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,V>, AbstractMap.SimpleImmutableEntry<K,V>

Nested classes/interfaces inherited from interface java.util.Map
Map.Entry<K,V>
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)

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 Details

IntervalTreeMap

IntervalTreeMap

Method Details

debugGetTree

clear

containsKey

containsKey

entrySet

equals

hashCode

get

get

isEmpty

put

remove

remove

size

containsOverlapping

getOverlapping

containsContained

getContained