org.broadinstitute.hellbender.utils

Class GenomeLocSortedSet

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractSet<GenomeLoc>

org.broadinstitute.hellbender.utils.GenomeLocSortedSet

All Implemented Interfaces:

java.lang.Iterable<GenomeLoc>, java.util.Collection<GenomeLoc>, java.util.Set<GenomeLoc>

public final class GenomeLocSortedSet
extends java.util.AbstractSet<GenomeLoc>

Class GenomeLocCollection

a set of genome locations. This collection is self sorting, and will merge genome locations that are overlapping. The remove function will also remove a region from the list, if the region to remove is a partial interval of a region in the collection it will remove the region from that element.

Constructor Summary

Constructors

Constructor and Description
GenomeLocSortedSet(GenomeLocParser parser) Create a new, empty GenomeLocSortedSet
GenomeLocSortedSet(GenomeLocParser parser, java.util.Collection<GenomeLoc> l) Create a new GenomeLocSortedSet containing locations l The elements in l can be in any order, and can be overlapping.
GenomeLocSortedSet(GenomeLocParser parser, GenomeLoc e) Create a new GenomeLocSortedSet containing location e

Method Summary

Modifier and Type	Method and Description
boolean	add(GenomeLoc loc) Adds a GenomeLoc to the collection, inserting at the correct sorted position into the set.
boolean	add(GenomeLoc loc, boolean mergeIfIntervalOverlaps) Adds a GenomeLoc to the collection, inserting at the correct sorted position into the set.
boolean	addRegion(GenomeLoc loc) Adds a GenomeLoc to the collection, merging it if it overlaps another region.
long	coveredSize() Return the size, in bp, of the genomic regions by all of the regions in this set
static GenomeLocSortedSet	createSetFromList(GenomeLocParser parser, java.util.List<GenomeLoc> locs) Create a sorted genome location set from a list of GenomeLocs.
static GenomeLocSortedSet	createSetFromSequenceDictionary(htsjdk.samtools.SAMSequenceDictionary dict) create a list of genomic locations, given a reference sequence
GenomeLocParser	getGenomeLocParser() Gets the GenomeLocParser used to create this sorted set.
java.util.List<GenomeLoc>	getOverlapping(GenomeLoc loc) Return a list of intervals overlapping loc
protected java.util.List<GenomeLoc>	getOverlappingFullSearch(GenomeLoc loc) Return a list of intervals overlapping loc by enumerating all locs and testing for overlap Purely for testing purposes -- this is way to slow for any production code
boolean	isEmpty() determine if the collection is empty
java.util.Iterator<GenomeLoc>	iterator() get an iterator over this collection
boolean	overlaps(GenomeLoc loc) Determine if the given loc overlaps any loc in the sorted set
void	remove(GenomeLoc location) a simple removal of an interval contained in this list.
int	size() return the size of the collection
long	sizeBeforeLoc(GenomeLoc loc) Return the number of bps before loc in the sorted set
GenomeLocSortedSet	subtractRegions(GenomeLocSortedSet toRemoveSet)
java.util.List<GenomeLoc>	toList() convert this object to a list
java.lang.String	toString()

Methods inherited from class java.util.AbstractSet

equals, hashCode, removeAll

Methods inherited from class java.util.AbstractCollection

addAll, clear, contains, containsAll, remove, retainAll, toArray, toArray

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Set

addAll, clear, contains, containsAll, remove, retainAll, spliterator, toArray, toArray

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream

Methods inherited from interface java.lang.Iterable

forEach

Constructor Detail

GenomeLocSortedSet

public GenomeLocSortedSet(GenomeLocParser parser)

Create a new, empty GenomeLocSortedSet

Parameters:

parser - a non-null the parser we use to create genome locs

GenomeLocSortedSet

public GenomeLocSortedSet(GenomeLocParser parser,
                          GenomeLoc e)

Create a new GenomeLocSortedSet containing location e

Parameters:

parser - a non-null the parser we use to create genome locs

e - a single genome locs to add to this set

GenomeLocSortedSet

public GenomeLocSortedSet(GenomeLocParser parser,
                          java.util.Collection<GenomeLoc> l)

Create a new GenomeLocSortedSet containing locations l The elements in l can be in any order, and can be overlapping. They will be sorted first and overlapping (but not contiguous) elements will be merged

Parameters:

parser - a non-null the parser we use to create genome locs

l - a collection of genome locs to add to this set

Method Detail

getGenomeLocParser

public GenomeLocParser getGenomeLocParser()

Gets the GenomeLocParser used to create this sorted set.

