net.sf.octet.collection
Class BasicPaddleWheelCollection

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

All Implemented Interfaces:

PaddleWheelCollection

public class BasicPaddleWheelCollection

extends java.lang.Object

implements PaddleWheelCollection

A default implementation of the PaddleWheelCollection interface backed by an ArraySequence

Author:

Richard Apodaca

Constructor Summary

BasicPaddleWheelCollection()
Constructs an empty, fully functional BasicPaddleWheelCollection.

BasicPaddleWheelCollection(java.util.Collection wheels)
Constructs a BasicPaddleWheelCollection from the elements contained in wheels.

BasicPaddleWheelCollection(PaddleWheel[] wheels)
Constructs a BasicPaddleWheelCollection from the elements contained in wheels.

Method Summary

boolean	containsPaddleWheel(Atom source, Atom target) Returns true if a PaddleWheel can be found containing an axis with source as its source and target as its target.
boolean	containsPaddleWheel(PaddleWheel paddleWheel) Returns true if the specified PaddleWheel is contained in this collection, and false otherwise.
int	countPaddleWheels() Returns the number of PaddleWheels contained in this collection.
PaddleWheel	getPaddleWheel(Atom source, Atom target) Returns the PaddleWheel containing an axis that consists of source and target.
PaddleWheel	getPaddleWheel(int index) Returns the PaddleWheel located at the specified zero-based index.
int	getPaddleWheelIndex(PaddleWheel paddleWheel) Returns the zero-based index of the specified PaddleWheel.
PaddleWheelIterator	iteratePaddleWheels() Returns an iterator over all PaddleWheels in this collection.
PaddleWheel[]	toPaddleWheelArray() Returns a copy of the PaddleWheels 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

BasicPaddleWheelCollection

public BasicPaddleWheelCollection()

Constructs an empty, fully functional BasicPaddleWheelCollection.

BasicPaddleWheelCollection

public BasicPaddleWheelCollection(java.util.Collection wheels)

Constructs a BasicPaddleWheelCollection from the elements contained in wheels.

Parameters:

wheels - the collection from which to get PaddleWheels

Throws:

java.lang.IllegalArgumentException - if wheels contains Objects that do not implement PaddleWheel

java.lang.NullPointerException - if wheels contains null

BasicPaddleWheelCollection

public BasicPaddleWheelCollection(PaddleWheel[] wheels)

Constructs a BasicPaddleWheelCollection from the elements contained in wheels.

Parameters:

wheels - the array from which to get PaddleWheels

Throws:

java.lang.IllegalArgumentException - if wheels contains Objects that do not implement PaddleWheel

java.lang.NullPointerException - if wheels contains null

Method Detail

containsPaddleWheel

public boolean containsPaddleWheel(PaddleWheel paddleWheel)

Description copied from interface: PaddleWheelCollection

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

Specified by:

containsPaddleWheel in interface PaddleWheelCollection

Parameters:

paddleWheel - the PaddleWheel

Returns:

true if contained, false otherwise

countPaddleWheels

public int countPaddleWheels()

Description copied from interface: PaddleWheelCollection

Returns the number of PaddleWheels contained in this collection.

Specified by:

countPaddleWheels in interface PaddleWheelCollection

Returns:

the number of PaddleWheels in this collection

getPaddleWheelIndex

public int getPaddleWheelIndex(PaddleWheel paddleWheel)

Description copied from interface: PaddleWheelCollection

Returns the zero-based index of the specified PaddleWheel.

Specified by:

getPaddleWheelIndex in interface PaddleWheelCollection

Parameters:

paddleWheel - the PaddleWheel

Returns:

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

getPaddleWheel

public PaddleWheel getPaddleWheel(int index)

Description copied from interface: PaddleWheelCollection

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

Specified by:

getPaddleWheel in interface PaddleWheelCollection

Parameters:

index - the index

Returns:

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

iteratePaddleWheels

public PaddleWheelIterator iteratePaddleWheels()

Description copied from interface: PaddleWheelCollection

Returns an iterator over all PaddleWheels in this collection.

Specified by:

iteratePaddleWheels in interface PaddleWheelCollection

Returns:

an iterator over all PaddleWheels in this collection

toPaddleWheelArray

public PaddleWheel[] toPaddleWheelArray()

Description copied from interface: PaddleWheelCollection

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

Specified by:

toPaddleWheelArray in interface PaddleWheelCollection

Returns:

a copy of the PaddleWheel array for this collection

containsPaddleWheel

public boolean containsPaddleWheel(Atom source,
                                   Atom target)

Description copied from interface: PaddleWheelCollection

Returns true if a PaddleWheel can be found containing an axis with source as its source and target as its target.

Specified by:

containsPaddleWheel in interface PaddleWheelCollection

Parameters:

source - the source Atom of the axis

target - the target Atom of the axis

Returns:

true if the PaddleWheel could be found, or false otherwise

getPaddleWheel

public PaddleWheel getPaddleWheel(Atom source,
                                  Atom target)

Description copied from interface: PaddleWheelCollection

Returns the PaddleWheel containing an axis that consists of source and target.

Specified by:

getPaddleWheel in interface PaddleWheelCollection

Parameters:

source - the source Atom

target - the target Atom

Returns:

the PaddleWheel accociated with the GammaSequence having source and target as endpoints