Package org.biopax.paxtools.util

Class BiopaxSafeSet<E extends BioPAXElement>

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractSet<E>

org.biopax.paxtools.util.BiopaxSafeSet<E>

All Implemented Interfaces:

Serializable, Iterable<E>, Collection<E>, Set<E>

public class BiopaxSafeSet<E extends BioPAXElement>
extends AbstractSet<E>
implements Serializable

A thread-safe Set of BioPAX objects that also prevents adding several elements having the same URI. This is backed by an internal Map (more memory but faster ~O(1) add/contains/remove operations).

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
BiopaxSafeSet()

Method Summary

Modifier and Type	Method	Description
boolean	add(E bpe)	Adds a new element to the collection unless it is null, wrong type, or URI is blank, or already contains an element with the same URI and model interface.
boolean	contains(Object o)	#
E	get(String uri)	Gets a BioPAX element by URI.
Iterator<E>	iterator()
boolean	remove(Object o)	#
int	size()

Methods inherited from class java.util.AbstractSet

equals, hashCode, removeAll

Methods inherited from class java.util.AbstractCollection

addAll, clear, containsAll, isEmpty, retainAll, toArray, toArray, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream, toArray

Methods inherited from interface java.lang.Iterable

forEach

Methods inherited from interface java.util.Set

addAll, clear, containsAll, isEmpty, retainAll, spliterator, toArray, toArray

Constructor Details

BiopaxSafeSet

public BiopaxSafeSet()

Method Details

iterator

public Iterator<E> iterator()

Specified by:

iterator in interface Collection<E extends BioPAXElement>

Specified by:

iterator in interface Iterable<E extends BioPAXElement>

Specified by:

iterator in interface Set<E extends BioPAXElement>

Specified by:

iterator in class AbstractCollection<E extends BioPAXElement>

size

public int size()

Specified by:

size in interface Collection<E extends BioPAXElement>

Specified by:

size in interface Set<E extends BioPAXElement>

Specified by:

size in class AbstractCollection<E extends BioPAXElement>

add

public boolean add(E bpe)

Adds a new element to the collection unless it is null, wrong type, or URI is blank, or already contains an element with the same URI and model interface. #

Specified by:

add in interface Collection<E extends BioPAXElement>

Specified by:

add in interface Set<E extends BioPAXElement>

Overrides:

add in class AbstractCollection<E extends BioPAXElement>

Parameters:

bpe - biopax object

Returns:

true when the element was actually added to the set

Throws:

NullPointerException - when bpe or uri is null

contains

public boolean contains(Object o)

#

Specified by:

contains in interface Collection<E extends BioPAXElement>

Specified by:

contains in interface Set<E extends BioPAXElement>

Overrides:

contains in class AbstractCollection<E extends BioPAXElement>

Throws:

NullPointerException - when o or o.uri is null

ClassCastException - when the o is not a BioPAX element

remove

public boolean remove(Object o)

#

Specified by:

remove in interface Collection<E extends BioPAXElement>

Specified by:

remove in interface Set<E extends BioPAXElement>

Overrides:

remove in class AbstractCollection<E extends BioPAXElement>

Throws:

NullPointerException - when o or o.uri is null

ClassCastException - when the o is not a BioPAX element

get

public E get(String uri)

Gets a BioPAX element by URI.

Parameters:

uri - absolute URI of a BioPAX individual

Returns:

BioPAX object or null