net.sf.octet.model
Class BasicAtomGraph

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

All Implemented Interfaces:

AtomCollection, AtomGraph, AtomPairCollection

public class BasicAtomGraph

extends java.lang.Object

implements AtomGraph

A default implementation of the AtomGraph interface that is suitable for representing Molecule subgraphs.

Author:

Richard Apodaca

Constructor Summary

BasicAtomGraph()
Constructs an empty BasicAtomGraph.

BasicAtomGraph(AtomCollection atoms, AtomPairCollection pairs)
Constructs a BasicAtomGraph from atoms and pairs.

BasicAtomGraph(AtomPairCollection pairs)
Constructs a BasicAtomGraph from the specified AtomPairCollection.

Method Summary

boolean	containsAtom(Atom atom) Returns true if the specified Atom is contained in this collection, and false otherwise.
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.
int	countAtoms() Returns the number of Atoms contained in this atom collection.
int	countNeighbors(Atom atom) Returns the number of Atoms connected to atom in the context of this AtomGraph.
boolean	equals(java.lang.Object object) Overrides Object.equals().
Atom	getAtom(int index) Returns the Atom located at the specified zero-based index.
int	getAtomIndex(Atom atom) Returns the zero-based index of the specified Atom.
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.
int	hashCode() Overrides Object.hashCode() due to override of Object.equals() .
AtomPairIterator	iterateAtomPairs() Returns an iterator over all AtomPairs in this collection.
AtomIterator	iterateAtoms() Returns an iterator over all Atoms in this collection.
AtomIterator	iterateNeighbors(Atom atom) Returns an iterator over all neighbors of atom in the context of this AtomGraph.
Atom[]	toAtomArray() Returns a copy of the Atoms contained in this collection as an array.
AtomPair[]	toAtomPairArray() Returns a copy of the atom pairs contained in this collection as an array.

Methods inherited from class java.lang.Object

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

Constructor Detail

BasicAtomGraph

public BasicAtomGraph()

Constructs an empty BasicAtomGraph.

BasicAtomGraph

public BasicAtomGraph(AtomPairCollection pairs)

Constructs a BasicAtomGraph from the specified AtomPairCollection. Atoms will be induced from pairs.

Parameters:

pairs - the set of AtomPairs

Throws:

java.lang.IllegalArgumentException - if pairs contains duplicate AtomPairs

BasicAtomGraph

public BasicAtomGraph(AtomCollection atoms,
                      AtomPairCollection pairs)

Constructs a BasicAtomGraph from atoms and pairs. Verifies that the Atoms implicit in pairs are all present in atoms. Preserves the indexing of atoms and pairs .

Parameters:

atoms - the Atom collection

pairs - the AtomPair collection

Throws:

java.lang.IllegalArgumentException - if atoms and pairs are not compatible

Method Detail

iterateNeighbors

public AtomIterator iterateNeighbors(Atom atom)

Description copied from interface: AtomGraph

Returns an iterator over all neighbors of atom in the context of this AtomGraph. This iterator may contain only a subset of the Atoms returned by atom.iterateNeighbors(), depending on the nature of this AtomGraph.

Specified by:

iterateNeighbors in interface AtomGraph

Parameters:

atom - the Atom to examine

Returns:

an iterator over all neighbors of atom

countNeighbors

public int countNeighbors(Atom atom)

Description copied from interface: AtomGraph

Returns the number of Atoms connected to atom in the context of this AtomGraph. This value will be less than or equal to the value returned by atom.countNeighbors().

Specified by:

countNeighbors in interface AtomGraph

Parameters:

atom - the Atom to examine

Returns:

the number of neighbors of atom

containsAtom

public boolean containsAtom(Atom atom)

Description copied from interface: AtomCollection

Returns true if the specified Atom is contained in this collection, and false otherwise.

Specified by:

containsAtom in interface AtomCollection

Parameters:

atom - the Atom

Returns:

true if contained, false otherwise

countAtoms

public int countAtoms()

Description copied from interface: AtomCollection

Returns the number of Atoms contained in this atom collection.

Specified by:

countAtoms in interface AtomCollection

Returns:

the number of atoms in this collection

getAtomIndex

public int getAtomIndex(Atom atom)

Description copied from interface: AtomCollection

Returns the zero-based index of the specified Atom.

Specified by:

getAtomIndex in interface AtomCollection

Parameters:

atom - the atom

Returns:

the index of the atom, or -1 if this collection does not contain atom

getAtom

public Atom getAtom(int index)

Description copied from interface: AtomCollection

Returns the Atom located at the specified zero-based index.

Specified by:

getAtom in interface AtomCollection

Parameters:

index - the index

Returns:

the Atom at index, or null if the index is invalid

iterateAtoms

public AtomIterator iterateAtoms()

Description copied from interface: AtomCollection

Returns an iterator over all Atoms in this collection.

Specified by:

iterateAtoms in interface AtomCollection

Returns:

an iterator over all Atoms in this collection

toAtomArray

public Atom[] toAtomArray()

Description copied from interface: AtomCollection

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

Specified by:

toAtomArray in interface AtomCollection

Returns:

a copy of the Atom array for this collection

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

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

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

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

equals

public boolean equals(java.lang.Object object)

Overrides Object.equals().

hashCode

public int hashCode()

Overrides Object.hashCode() due to override of Object.equals() .