Returns:

The parser. Will never be null.

iterator

public java.util.Iterator<GenomeLoc> iterator()

get an iterator over this collection

Specified by:

iterator in interface java.lang.Iterable<GenomeLoc>

Specified by:

iterator in interface java.util.Collection<GenomeLoc>

Specified by:

iterator in interface java.util.Set<GenomeLoc>

Specified by:

iterator in class java.util.AbstractCollection<GenomeLoc>

Returns:

an iterator

size

public int size()

return the size of the collection

Specified by:

size in interface java.util.Collection<GenomeLoc>

Specified by:

size in interface java.util.Set<GenomeLoc>

Specified by:

size in class java.util.AbstractCollection<GenomeLoc>

Returns:

the size of the collection

coveredSize

public long coveredSize()

Return the size, in bp, of the genomic regions by all of the regions in this set

Returns:

size in bp of the covered regions

sizeBeforeLoc

public long sizeBeforeLoc(GenomeLoc loc)

Return the number of bps before loc in the sorted set

Parameters:

loc - the location before which we are counting bases

Returns:

the number of base pairs over all previous intervals

isEmpty

public boolean isEmpty()

determine if the collection is empty

Specified by:

isEmpty in interface java.util.Collection<GenomeLoc>

Specified by:

isEmpty in interface java.util.Set<GenomeLoc>

Overrides:

isEmpty in class java.util.AbstractCollection<GenomeLoc>

Returns:

true if we have no elements

overlaps

public boolean overlaps(GenomeLoc loc)

Determine if the given loc overlaps any loc in the sorted set

Parameters:

loc - the location to test

Returns:

trip if the location overlaps any loc

getOverlapping

public java.util.List<GenomeLoc> getOverlapping(GenomeLoc loc)

Return a list of intervals overlapping loc

Parameters:

loc - the location we want overlapping intervals

Returns:

a non-null list of locations that overlap loc

getOverlappingFullSearch

protected java.util.List<GenomeLoc> getOverlappingFullSearch(GenomeLoc loc)

Return a list of intervals overlapping loc by enumerating all locs and testing for overlap Purely for testing purposes -- this is way to slow for any production code

Parameters:

loc - the location we want overlapping intervals

Returns:

a non-null list of locations that overlap loc

add

public boolean add(GenomeLoc loc)

Adds a GenomeLoc to the collection, inserting at the correct sorted position into the set. Throws an exception if the loc overlaps another loc already in the set.

Specified by:

add in interface java.util.Collection<GenomeLoc>

Specified by:

add in interface java.util.Set<GenomeLoc>

Overrides:

add in class java.util.AbstractCollection<GenomeLoc>

Parameters:

loc - the GenomeLoc to add

Returns:

true if the loc was added or false otherwise (if the loc was null)

addRegion

public boolean addRegion(GenomeLoc loc)

Adds a GenomeLoc to the collection, merging it if it overlaps another region. If it's not overlapping then we insert it at the correct sorted position into the set.

Parameters:

loc - the GenomeLoc to add

Returns:

true if the loc was added or false otherwise (if the loc was null)

add

public boolean add(GenomeLoc loc,
                   boolean mergeIfIntervalOverlaps)

Adds a GenomeLoc to the collection, inserting at the correct sorted position into the set.

Parameters:

loc - the GenomeLoc to add

mergeIfIntervalOverlaps - if true we merge the interval if it overlaps another one already in the set, otherwise we throw an exception

Returns:

true if the loc was added or false otherwise (if the loc was null or an exact duplicate)

subtractRegions

public GenomeLocSortedSet subtractRegions(GenomeLocSortedSet toRemoveSet)

remove

public void remove(GenomeLoc location)

a simple removal of an interval contained in this list. The interval must be identical to one in the list (no partial locations or overlapping)

Parameters:

location - the GenomeLoc to remove

createSetFromSequenceDictionary

public static GenomeLocSortedSet createSetFromSequenceDictionary(htsjdk.samtools.SAMSequenceDictionary dict)

create a list of genomic locations, given a reference sequence

Parameters:

dict - the sequence dictionary to create a collection from

Returns:

the GenomeLocSet of all references sequences as GenomeLoc's

createSetFromList

public static GenomeLocSortedSet createSetFromList(GenomeLocParser parser,
                                                   java.util.List<GenomeLoc> locs)

Create a sorted genome location set from a list of GenomeLocs.

Parameters:

locs - the list

Returns:

the sorted genome loc list

toList

public java.util.List<GenomeLoc> toList()

convert this object to a list

Returns:

the lists

toString

public java.lang.String toString()

Overrides:

toString in class java.util.AbstractCollection<GenomeLoc>