/*******************************************************************************
* 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.dataStructure.list.genomeWideList.SCWList;
import java.security.InvalidParameterException;
import java.util.List;
import java.util.concurrent.ExecutionException;
import edu.yu.einstein.genplay.dataStructure.chromosome.Chromosome;
import edu.yu.einstein.genplay.dataStructure.list.chromosomeWideList.SCWListView.SCWListViewBuilder;
import edu.yu.einstein.genplay.dataStructure.list.chromosomeWideList.SCWListView.bin.BinListView;
import edu.yu.einstein.genplay.dataStructure.list.chromosomeWideList.SCWListView.bin.BinListViewBuilder;
import edu.yu.einstein.genplay.dataStructure.list.chromosomeWideList.SCWListView.dense.DenseSCWListViewBuilder;
import edu.yu.einstein.genplay.dataStructure.list.chromosomeWideList.SCWListView.generic.GenericSCWListViewBuilder;
import edu.yu.einstein.genplay.dataStructure.list.chromosomeWideList.SCWListView.mask.MaskListViewBuilder;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.ListOfListViewBuilder;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.SCWList.SimpleSCWList.SimpleSCWList;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.SCWList.binList.BinList;
import edu.yu.einstein.genplay.dataStructure.list.listView.ListView;
import edu.yu.einstein.genplay.dataStructure.list.listView.ListViewBuilder;
import edu.yu.einstein.genplay.dataStructure.scoredChromosomeWindow.ScoredChromosomeWindow;
import edu.yu.einstein.genplay.exception.exceptions.InvalidChromosomeException;
import edu.yu.einstein.genplay.exception.exceptions.ObjectAlreadyBuiltException;
/**
* Builder that creates {@link SCWList} objects.
* @author Julien Lajugie
*/
public class SCWListBuilder {
/**
* @param list an object instance of {@link SCWList}.
* @return A {@link ListViewBuilder} that creates ListView objects the same kind of the ones from the specified list
*/
private static final SCWListViewBuilder createSCWLVBuilderPrototype(SCWList list) {
switch (list.getSCWListType()) {
case BIN:
BinList binList = (BinList) list;
return new BinListViewBuilder(binList.getBinSize());
case DENSE:
return new DenseSCWListViewBuilder();
case GENERIC:
return new GenericSCWListViewBuilder();
case MASK:
return new MaskListViewBuilder();
default:
throw new InvalidParameterException("The specified list is not a valid SCWList");
}
}
/** Builder used to build the data of the SCWList */
protected final ListOfListViewBuilder<ScoredChromosomeWindow> builders;
/**
* Creates an instance of {@link SCWListBuilder}
* @param list list used as a model for the result list.
* The result list will be the same type of the specified list and have similar attributes
* (eg: same bin size in the case of BinList)
* @throws CloneNotSupportedException
*/
public SCWListBuilder(SCWList list) throws CloneNotSupportedException {
this(createSCWLVBuilderPrototype(list));
}
/**
* Creates an instance of {@link SCWListBuilder}
* @param builderPrototype prototype of the builder that will create the {@link ListView} objects.
* @throws CloneNotSupportedException
*/
public SCWListBuilder(SCWListViewBuilder builderPrototype) throws CloneNotSupportedException {
super();
builders = new ListOfListViewBuilder<ScoredChromosomeWindow>(builderPrototype);
}
/**
* Adds an element to the {@link SCWList} to be built.
* @param chromosome chromosome of the element to add
* @param start start position of the window to add
* @param stop stop position of the window to add
* @param score score of the window to add
* @throws InvalidChromosomeException if the chromosome is not valid
* @throws ObjectAlreadyBuiltException if the SCWList has already been created
*/
public void addElementToBuild(Chromosome chromosome, int start, int stop, float score) throws InvalidChromosomeException, ObjectAlreadyBuiltException {
SCWListViewBuilder scwLVB = (SCWListViewBuilder) builders.getBuilder(chromosome);
scwLVB.addElementToBuild(start, stop, score);
}
/**
* Adds an element to the {@link SCWList} to be built.
* @param chromosome chromosome of the element to add
* @param element element to add to the SCWList to be built
* @throws InvalidChromosomeException if the chromosome is not valid
* @throws ObjectAlreadyBuiltException if the SCWList has already been created
*/
public void addElementToBuild(Chromosome chromosome, ScoredChromosomeWindow element) throws InvalidChromosomeException, ObjectAlreadyBuiltException {
builders.addElementToBuild(chromosome, element);
}
/**
* Creates an instance of {@link SCWList} that can either be an instance of {@link BinList} or of {@link SimpleSCWList} depending
* on the specified {@link ListView} objects
* @return An instance of {@link ScoredChromosomeWindow}
* @throws ExecutionException
* @throws InterruptedException
* @throws InvalidParameterException
* @throws CloneNotSupportedException
* @throws Exception
*/
private final SCWList createSCWList(List<ListView<ScoredChromosomeWindow>> data) throws InvalidParameterException, InterruptedException, ExecutionException, CloneNotSupportedException {
if ((data == null) || data.isEmpty()) {
return null;
}
if (data.get(0) instanceof BinListView) {
return new BinList(data);
} else {
return new SimpleSCWList(data);
}
}
/**
* @return the list of {@link ListView} objects created by this builder
* Note: the {@link #getSCWList()} method can be used to retrieve a {@link SCWList}
* object instead.
*/
public List<ListView<ScoredChromosomeWindow>> getListOfListViews() {
return builders.getGenomicList();
}
/**
* @return A SCWList containing the items added using the {@link #addElementToBuild(Chromosome, ScoredChromosomeWindow)}.<br>
* The type of the SCWList will be the same as the one from the list specified in the {@link #SCWListBuilder(SCWList)} constructor.
* @throws ExecutionException
* @throws InterruptedException
* @throws InvalidParameterException
* @throws CloneNotSupportedException
*/
public SCWList getSCWList() throws InvalidParameterException, InterruptedException, ExecutionException, CloneNotSupportedException {
SCWList list = createSCWList(getListOfListViews());
return list;
}
}