net.sf.octet.collection
Class BasicAtomPairCollection

java.lang.Object
  net.sf.octet.collection.BasicAtomPairCollection

All Implemented Interfaces:

AtomPairCollection

public class BasicAtomPairCollection

extends java.lang.Object

implements AtomPairCollection

A default implementation of the AtomPairCollection interface backed by an ArraySequence.

Author:

Richard Apodaca

Constructor Summary

BasicAtomPairCollection()
Constructs an empty, fully functional BasicAtomPairCollection.

BasicAtomPairCollection(AtomPair[] pairs)
Constructs a BasicAtomPairCollection from the elements contained in pairs.

BasicAtomPairCollection(java.util.Collection pairs)
Constructs a BasicAtomPairCollection from the elements contained in pairs.

Method Summary

boolean	containsAtomPair(Atom source, Atom target) Returns true if an AtomPair connecting source and target is contained in this collection.
boolean	containsAtomPair(AtomPair pair) Returns true if an AtomPair matching pair is contained in this collection.
int	countAtomPairs() Returns the number of AtomPairs contained in this collection.
AtomPair	getAtomPair(Atom source, Atom target) Returns an AtomPair containing the specified source and target Atoms.
AtomPair	getAtomPair(int index) Returns the AtomPair corresponding to the specified integer index.
int	getAtomPairIndex(AtomPair pair) Returns the index of the specified AtomPair.
AtomPairIterator	iterateAtomPairs() Returns an iterator over all AtomPairs in this collection.
AtomPair[]	toAtomPairArray() Returns a copy of the atom pairs contained in this collection as an array.

Methods inherited from class java.lang.Object

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

Constructor Detail

BasicAtomPairCollection

public BasicAtomPairCollection()

Constructs an empty, fully functional BasicAtomPairCollection.

BasicAtomPairCollection

public BasicAtomPairCollection(java.util.Collection pairs)

Constructs a BasicAtomPairCollection from the elements contained in pairs.

Parameters:

pairs - the collection from which to get AtomPairs

Throws:

java.lang.IllegalArgumentException - if pairs contains Objects that do not implement AtomPair

java.lang.NullPointerException - if pairs contains null

BasicAtomPairCollection

public BasicAtomPairCollection(AtomPair[] pairs)

Constructs a BasicAtomPairCollection from the elements contained in pairs.

Parameters:

pairs - the array from which to get AtomPairs

Throws:

java.lang.IllegalArgumentException - if pairs contains Objects that do not implement AtomPair

java.lang.NullPointerException - if pairs contains null

Method Detail

containsAtomPair

public boolean containsAtomPair(AtomPair pair)

Description copied from interface: AtomPairCollection

Returns true if an AtomPair matching pair is contained in this collection.

Specified by:

containsAtomPair in interface AtomPairCollection

Parameters:

pair - the AtomPair to search for

Returns:

true if found, false otherwise

containsAtomPair

public boolean containsAtomPair(Atom source,
                                Atom target)

Description copied from interface: AtomPairCollection

Returns true if an AtomPair connecting source and target is contained in this collection.

Specified by:

containsAtomPair in interface AtomPairCollection

Parameters:

source - the source atom

target - the target atom

Returns:

true if the atom pair exists, false otherwise

getAtomPair

public AtomPair getAtomPair(Atom source,
                            Atom target)

Description copied from interface: AtomPairCollection

Returns an AtomPair containing the specified source and target Atoms. If no such pair is found, null is returned.

Specified by:

getAtomPair in interface AtomPairCollection

Parameters:

source - the source atom

target - the target atom

Returns:

the matching AtomPair

countAtomPairs

public int countAtomPairs()

Description copied from interface: AtomPairCollection

Returns the number of AtomPairs contained in this collection.

Specified by:

countAtomPairs in interface AtomPairCollection

Returns:

the number of AtomPairs contained in this collection.

iterateAtomPairs

public AtomPairIterator iterateAtomPairs()

Description copied from interface: AtomPairCollection

Returns an iterator over all AtomPairs in this collection.

Specified by:

iterateAtomPairs in interface AtomPairCollection

Returns:

an iterator over all AtomPairs in this collection

getAtomPair

public AtomPair getAtomPair(int index)

Description copied from interface: AtomPairCollection

Returns the AtomPair corresponding to the specified integer index.

Specified by:

getAtomPair in interface AtomPairCollection

Parameters:

index - the index to search for

Returns:

the AtomPair at the specified index

getAtomPairIndex

public int getAtomPairIndex(AtomPair pair)

Description copied from interface: AtomPairCollection

Returns the index of the specified AtomPair.

Specified by:

getAtomPairIndex in interface AtomPairCollection

Parameters:

pair - the AtomPair to search for

Returns:

the index of the AtomPair

toAtomPairArray

public AtomPair[] toAtomPairArray()

Description copied from interface: AtomPairCollection

Returns a copy of the atom pairs contained in this collection as an array. The resulting array may be modified without changing the state of this collection.

Specified by:

toAtomPairArray in interface AtomPairCollection

Returns:

a copy of the atom pair array for this collection