Package org.openscience.cdk

Class ChemSequence

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.ChemSequence

All Implemented Interfaces:

Serializable, Cloneable, ICDKObject, IChemObject, IChemObjectListener, IChemSequence

Direct Known Subclasses:

DebugChemSequence

public class ChemSequence
extends ChemObject
implements Serializable, IChemSequence, IChemObjectListener, Cloneable

A sequence of ChemModels, which can, for example, be used to store the course of a reaction. Each state of the reaction would be stored in one ChemModel.

See Also:

• Serialized Form

Keywords:

animation, reaction

Field Summary

Fields

Modifier and Type	Field	Description
protected int	chemModelCount	Number of ChemModels contained by this container.
protected IChemModel[]	chemModels	Array of ChemModels.
protected final int	growArraySize	Amount by which the chemModels array grows when elements are added and the array is not large enough for that.

Fields inherited from interface org.openscience.cdk.interfaces.IChemObject

ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, MARKUSH, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED

Constructor Summary

Constructors

Constructor	Description
ChemSequence()	Constructs an empty ChemSequence.

Method Summary

Modifier and Type	Method	Description
void	addChemModel(IChemModel chemModel)	Adds an chemModel to this container.
Iterable<IChemModel>	chemModels()	Returns an Iterable to ChemModels in this container.
Object	clone()	Clones this IChemObject.
IChemModel	getChemModel(int number)	Returns the ChemModel at position number in the container.
int	getChemModelCount()	Returns the number of ChemModels in this Container.
protected void	growChemModelArray()	Grows the chemModel array by a given size.
void	removeChemModel(int pos)	Remove a ChemModel from this ChemSequence.
void	stateChanged(IChemObjectChangeEvent event)	Called by objects to which this object has registered as a listener.
String	toString()	Returns a one line description of this IChemObject.

Methods inherited from class org.openscience.cdk.ChemObject

addListener, addProperties, clear, compare, flags, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

getBuilder

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject

addListener, addProperties, clear, flags, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Field Details

chemModels

protected IChemModel[] chemModels

Array of ChemModels.

chemModelCount

protected int chemModelCount

Number of ChemModels contained by this container.

growArraySize

protected final int growArraySize

Amount by which the chemModels array grows when elements are added and the array is not large enough for that.

See Also:

• Constant Field Values

Constructor Details

ChemSequence

public ChemSequence()

Constructs an empty ChemSequence.

Method Details

addChemModel

public void addChemModel(IChemModel chemModel)

Adds an chemModel to this container.

Specified by:

addChemModel in interface IChemSequence

Parameters:

chemModel - The chemModel to be added to this container

See Also:

• getChemModel(int)

removeChemModel

public void removeChemModel(int pos)

Remove a ChemModel from this ChemSequence.

Specified by:

removeChemModel in interface IChemSequence

Parameters:

pos - The position of the ChemModel to be removed.

chemModels

public Iterable<IChemModel> chemModels()

Returns an Iterable to ChemModels in this container.

Specified by:

chemModels in interface IChemSequence

Returns:

The Iterable to ChemModels in this container

See Also:

• addChemModel(org.openscience.cdk.interfaces.IChemModel)

getChemModel

public IChemModel getChemModel(int number)

Returns the ChemModel at position number in the container.

Specified by:

getChemModel in interface IChemSequence

Parameters:

number - The position of the ChemModel to be returned.

Returns:

The ChemModel at position number.

See Also:

• addChemModel(org.openscience.cdk.interfaces.IChemModel)

growChemModelArray

protected void growChemModelArray()

Grows the chemModel array by a given size.

See Also:

• growArraySize

getChemModelCount

public int getChemModelCount()

Returns the number of ChemModels in this Container.

Specified by:

getChemModelCount in interface IChemSequence

Returns:

The number of ChemModels in this Container

toString

public String toString()

Description copied from interface: IChemObject

Returns a one line description of this IChemObject.

Specified by:

toString in interface IChemObject

Overrides:

toString in class Object

Returns:

a String representation of this object

clone

public Object clone()
             throws CloneNotSupportedException

Description copied from class: ChemObject

Clones this IChemObject. It clones the identifier, flags, properties and pointer vectors. The ChemObjectListeners are not cloned, and neither is the content of the pointer vectors.

Specified by:

clone in interface IChemObject

Overrides:

clone in class ChemObject

Returns:

The cloned object

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned

stateChanged

public void stateChanged(IChemObjectChangeEvent event)

Called by objects to which this object has registered as a listener.

Specified by:

stateChanged in interface IChemObjectListener

Parameters:

event - A change event pointing to the source of the change