net.sf.octet.collection
Class BasicNucleusCollection

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

All Implemented Interfaces:

NucleusCollection

public class BasicNucleusCollection

extends java.lang.Object

implements NucleusCollection

A default implementation of the NucleusCollection interface backed by a ArraySequence.

Author:

Richard Apodaca

Constructor Summary

BasicNucleusCollection()
Constructs an empty BasicNucleusCollection.

BasicNucleusCollection(java.util.Collection nuclei)
Constructs a BasicNucleusCollection from the elements contained in nuclei.

BasicNucleusCollection(Nucleus[] nuclei)
Constructs a BasicNucleusCollection from the elements contained in nuclei.

Method Summary

boolean	containsNucleus(Nucleus nucleus) Returns true if the specified Nucleus is contained in this collection, and false otherwise.
int	countNuclei() Returns the number of Nuclei contained in this collection.
Nucleus	getNucleus(int index) Returns the isotope located at the specified zero-based index.
int	getNucleusIndex(Nucleus nucleus) Returns the zero-based index of the specified Nucleus.
NucleusIterator	iterateNuclei() Returns an iterator over all Nuclei in this collection.
Nucleus[]	toNucleusArray() Returns a copy of the Nuclei 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

BasicNucleusCollection

public BasicNucleusCollection()

Constructs an empty BasicNucleusCollection.

BasicNucleusCollection

public BasicNucleusCollection(java.util.Collection nuclei)

Constructs a BasicNucleusCollection from the elements contained in nuclei.

Parameters:

nuclei - the collection from which to get Nuclei

Throws:

java.lang.IllegalArgumentException - if nuclei contains Objects that do not implement Nucleus

java.lang.NullPointerException - if nuclei contains null

BasicNucleusCollection

public BasicNucleusCollection(Nucleus[] nuclei)

Constructs a BasicNucleusCollection from the elements contained in nuclei.

Parameters:

nuclei - the array from which to get Nuclei

Throws:

java.lang.IllegalArgumentException - if nuclei contains Objects that do not implement Nucleus

java.lang.NullPointerException - if nuclei contains null

Method Detail

containsNucleus

public boolean containsNucleus(Nucleus nucleus)

Description copied from interface: NucleusCollection

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

Specified by:

containsNucleus in interface NucleusCollection

Parameters:

nucleus - the Nucleus

Returns:

true if contained, false otherwise

countNuclei

public int countNuclei()

Description copied from interface: NucleusCollection

Returns the number of Nuclei contained in this collection.

Specified by:

countNuclei in interface NucleusCollection

Returns:

the number of Nuclei in this collection

getNucleusIndex

public int getNucleusIndex(Nucleus nucleus)

Description copied from interface: NucleusCollection

Returns the zero-based index of the specified Nucleus.

Specified by:

getNucleusIndex in interface NucleusCollection

Parameters:

nucleus - the nucleus

Returns:

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

getNucleus

public Nucleus getNucleus(int index)

Description copied from interface: NucleusCollection

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

Specified by:

getNucleus in interface NucleusCollection

Parameters:

index - the index

Returns:

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

iterateNuclei

public NucleusIterator iterateNuclei()

Description copied from interface: NucleusCollection

Returns an iterator over all Nuclei in this collection.

Specified by:

iterateNuclei in interface NucleusCollection

Returns:

an iterator over all Nuclei in this collection

toNucleusArray

public Nucleus[] toNucleusArray()

Description copied from interface: NucleusCollection

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

Specified by:

toNucleusArray in interface NucleusCollection

Returns:

a copy of the Nucleus array for this collection