htsjdk.samtools.util

Class IntervalTreeMap<T>

java.lang.Object

java.util.AbstractMap<Interval,T>

htsjdk.samtools.util.IntervalTreeMap<T>

All Implemented Interfaces:

java.util.Map<Interval,T>

public class IntervalTreeMap<T>
extends java.util.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

java.util.AbstractMap.SimpleEntry<K,V>, java.util.AbstractMap.SimpleImmutableEntry<K,V>

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

java.util.Map.Entry<K,V>

Constructor Summary

Constructors

Constructor and Description
IntervalTreeMap()
IntervalTreeMap(java.util.Map<? extends Interval,? extends T> map)

Method Summary

Methods

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

Constructor Detail

IntervalTreeMap

public IntervalTreeMap()

IntervalTreeMap

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

Method Detail

debugGetTree

public IntervalTree<T> debugGetTree(java.lang.String sequence)

clear

public void clear()

Specified by:

clear in interface java.util.Map<Interval,T>

Overrides:

clear in class java.util.AbstractMap<Interval,T>

containsKey

public boolean containsKey(java.lang.Object object)

Specified by:

containsKey in interface java.util.Map<Interval,T>

Overrides:

containsKey in class java.util.AbstractMap<Interval,T>

containsKey

public boolean containsKey(Interval key)

entrySet

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

Specified by:

entrySet in interface java.util.Map<Interval,T>

Specified by:

entrySet in class java.util.AbstractMap<Interval,T>

equals

public boolean equals(java.lang.Object o)

Specified by:

equals in interface java.util.Map<Interval,T>

Overrides:

equals in class java.util.AbstractMap<Interval,T>

hashCode

public int hashCode()

Specified by:

hashCode in interface java.util.Map<Interval,T>

Overrides:

hashCode in class java.util.AbstractMap<Interval,T>

get

public T get(java.lang.Object object)

Specified by:

get in interface java.util.Map<Interval,T>

Overrides:

get in class java.util.AbstractMap<Interval,T>

get

public T get(Interval key)

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface java.util.Map<Interval,T>

Overrides:

isEmpty in class java.util.AbstractMap<Interval,T>

put

public T put(Interval key,
    T value)

Specified by:

put in interface java.util.Map<Interval,T>

Overrides:

put in class java.util.AbstractMap<Interval,T>

remove

public T remove(java.lang.Object object)

Specified by:

remove in interface java.util.Map<Interval,T>

Overrides:

remove in class java.util.AbstractMap<Interval,T>

remove

public T remove(Interval key)

size

public int size()

Specified by:

size in interface java.util.Map<Interval,T>

Overrides:

size in class java.util.AbstractMap<Interval,T>

containsOverlapping

public boolean containsOverlapping(Interval key)

Test overlapping interval

Parameters:

key - the interval

Returns:

true if it contains an object overlapping the interval

getOverlapping

public java.util.Collection<T> getOverlapping(Interval key)

containsContained

public boolean containsContained(Interval key)

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

Parameters:

key - the interval

Returns:

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

getContained

public java.util.Collection<T> getContained(Interval key)