Package htsjdk.samtools.util

Class IntervalTreeMap<T>

java.lang.Object

java.util.AbstractMap<Interval,T>

htsjdk.samtools.util.IntervalTreeMap<T>

All Implemented Interfaces:

Map<Interval,T>

public class IntervalTreeMap<T>
extends AbstractMap<Interval,T>

Utility class that implements an interval map. This class functions as a java map but also supports efficient interval overlap queries.

Nested Class Summary

Nested classes/interfaces inherited from class java.util.AbstractMap

AbstractMap.SimpleEntry<K extends Object,V extends Object>, AbstractMap.SimpleImmutableEntry<K extends Object,V extends Object>

Nested classes/interfaces inherited from interface java.util.Map

Map.Entry<K extends Object,V extends Object>

Constructor Summary

Constructors

Constructor	Description
IntervalTreeMap()
IntervalTreeMap(Map<? extends Interval,? extends T> map)

Method Summary

Modifier and Type	Method	Description
void	clear()
boolean	containsContained(Locatable key)	Test if this contains an object that is contained by 'key'
boolean	containsKey(Interval key)
boolean	containsKey(Object object)
boolean	containsOverlapping(Locatable key)	Test overlapping interval
IntervalTree<T>	debugGetTree(String sequence)
Set<Map.Entry<Interval,T>>	entrySet()
boolean	equals(Object o)
T	get(Interval key)
T	get(Object object)
Collection<T>	getContained(Locatable key)
Collection<T>	getOverlapping(Locatable key)
int	hashCode()
boolean	isEmpty()
T	put(Interval key, T value)
T	remove(Interval key)
T	remove(Object object)
int	size()

Methods inherited from class java.util.AbstractMap

clone, containsValue, keySet, putAll, toString, values

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Map

compute, computeIfAbsent, computeIfPresent, forEach, getOrDefault, merge, putIfAbsent, remove, replace, replace, replaceAll

Constructor Details

IntervalTreeMap

public IntervalTreeMap()

IntervalTreeMap

public IntervalTreeMap(Map<? extends Interval,? extends T> map)

Method Details

debugGetTree

public IntervalTree<T> debugGetTree(String sequence)

clear

public void clear()

Specified by:

clear in interface Map<Interval,T>

Overrides:

clear in class AbstractMap<Interval,T>

containsKey

public boolean containsKey(Object object)

Specified by:

containsKey in interface Map<Interval,T>

Overrides:

containsKey in class AbstractMap<Interval,T>

containsKey

public boolean containsKey(Interval key)

entrySet

public Set<Map.Entry<Interval,T>> entrySet()

Specified by:

entrySet in interface Map<Interval,T>

Specified by:

entrySet in class AbstractMap<Interval,T>

equals

public boolean equals(Object o)

Specified by:

equals in interface Map<Interval,T>

Overrides:

equals in class AbstractMap<Interval,T>

hashCode

public int hashCode()

Specified by:

hashCode in interface Map<Interval,T>

Overrides:

hashCode in class AbstractMap<Interval,T>

get

public T get(Object object)

Specified by:

get in interface Map<Interval,T>

Overrides:

get in class AbstractMap<Interval,T>

get

public T get(Interval key)

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface Map<Interval,T>

Overrides:

isEmpty in class AbstractMap<Interval,T>

put

public T put(Interval key,
 T value)

Specified by:

put in interface Map<Interval,T>

Overrides:

put in class AbstractMap<Interval,T>

remove

public T remove(Object object)

Specified by:

remove in interface Map<Interval,T>

Overrides:

remove in class AbstractMap<Interval,T>

remove

public T remove(Interval key)

size

public int size()

Specified by:

size in interface Map<Interval,T>

Overrides:

size in class AbstractMap<Interval,T>

containsOverlapping

public boolean containsOverlapping(Locatable key)

Test overlapping interval

Parameters:

key - the Locatable

Returns:

true if it contains an object overlapping the interval

getOverlapping

public Collection<T> getOverlapping(Locatable key)

containsContained

public boolean containsContained(Locatable key)

Test if this contains an object that is contained by 'key'

Parameters:

key - the Locatable

Returns:

true if it contains an object is contained by 'key'

getContained

public Collection<T> getContained(Locatable key)