net.sf.octet.model
Class BasicConformation

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

All Implemented Interfaces:

Conformation, GammaSequenceCollection, PaddleWheelCollection

public class BasicConformation

extends java.lang.Object

implements Conformation

A default implementation of the Conformation interface.

Author:

Richard Apodaca

Constructor Summary

BasicConformation(PaddleWheelCollection wheels, GammaSequenceCollection sequences)
Constructs a BasicConformation from wheels and sequences.

Method Summary

boolean	containsGammaSequence(Atom source, Atom target) Returns true if a GammaSequence containing an axis with source as its source and target as its target can be found, or false otherwise.
boolean	containsGammaSequence(GammaSequence sequence) Returns true if the specified GammaSequence is contained in this collection, and false otherwise.
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	countGammaSequences() Returns the number of GammaSequences contained in this collection.
int	countPaddleWheels() Returns the number of PaddleWheels contained in this collection.
GammaSequence	getGammaSequence(Atom source, Atom target) Returns the GammaSequence having source and target axis Atoms.
GammaSequence	getGammaSequence(int index) Returns the GammaSequence located at the specified zero-based index.
GammaSequence	getGammaSequence(PaddleWheel wheel) Returns the GammaSequence associated with the specified PaddleWheel.
int	getGammaSequenceIndex(GammaSequence sequence) Returns the zero-based index of the specified GammaSequence.
static Conformation	getNullInstance()
PaddleWheel	getPaddleWheel(Atom source, Atom target) Returns the PaddleWheel containing an axis that consists of source and target.
PaddleWheel	getPaddleWheel(GammaSequence sequence) Returns the PaddleWheel associated with the specified GammaSequence.
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.
GammaSequenceIterator	iterateGammaSequences() Returns an iterator over all GammaSequences in this collection.
PaddleWheelIterator	iteratePaddleWheels() Returns an iterator over all PaddleWheels in this collection.
GammaSequence[]	toGammaSequenceArray() Returns a copy of the GammaSequences contained in this collection as an array.
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

BasicConformation

public BasicConformation(PaddleWheelCollection wheels,
                         GammaSequenceCollection sequences)

Constructs a BasicConformation from wheels and sequences.

Parameters:

wheels - the PaddleWheelCollection to be used

sequences - the GammaSequenceCollection to be used

Throws:

IllegalRepresentationException - if the number of elements in wheels and sequences differs

Method Detail

getPaddleWheel

public PaddleWheel getPaddleWheel(GammaSequence sequence)

Description copied from interface: Conformation

Returns the PaddleWheel associated with the specified GammaSequence.

Specified by:

getPaddleWheel in interface Conformation

Parameters:

sequence - the GammaSequence to search

Returns:

the PaddleWheel associated with sequence

getGammaSequence

public GammaSequence getGammaSequence(PaddleWheel wheel)

Description copied from interface: Conformation

Returns the GammaSequence associated with the specified PaddleWheel.

Specified by:

getGammaSequence in interface Conformation

Parameters:

wheel - the PaddleWheel to search

Returns:

the GammaSequence associated with wheel

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

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

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

containsGammaSequence

public boolean containsGammaSequence(GammaSequence sequence)

Description copied from interface: GammaSequenceCollection

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

Specified by:

containsGammaSequence in interface GammaSequenceCollection

Parameters:

sequence - the PaddleWheel

Returns:

true if contained, false otherwise

countGammaSequences

public int countGammaSequences()

Description copied from interface: GammaSequenceCollection

Returns the number of GammaSequences contained in this collection.

Specified by:

countGammaSequences in interface GammaSequenceCollection

Returns:

the number of GammaSequences in this collection

getGammaSequenceIndex

public int getGammaSequenceIndex(GammaSequence sequence)

Description copied from interface: GammaSequenceCollection

Returns the zero-based index of the specified GammaSequence.

Specified by:

getGammaSequenceIndex in interface GammaSequenceCollection

Parameters:

sequence - the GammaSequence

Returns:

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

getGammaSequence

public GammaSequence getGammaSequence(int index)

Description copied from interface: GammaSequenceCollection

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

Specified by:

getGammaSequence in interface GammaSequenceCollection

Parameters:

index - the index

Returns:

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

getGammaSequence

public GammaSequence getGammaSequence(Atom source,
                                      Atom target)

Description copied from interface: GammaSequenceCollection

Returns the GammaSequence having source and target axis Atoms.

Specified by:

getGammaSequence in interface GammaSequenceCollection

Parameters:

source - the source Atom

target - the target Atom

Returns:

the GammaSequence having source and target as axis Atoms

containsGammaSequence

public boolean containsGammaSequence(Atom source,
                                     Atom target)

Description copied from interface: GammaSequenceCollection

Returns true if a GammaSequence containing an axis with source as its source and target as its target can be found, or false otherwise.

Specified by:

containsGammaSequence in interface GammaSequenceCollection

Parameters:

source - the axis source Atom

target - the axid target Atom

Returns:

true if the GammaSequence was found, or false otherwise

iterateGammaSequences

public GammaSequenceIterator iterateGammaSequences()

Description copied from interface: GammaSequenceCollection

Returns an iterator over all GammaSequences in this collection.

Specified by:

iterateGammaSequences in interface GammaSequenceCollection

Returns:

an iterator over all GammaSequences in this collection

toGammaSequenceArray

public GammaSequence[] toGammaSequenceArray()

Description copied from interface: GammaSequenceCollection

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

Specified by:

toGammaSequenceArray in interface GammaSequenceCollection

Returns:

a copy of the GammaSequence array for this collection

getNullInstance

public static Conformation getNullInstance()