htsjdk.samtools.util

Class OverlapDetector<T>

java.lang.Object

htsjdk.samtools.util.OverlapDetector<T>

public class OverlapDetector<T>
extends java.lang.Object

Utility class to efficiently do in memory overlap detection between a large set of mapping like objects, and one or more candidate mappings.

Constructor Summary

Constructors

Constructor and Description
OverlapDetector(int lhsBuffer, int rhsBuffer) Constructs an overlap detector.

Method Summary

Methods

Modifier and Type	Method and Description
void	addAll(java.util.List<T> objects, java.util.List<Interval> intervals) Adds all items to the overlap detector.
void	addLhs(T object, Interval interval) Adds a mapping to the set of mappings against which to match candidates.
java.util.Collection<T>	getAll() Gets all the objects that could be returned by the overlap detector.
java.util.Collection<T>	getOverlaps(Interval rhs) Gets the collection of objects that overlap the provided mapping.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

OverlapDetector

public OverlapDetector(int lhsBuffer,
               int rhsBuffer)

Constructs an overlap detector.

Parameters:

lhsBuffer - the amount by which to "trim" coordinates of mappings on the left hand side when calculating overlaps

rhsBuffer - the amount by which to "trim" coordinates of mappings on the right hand side when calculating overlaps

Method Detail

addLhs

public void addLhs(T object,
          Interval interval)

Adds a mapping to the set of mappings against which to match candidates.

addAll

public void addAll(java.util.List<T> objects,
          java.util.List<Interval> intervals)

Adds all items to the overlap detector.

getAll

public java.util.Collection<T> getAll()

Gets all the objects that could be returned by the overlap detector.

getOverlaps

public java.util.Collection<T> getOverlaps(Interval rhs)

Gets the collection of objects that overlap the provided mapping.