net.sf.octet.collection
Interface AtomPairCollection

All Known Subinterfaces:

AtomGraph, BondingSystem, GammaSequence, Molecule

All Known Implementing Classes:

AtomGraphDecorator, BasicAtomGraph, BasicAtomPairCollection, BasicBondingSystem, BasicGammaSequence, MoleculeDecorator, SimpleBondingSystem

public interface AtomPairCollection

AtomPairCollection represents an immutable group of AtomPairs. Any AtomPair may be present, but null is disallowed. AtomPairs from different Molecules may or may not be present, depending on implementation.

AtomPairCollection places the additional restriction on implementors that all methods are consistent - they can be assumed to return the same results throughout the Object's lifetime.

Author:

Richard Apodaca

See Also:

"Immutable Pattern (Grand98)"

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.

Method Detail

containsAtomPair

public boolean containsAtomPair(AtomPair pair)

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

Parameters:

pair - the AtomPair to search for

Returns:

true if found, false otherwise

containsAtomPair

public boolean containsAtomPair(Atom source,
                                Atom target)

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

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)

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

Parameters:

source - the source atom

target - the target atom

Returns:

the matching AtomPair

Throws:

NoSuchAtomPairException - if no AtomPair connecting source and target could be found

countAtomPairs

public int countAtomPairs()

Returns the number of AtomPairs contained in this collection.

Returns:

the number of AtomPairs contained in this collection.

iterateAtomPairs

public AtomPairIterator iterateAtomPairs()

Returns an iterator over all AtomPairs in this collection.

Returns:

an iterator over all AtomPairs in this collection

getAtomPairIndex

public int getAtomPairIndex(AtomPair pair)

Returns the index of the specified AtomPair.

Parameters:

pair - the AtomPair to search for

Returns:

the index of the AtomPair

getAtomPair

public AtomPair getAtomPair(int index)

Returns the AtomPair corresponding to the specified integer index.

Parameters:

index - the index to search for

Returns:

the AtomPair at the specified index

Throws:

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

toAtomPairArray

public AtomPair[] toAtomPairArray()

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.

Returns:

a copy of the atom pair array for this collection