/*******************************************************************************
* 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.dense;
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.ElementAddedOverlapException;
import edu.yu.einstein.genplay.exception.exceptions.ObjectAlreadyBuiltException;
/**
* Implementation of the {@link ListViewBuilder} interface vending
* {@link DenseSCWListView} objects.
* @author Julien Lajugie
*/
public final class DenseSCWListViewBuilder implements ListViewBuilder<ScoredChromosomeWindow>, SCWListViewBuilder {
/** List of the stop positions of the SCWs */
private List<Integer> windowStops;
/** List of the score values of the SCWs */
private List<Float> windowScores;
/**
* Creates an instance of {@link DenseSCWListViewBuilder}
*/
public DenseSCWListViewBuilder() {
windowStops = new PrimitiveList<Integer>(Integer.class);
windowScores = new PrimitiveList<Float>(Float.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 SCW to add
* @param stop stop position of the SCW to add
* @param score score value of the SCW to add
* @throws ObjectAlreadyBuiltException
* @throws ElementAddedNotSortedException If elements are not added in sorted order
* @throws ElementAddedOverlapException If elements added overlaps
*/
@Override
public void addElementToBuild(int start, int stop, float score)
throws ObjectAlreadyBuiltException, ElementAddedNotSortedException, ElementAddedOverlapException {
if (windowStops == null) {
throw new ObjectAlreadyBuiltException();
}
if (windowStops.size() > 0) {
int lastElementIndex = windowStops.size() -1;
int lastStart = 1;
if (windowStops.size() > 1) {
lastStart = windowStops.get(lastElementIndex - 1);
}
int lastStop = windowStops.get(lastElementIndex);
if (start < lastStart) {
// case where the elements added are not sorted
throw new ElementAddedNotSortedException();
} else if (start < lastStop) {
// case where the elements added overlap
throw new ElementAddedOverlapException();
}
if (lastStop != start) {
windowStops.add(start);
windowScores.add(0f);
} else if (windowScores.get(lastElementIndex) == score) {
// if the current window and the previous one have the same same score
// and are adjacent we merge them
windowStops.set(lastElementIndex, stop);
return;
}
} else if (start != 1) {
windowStops.add(start);
windowScores.add(0f);
}
windowStops.add(stop);
windowScores.add(score);
}
@Override
public void addElementToBuild(ScoredChromosomeWindow element)
throws ObjectAlreadyBuiltException, ElementAddedNotSortedException, ElementAddedOverlapException {
addElementToBuild(element.getStart(), element.getStop(), element.getScore());
}
@Override
public DenseSCWListViewBuilder clone() {
DenseSCWListViewBuilder clone = new DenseSCWListViewBuilder();
return clone;
}
@Override
public ListView<ScoredChromosomeWindow> getListView() {
trimListsToSize();
ListView<ScoredChromosomeWindow> listView = new DenseSCWListView(windowStops, windowScores);
windowStops = null;
windowScores = null;
return listView;
}
/**
* Trims the lists to their sizes in order to improve the memory usage of the list view
*/
private void trimListsToSize() {
if (windowStops instanceof PrimitiveList<?>) {
((PrimitiveList<?>) windowStops).trimToSize();
}
if (windowScores instanceof PrimitiveList<?>) {
((PrimitiveList<?>) windowScores).trimToSize();
}
}
}