/*******************************************************************************
* 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.gui.MGDisplaySettings;
import java.awt.Color;
import java.awt.FlowLayout;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serializable;
import java.util.List;
import javax.swing.JLabel;
import javax.swing.JPanel;
import edu.yu.einstein.genplay.dataStructure.enums.AlleleType;
import edu.yu.einstein.genplay.dataStructure.enums.VariantType;
/**
* Settings of a variant layer containing the name of the genome displayed,
* the type of variants displayed and the color used to display them
* @author Nicolas Fourel
*/
public class VariantLayerDisplaySettings implements Serializable {
/** Generated serial version ID */
private static final long serialVersionUID = 2604583442089053519L;
private static final int SAVED_FORMAT_VERSION_NUMBER = 0; // saved format version
/** Index used for Genome column */
public static final int GENOME_INDEX = 1;
/** Index used for Allele column */
public static final int ALLELE_INDEX = 2;
/** Index used for variant column */
public static final int VARIANT_INDEX = 3;
private String genome; // name of the genome
private AlleleType alleleType; // type of allele (paternal, maternal or both)
private List<VariantType> variationTypeList; // list of variation
private List<Color> colorList; // list of color
private boolean hasChanged;
/**
* Constructor of {@link VariantLayerDisplaySettings}
*/
protected VariantLayerDisplaySettings() {
genome = null;
alleleType = null;
variationTypeList = null;
colorList = null;
}
/**
* Constructor of {@link VariantLayerDisplaySettings}
* @param genome name of the genome
* @param alleleType type of the allele
* @param variantList list of variation
* @param colorList list of color
*/
public VariantLayerDisplaySettings(String genome, AlleleType alleleType, List<VariantType> variantList, List<Color> colorList) {
this.genome = genome;
this.alleleType = alleleType;
variationTypeList = variantList;
this.colorList = colorList;
hasChanged = false;
}
@Override
public boolean equals(Object obj) {
if(this == obj){
return true;
}
if((obj == null) || (obj.getClass() != this.getClass())) {
return false;
}
// object must be Test at this point
VariantLayerDisplaySettings test = (VariantLayerDisplaySettings)obj;
return genome.equals(test.getGenome()) &&
(alleleType == test.getAlleleType()) &&
hasSameVariationTypeList(test.getVariationTypeList()) &&
hasSameColorList(test.getColorList());
}
/**
* @return the alleleType
*/
public AlleleType getAlleleType() {
return alleleType;
}
/**
* @return the allele type
*/
public String getAlleleTypeForDisplay() {
return alleleType.toString();
}
/**
* @return the colorList
*/
public List<Color> getColorList() {
return colorList;
}
/**
* @return a description of the {@link VariantLayerDisplaySettings} settings
*/
public String getDescription() {
String description = (genome + " ("); // add the name and " ("
for (int i = 0; i < variationTypeList.size(); i++) {
VariantType type = variationTypeList.get(i);
// Add the variant type shortcut
if (type == VariantType.INSERTION) {
description += "I";
} else if (type == VariantType.DELETION) {
description += "D";
} else if (type == VariantType.SNPS) {
description += "SNPs";
}
if (i < (variationTypeList.size() - 1)) {
description += ", ";
}
}
description += ")"; // add a ")" for closing
return description;
}
//////////////////// Getters
/**
* @return the genome
*/
public String getGenome() {
return genome;
}
//////////////////// Getters for display
/**
* @return the genome
*/
public String getGenomeForDisplay() {
return genome;
}
/**
* @return the variantList
*/
public List<VariantType> getVariationTypeList() {
return variationTypeList;
}
/**
* @return the variantList
*/
public JPanel getVariationTypeListForDisplay() {
JPanel panel = new JPanel();
FlowLayout layout = new FlowLayout(FlowLayout.LEFT, 0, 0);
panel.setLayout(layout);
for (int i = 0; i < variationTypeList.size(); i++) {
JLabel label = new JLabel(variationTypeList.get(i).toString());
label.setForeground(colorList.get(i));
panel.add(label);
if (i < (variationTypeList.size() - 1)) {
panel.add(new JLabel(", "));
}
}
return panel;
}
/**
* @return the hasChanged
*/
public boolean hasChanged() {
return hasChanged;
}
/**
* Compare a list of color to the current one
* @param colorList the list of color to compare
* @return true if both list contain same values, false otherwise
*/
private boolean hasSameColorList (List<Color> colorList) {
if ((this.colorList == null) && (colorList == null)) {
return true;
} else if ((this.colorList != null) && (colorList == null)) {
return false;
} else if ((this.colorList == null) && (colorList != null)) {
return false;
} else {
if (this.colorList.size() != colorList.size()) {
return false;
} else {
for (Color color: colorList) {
if (!this.colorList.contains(color)) {
return false;
}
}
return true;
}
}
}
/**
* Compare a variation type list to the current one
* @param variationTypeList the variation list to compare
* @return true if both list contain same values, false otherwise
*/
private boolean hasSameVariationTypeList (List<VariantType> variationTypeList) {
if ((this.variationTypeList == null) && (variationTypeList == null)) {
return true;
} else if ((this.variationTypeList != null) && (variationTypeList == null)) {
return false;
} else if ((this.variationTypeList == null) && (variationTypeList != null)) {
return false;
} else {
if (this.variationTypeList.size() != variationTypeList.size()) {
return false;
} else {
for (VariantType variantType: variationTypeList) {
if (!this.variationTypeList.contains(variantType)) {
return false;
}
}
return true;
}
}
}
/**
* Method used for unserialization
* @param in
* @throws IOException
* @throws ClassNotFoundException
*/
@SuppressWarnings("unchecked")
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
in.readInt();
genome = (String) in.readObject();
alleleType = (AlleleType) in.readObject();
variationTypeList = (List<VariantType>) in.readObject();
colorList = (List<Color>) in.readObject();
}
/**
* @param alleleType the alleleType to set
*/
public void setAlleleType(AlleleType alleleType) {
this.alleleType = alleleType;
}
/**
* @param colorList the colorList to set
*/
public void setColorList(List<Color> colorList) {
this.colorList = colorList;
}
//////////////////// Setters
/**
* @param genome the genome to set
*/
public void setGenome(String genome) {
this.genome = genome;
}
/**
* @param hasChanged the hasChanged to set
*/
public void setHasChanged(boolean hasChanged) {
this.hasChanged = hasChanged;
}
/**
* @param variantList the variantList to set
*/
public void setVariationTypeList(List<VariantType> variantList) {
variationTypeList = variantList;
}
@Override
public String toString () {
String info = "";
info += genome;
info += " " + alleleType.toString();
for (int i = 0; i < variationTypeList.size(); i++) {
info += " [" + variationTypeList.get(i) + ", ";
info += colorList.get(i) + "]";
}
return info;
}
/**
* Method used for serialization
* @param out
* @throws IOException
*/
private void writeObject(ObjectOutputStream out) throws IOException {
out.writeInt(SAVED_FORMAT_VERSION_NUMBER);
out.writeObject(genome);
out.writeObject(alleleType);
out.writeObject(variationTypeList);
out.writeObject(colorList);
}
}