolean isReference () {
return (this instanceof ReferenceVariant);
}
/**
* Method used for unserialization
* @param in
* @throws IOException
* @throws ClassNotFoundException
*/
protected void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
in.readInt();
chromosomeContent = (MGChromosomeContent) in.readObject();
referencePositionIndex = in.readInt();
start = in.readInt();
}
/**
* @param start start position to set
*/
public void setStart (int start) {
this.start = start;
}
/**
* @param stop stop position to set
*/
public abstract void setStop (int stop);
/**
* Method used for serialization
* @param out
* @throws IOException
*/
protected void writeObject(ObjectOutputStream out) throws IOException {
out.writeInt(SAVED_FORMAT_VERSION_NUMBER);
out.writeObject(chromosomeContent);
out.writeInt(referencePositionIndex);
out.writeInt(start);
}
}