net.sf.octet.collection
Interface AtomCollection

All Known Subinterfaces:

AtomGraph, BondingSystem, GammaSequence, Molecule

All Known Implementing Classes:

AtomGraphDecorator, BasicAtomCollection, BasicAtomGraph, BasicBondingSystem, BasicGammaSequence, MoleculeDecorator, SimpleBondingSystem

public interface AtomCollection

AtomCollection represents an immutable group of Atoms. Any Atom may be present, but null is disallowed. Atoms from different Molecules may or not be present, depending on implementation.

AtomCollection places the additional restriction on implementors that all methods are consistent - they can be assumed to return the same results throughout the lifetime of the AtomCollection.

Author:

Richard Apodaca

See Also:

"Immutable Pattern (Grand98)"

Method Summary

boolean	containsAtom(Atom atom) Returns true if the specified Atom is contained in this collection, and false otherwise.
int	countAtoms() Returns the number of Atoms contained in this atom collection.
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.
AtomIterator	iterateAtoms() Returns an iterator over all Atoms in this collection.
Atom[]	toAtomArray() Returns a copy of the Atoms contained in this collection as an array.

Method Detail

containsAtom

public boolean containsAtom(Atom atom)

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

Parameters:

atom - the Atom

Returns:

true if contained, false otherwise

countAtoms

public int countAtoms()

Returns the number of Atoms contained in this atom collection.

Returns:

the number of atoms in this collection

getAtomIndex

public int getAtomIndex(Atom atom)

Returns the zero-based index of the specified Atom.

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)

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

Parameters:

index - the index

Returns:

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

Throws:

java.lang.IndexOutOfBoundsException - if index is less than zero or greater than or equal to the number of Atoms

iterateAtoms

public AtomIterator iterateAtoms()

Returns an iterator over all Atoms in this collection.

Returns:

an iterator over all Atoms in this collection

toAtomArray

public Atom[] toAtomArray()

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.

Returns:

a copy of the Atom array for this collection