/*******************************************************************************
* 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.chromosomeWideList.SCWListView.mask;
import java.util.List;
import edu.yu.einstein.genplay.dataStructure.list.chromosomeWideList.SCWListView.SCWListViewBuilder;
import edu.yu.einstein.genplay.dataStructure.list.listView.ListView;
import edu.yu.einstein.genplay.dataStructure.list.listView.ListViewBuilder;
import edu.yu.einstein.genplay.dataStructure.list.primitiveList.PrimitiveList;
import edu.yu.einstein.genplay.dataStructure.scoredChromosomeWindow.ScoredChromosomeWindow;
import edu.yu.einstein.genplay.exception.exceptions.ElementAddedNotSortedException;
import edu.yu.einstein.genplay.exception.exceptions.ObjectAlreadyBuiltException;
/**
* Implementation of the {@link ListViewBuilder} interface vending
* {@link MaskListView} objects.
* @author Julien Lajugie
*/
public final class MaskListViewBuilder implements ListViewBuilder<ScoredChromosomeWindow>, SCWListViewBuilder {
/** List of the start positions of the masks */
private List<Integer> maskStarts;
/** List of the stop positions of the masks */
private List<Integer> maskStops;
/**
* Creates an instance of {@link MaskListViewBuilder}
*/
public MaskListViewBuilder() {
maskStarts = new PrimitiveList<Integer>(Integer.class);
maskStops = new PrimitiveList<Integer>(Integer.class);
}
/**
* Adds an element to the ListView that will be built.
* To assure that ListView objects are immutable, this method
* will throw an exception if called after the getListView() has been called.
* Checks that the elements are added in start position order.
* @param start start position of the mask to add
* @param stop stop position of the mask to add
* @throws ObjectAlreadyBuiltException
* @throws ElementAddedNotSortedException If elements are not added in sorted order
*/
public void addElementToBuild(int start, int stop)
throws ObjectAlreadyBuiltException, ElementAddedNotSortedException {
if (maskStarts == null) {
throw new ObjectAlreadyBuiltException();
}
if (maskStarts.isEmpty()) {
maskStarts.add(start);
maskStops.add(stop);
} else {
int lastElementIndex = maskStarts.size() -1;
int lastStart = maskStarts.get(lastElementIndex);
int lastStop = maskStops.get(lastElementIndex);
if (start < lastStart) {
// case where the element added are not sorted
throw new ElementAddedNotSortedException();
} else if (start <= lastStop) {
// if the current start is smaller than the previous stop we merge the masks
stop = Math.max(stop, lastStop);
maskStops.set(lastElementIndex, stop);
} else {
maskStarts.add(start);
maskStops.add(stop);
}
}
}
/**
* {@inheritDoc}
* The score parameter is not used.
*/
@Override
public void addElementToBuild(int start, int stop, float score) throws ObjectAlreadyBuiltException {
addElementToBuild(start, stop);
}
@Override
public void addElementToBuild(ScoredChromosomeWindow element)
throws ObjectAlreadyBuiltException, ElementAddedNotSortedException {
addElementToBuild(element.getStart(), element.getStop());
}
/**
* Creates a clone of this {@link MaskListViewBuilder} prototype
* containing no elements.
*/
@Override
public MaskListViewBuilder clone() {
MaskListViewBuilder clone = new MaskListViewBuilder();
return clone;
}
@Override
public ListView<ScoredChromosomeWindow> getListView() {
trimListsToSize();
ListView<ScoredChromosomeWindow> listView = new MaskListView(maskStarts, maskStops);
maskStarts = null;
maskStops = null;
return listView;
}
/**
* Trims the lists to their sizes in order to improve the memory usage of the list view
*/
private void trimListsToSize() {
if (maskStarts instanceof PrimitiveList<?>) {
((PrimitiveList<?>) maskStarts).trimToSize();
}
if (maskStops instanceof PrimitiveList<?>) {
((PrimitiveList<?>) maskStops).trimToSize();
}
}
}