/*******************************************************************************
* 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.manager.project;
import java.io.File;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import edu.yu.einstein.genplay.core.multiGenome.utils.FormattedMultiGenomeName;
import edu.yu.einstein.genplay.dataStructure.chromosome.Chromosome;
import edu.yu.einstein.genplay.dataStructure.enums.ScorePrecision;
import edu.yu.einstein.genplay.dataStructure.genome.Assembly;
import edu.yu.einstein.genplay.dataStructure.gwBookmark.GWBookmark;
import edu.yu.einstein.genplay.dataStructure.list.primitiveList.PrimitiveList;
/**
* This class manages information about the project.
* @author Nicolas Fourel
*/
public class ProjectManager implements Serializable {
private static final long serialVersionUID = -8900126340763056646L; // generated ID
private static final int SAVED_FORMAT_VERSION_NUMBER = 2; // saved format version
private static ProjectManager instance = null; // unique instance of the singleton
/**
* @return an instance of a {@link ProjectManager}.
* Makes sure that there is only one unique instance as specified in the singleton pattern
*/
public static ProjectManager getInstance() {
if (instance == null) {
synchronized(ProjectManager.class) {
if (instance == null) {
instance = new ProjectManager();
}
}
}
return instance;
}
private String projectName; // project name
private transient File projectDirectory = null; // directory where the project is saved
private String cladeName; // clade name
private String genomeName; // genome name
private Assembly assembly; // assembly name
private boolean isMultiGenome; // True if it is a multi genome project, false if it is a simple genome project
private ScorePrecision projectScorePrecision; // precision of the scores of the project (16 / 32 BIT)
private final ProjectWindow projectWindow; // Instance of the Genome Window Manager
private final ProjectZoom projectZoom; // Instance of the Zoom Manager
private final ProjectChromosomes projectChromosomes; // Instance of the Chromosome Manager
private MultiGenomeProject multiGenomeProject; // Instance of the Multi Genome Project
private List<GWBookmark> projectBookmarks; // Genome windows bookmarked for the project
/**
* Private constructor of the singleton. Creates an instance of a {@link ProjectManager}.
*/
private ProjectManager() {
isMultiGenome = false;
projectZoom = new ProjectZoom();
projectChromosomes = new ProjectChromosomes();
projectWindow = new ProjectWindow();
projectBookmarks = new ArrayList<GWBookmark>();
}
/**
* @return the assembly
*/
public Assembly getAssembly() {
return assembly;
}
/**
* @return the cladeName
*/
public String getCladeName() {
return cladeName;
}
/**
* @return the genomeName
*/
public String getGenomeName() {
return genomeName;
}
/**
* @return the genomeSynchroniser
*/
public MultiGenomeProject getMultiGenomeProject() {
if (isMultiGenome && (multiGenomeProject == null)) {
multiGenomeProject = new MultiGenomeProject();
FormattedMultiGenomeName.REFERENCE_GENOME_NAME = assembly.getDisplayName();
}
return multiGenomeProject;
}
/**
* @return the list of the genome windows bookmarked
*/
public List<GWBookmark> getProjectBookmarks() {
return projectBookmarks;
}
/**
* @return the chromosomeManager
*/
public ProjectChromosomes getProjectChromosomes() {
return projectChromosomes;
}
/**
* @return the directory where the project is saved
*/
public File getProjectDirectory() {
return projectDirectory;
}
/**
* @return the projectName
*/
public String getProjectName() {
return projectName;
}
/**
* @return the precision of the scores of the project
*/
public ScorePrecision getProjectScorePrecision() {
return projectScorePrecision;
}
/**
* @return the Genome Window Manager
*/
public ProjectWindow getProjectWindow() {
return projectWindow;
}
/**
* @return the Zoom Manager
*/
public ProjectZoom getProjectZoom() {
return projectZoom;
}
/**
* @return the multiGenomeProject
*/
public boolean isMultiGenomeProject() {
return isMultiGenome;
}
/**
* @param in
* @throws IOException
* @throws ClassNotFoundException
*/
public void readMultiGenomeObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
if (instance.isMultiGenomeProject()) {
instance.getMultiGenomeProject().setMultiGenomeProject((MultiGenomeProject) in.readObject());
}
}
/**
* Method used for unserialization
* @param in
* @throws IOException
* @throws ClassNotFoundException
*/
@SuppressWarnings("unchecked")
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
getInstance();
int savedVersion = in.readInt();
instance.setProjectName((String) in.readObject());
instance.setCladeName((String) in.readObject());
instance.setGenomeName((String) in.readObject());
instance.setAssembly((Assembly) in.readObject());
instance.setMultiGenomeProject(in.readBoolean());
if (savedVersion >= 1) {
instance.setProjectScorePrecision((ScorePrecision) in.readObject());
}
instance.getProjectWindow().setProjectWindow((ProjectWindow) in.readObject());
instance.getProjectChromosomes().setProjectChromosomes((ProjectChromosomes) in.readObject());
if (savedVersion >= 2) {
instance.projectBookmarks = (List<GWBookmark>) in.readObject();
} else {
instance.projectBookmarks = new ArrayList<GWBookmark>();
}
}
/**
* @param assembly the assembly to set
*/
public void setAssembly(Assembly assembly) {
this.assembly = assembly;
}
/**
* @param cladeName the cladeName to set
*/
public void setCladeName(String cladeName) {
this.cladeName = cladeName;
}
/**
* @param genomeName the genomeName to set
*/
public void setGenomeName(String genomeName) {
this.genomeName = genomeName;
}
/**
* @param multiGenome the multiGenomeProject to set
*/
public void setMultiGenomeProject(boolean multiGenome) {
isMultiGenome = multiGenome;
if (!multiGenome) {
multiGenomeProject = null;
}
}
/**
* Sets the directory where the project is saved
* @param projectDirectory
*/
public void setProjectDirectory(File projectDirectory) {
this.projectDirectory = projectDirectory;
}
/**
* @param projectName the projectName to set
*/
public void setProjectName(String projectName) {
this.projectName = projectName;
}
/**
* @param projectScorePrecision the ScorePrecision of the scores of the project
*/
public void setProjectScorePrecision(ScorePrecision projectScorePrecision) {
PrimitiveList.setScorePrecision(projectScorePrecision);
this.projectScorePrecision = projectScorePrecision;
}
/**
* Updates the chromosome list
*/
public void updateChromosomeList () {
List<Chromosome> chromosomeList;
chromosomeList = getAssembly().getChromosomeList();
projectChromosomes.setChromosomeList(chromosomeList);
}
/**
* Method used for serialization
* @param out
* @throws IOException
*/
private void writeObject(ObjectOutputStream out) throws IOException {
out.writeInt(SAVED_FORMAT_VERSION_NUMBER);
out.writeObject(projectName);
out.writeObject(cladeName);
out.writeObject(genomeName);
out.writeObject(assembly);
out.writeBoolean(isMultiGenome);
out.writeObject(projectScorePrecision);
out.writeObject(projectWindow);
out.writeObject(projectChromosomes);
out.writeObject(projectBookmarks);
}
}