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

All Methods Instance Methods Concrete Methods
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 Detail
  - IntervalTreeMap
```
public IntervalTreeMap()
```
  - IntervalTreeMap
```
public IntervalTreeMap(Map<? extends Interval,? extends T> map)
```
- Method Detail
  - 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)
```

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

Class IntervalTreeMap<T>

Nested Class Summary

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

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

Constructor Summary

Method Summary

Methods inherited from class java.util.AbstractMap

Methods inherited from class java.lang.Object

Methods inherited from interface java.util.Map

Constructor Detail

IntervalTreeMap

IntervalTreeMap

Method Detail

debugGetTree

clear

containsKey

containsKey

entrySet

equals

hashCode

get

get

isEmpty

put

remove

remove

size

containsOverlapping

getOverlapping

containsContained

getContained