net.sf.octet.model
Class BasicAtomPair

java.lang.Object
  net.sf.octet.model.BasicAtomPair

All Implemented Interfaces:

AtomPair

public class BasicAtomPair

extends java.lang.Object

implements AtomPair

A default implementation of the AtomPair interface. The equals method does not distinguish between source and target atoms, so BasicAtomPair is suitable for undirected graph representations.

Author:

Richard Apodaca

Constructor Summary

BasicAtomPair(Atom source, Atom target)
Creates a new BasicAtomPair from source and target.

Method Summary

boolean	connects(Atom atom1, Atom atom2) Returns true if the specified atoms are connected by this AtomPair.
boolean	contains(Atom atom) Returns true if the spacified Atom is linked by this AtomPair.
boolean	equals(java.lang.Object object) Returns true if object has the same two atoms as this AtomPair.
Atom	getMate(Atom atom) Returns the mate for the specified atom.
Atom	getSource() Returns the source Atom.
Atom	getTarget() Returns the target Atom.
int	hashCode() Required due to override of Object.equals().

Methods inherited from class java.lang.Object

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

Constructor Detail

BasicAtomPair

public BasicAtomPair(Atom source,
                     Atom target)

Creates a new BasicAtomPair from source and target.

Parameters:

source - the source Atom

target - the target Atom

Throws:

java.lang.IllegalArgumentException - if source and target are equal by Object.equals

Method Detail

getSource

public Atom getSource()

Description copied from interface: AtomPair

Returns the source Atom.

Specified by:

getSource in interface AtomPair

Returns:

the source atom

getTarget

public Atom getTarget()

Description copied from interface: AtomPair

Returns the target Atom.

Specified by:

getTarget in interface AtomPair

Returns:

the target atom

getMate

public Atom getMate(Atom atom)

Description copied from interface: AtomPair

Returns the mate for the specified atom. Returns null if the specified atom is not connected by this Bond.

Specified by:

getMate in interface AtomPair

Parameters:

atom - the atom for which the mate will be returned

Returns:

the mate to the specified atom

contains

public boolean contains(Atom atom)

Description copied from interface: AtomPair

Returns true if the spacified Atom is linked by this AtomPair.

Specified by:

contains in interface AtomPair

Parameters:

atom - the atom to examine

Returns:

true if the atom is linked by this bond, false otherwise

connects

public boolean connects(Atom atom1,
                        Atom atom2)

Description copied from interface: AtomPair

Returns true if the specified atoms are connected by this AtomPair.

Specified by:

connects in interface AtomPair

Parameters:

atom1 - the first atom

atom2 - the second atom

Returns:

true if the two atoms are connected by this AtomPair, false otherwise

equals

public boolean equals(java.lang.Object object)

Returns true if object has the same two atoms as this AtomPair. Returns false otherwise, or if the source and target atoms of object are equal.

Parameters:

object - the Object to compare

Returns:

true if source and target are contained in this AtomPair, false otherwise

hashCode

public int hashCode()

Required due to override of Object.equals(). Currently, invokes super.hashCode().