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/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools.util;
import java.util.AbstractMap;
import java.util.AbstractSet;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.NoSuchElementException;
import java.util.Set;
/**
* Utility class that implements an interval map.
* This class functions as a java map but also supports efficient interval overlap queries.
*
* @author Bob Handsaker
*/
public class IntervalTreeMap
extends AbstractMap
{
private final Map> mSequenceMap = new HashMap>();
private final EntrySet mEntrySet = new EntrySet();
public IntervalTree debugGetTree(final String sequence) {
return mSequenceMap.get(sequence);
}
public IntervalTreeMap() {
}
public IntervalTreeMap(final Map map) {
for (final Map.Entry entry : map.entrySet()) {
put(entry.getKey(), entry.getValue());
}
}
@Override
public void clear() {
mSequenceMap.clear();
}
@Override
public boolean containsKey(final Object object) {
if (!(object instanceof Interval)) {
return false;
}
return containsKey((Interval) object);
}
public boolean containsKey(final Interval key) {
final IntervalTree tree = mSequenceMap.get(key.getContig());
if (tree == null) {
return false;
}
return (tree.find(key.getStart(), key.getEnd()) != null);
}
@Override
public Set> entrySet() {
return mEntrySet;
}
@SuppressWarnings("rawtypes")
public boolean equals(final Object o) {
if (!(o instanceof IntervalTreeMap)) {
return false;
}
return mSequenceMap.equals(((IntervalTreeMap)o).mSequenceMap);
}
public int hashCode() {
return mSequenceMap.hashCode();
}
@Override
public T get(final Object object) {
if (!(object instanceof Interval)) {
return null;
}
return get((Interval) object);
}
public T get(final Interval key) {
final IntervalTree tree = mSequenceMap.get(key.getContig());
if (tree == null) {
return null;
}
final IntervalTree.Node node = tree.find(key.getStart(), key.getEnd());
if (node == null) {
return null;
}
return node.getValue();
}
@Override
public boolean isEmpty() {
for (final IntervalTree tree : mSequenceMap.values()) {
if (tree.size() > 0) {
return false;
}
}
return true;
}
@Override
public T put(final Interval key, final T value) {
IntervalTree tree = mSequenceMap.get(key.getContig());
if (tree == null) {
tree = new IntervalTree();
mSequenceMap.put(key.getContig(), tree);
}
return tree.put(key.getStart(), key.getEnd(), value);
}
@Override
public T remove(final Object object) {
if (!(object instanceof Interval)) {
return null;
}
return remove((Interval)object);
}
public T remove(final Interval key) {
final IntervalTree tree = mSequenceMap.get(key.getContig());
if (tree == null) {
return null;
}
return tree.remove(key.getStart(), key.getEnd());
}
@Override
public int size() {
// Note: We should think about caching the size to avoid having to recompute it.
int size = 0;
for (final IntervalTree tree : mSequenceMap.values()) {
size += tree.size();
}
return size;
}
/**
* Test overlapping interval
* @param key the Locatable
* @return true if it contains an object overlapping the interval
*/
public boolean containsOverlapping(final Locatable key) {
final IntervalTree tree = mSequenceMap.get(key.getContig());
return tree!=null && tree.overlappers(key.getStart(), key.getEnd()).hasNext();
}
public Collection getOverlapping(final Locatable key) {
final List result = new ArrayList();
final IntervalTree tree = mSequenceMap.get(key.getContig());
if (tree != null) {
final Iterator> iterator = tree.overlappers(key.getStart(), key.getEnd());
while (iterator.hasNext()) {
result.add(iterator.next().getValue());
}
}
return result;
}
/**
* Test if this contains an object that is contained by 'key'
* @param key the Locatable
* @return true if it contains an object is contained by 'key'
*/
public boolean containsContained(final Locatable key) {
final IntervalTree tree = mSequenceMap.get(key.getContig());
if(tree==null) return false;
final Iterator> iterator = tree.overlappers(key.getStart(), key.getEnd());
while (iterator.hasNext()) {
final IntervalTree.Node node = iterator.next();
if (node.getStart() >= key.getStart() && node.getEnd() <= key.getEnd()) {
return true;
}
}
return false;
}
public Collection getContained(final Locatable key) {
final List result = new ArrayList();
final IntervalTree tree = mSequenceMap.get(key.getContig());
if (tree != null) {
final Iterator> iterator = tree.overlappers(key.getStart(), key.getEnd());
while (iterator.hasNext()) {
final IntervalTree.Node node = iterator.next();
if (node.getStart() >= key.getStart() && node.getEnd() <= key.getEnd()) {
result.add(node.getValue());
}
}
}
return result;
}
private class EntrySet
extends AbstractSet> {
@Override
public void clear() {
IntervalTreeMap.this.clear();
}
public boolean contains(final Map.Entry entry) {
if (entry == null) {
return false;
}
return entry.getValue().equals(IntervalTreeMap.this.get(entry.getKey()));
}
@Override
public boolean isEmpty() {
return IntervalTreeMap.this.isEmpty();
}
@Override
public Iterator> iterator() {
return new EntryIterator();
}
@Override
@SuppressWarnings("unchecked")
public boolean remove(final Object object) {
// Note: Could not figure out how to eliminate the unchecked cast.
if (!(object instanceof Map.Entry)) {
return false;
}
return remove((Map.Entry)object);
}
public boolean remove(final Map.Entry entry) {
if (this.contains(entry)) {
IntervalTreeMap.this.remove(entry.getKey());
return true;
} else {
return false;
}
}
@Override
public int size() {
return IntervalTreeMap.this.size();
}
}
private class EntryIterator
implements Iterator> {
private String mSequence = null;
private Iterator mSequenceIterator = null;
private Iterator> mTreeIterator = null;
EntryIterator() {
mSequenceIterator = mSequenceMap.keySet().iterator();
advanceSequence();
}
@Override
public boolean hasNext() {
return (mTreeIterator != null && mTreeIterator.hasNext());
}
@Override
public Map.Entry next() {
if (!hasNext()) {
throw new NoSuchElementException("Iterator exhausted");
}
final IntervalTree.Node node = mTreeIterator.next();
final String sequence = mSequence;
if (!mTreeIterator.hasNext()) {
advanceSequence();
}
final Interval key = new Interval(sequence, node.getStart(), node.getEnd());
final T value = node.getValue();
return new MapEntry(key, value);
}
@Override
public void remove() {
if (mTreeIterator == null) {
throw new IllegalStateException("Iterator.next() has not been called");
}
mTreeIterator.remove();
}
private void advanceSequence() {
while (mSequenceIterator.hasNext()) {
mSequence = mSequenceIterator.next();
mTreeIterator = mSequenceMap.get(mSequence).iterator();
if (mTreeIterator.hasNext()) {
break;
}
}
}
}
private class MapEntry
implements Map.Entry {
private final Interval mKey;
private T mValue;
MapEntry(final Interval key, final T value) {
mKey = key;
mValue = value;
}
@Override
public Interval getKey() {
return mKey;
}
@Override
public T getValue() {
return mValue;
}
@Override
public T setValue(final T value) {
mValue = value;
return IntervalTreeMap.this.put(mKey, mValue);
}
}
}
