Package org.openscience.cdk

Class ChemFile

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.ChemFile

All Implemented Interfaces:

Serializable, Cloneable, ICDKObject, IChemFile, IChemObject, IChemObjectListener

public class ChemFile
extends ChemObject
implements Serializable, Cloneable, IChemFile, IChemObjectListener

A Object containing a number of ChemSequences. This is supposed to be the top level container, which can contain all the concepts stored in a chemical document

Author:

steinbeck

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected int	chemSequenceCount	Number of ChemSequences contained by this container.
protected IChemSequence[]	chemSequences	Array of ChemSquences.
protected int	growArraySize	Amount by which the chemsequence 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
ChemFile()	Constructs an empty ChemFile.

Method Summary

Modifier and Type	Method	Description
void	addChemSequence(IChemSequence chemSequence)	Adds a ChemSequence to this container.
Iterable<IChemSequence>	chemSequences()	Returns the Iterable to ChemSequences of this container.
Object	clone()	Allows for getting an clone of this object.
IChemSequence	getChemSequence(int number)	Returns the ChemSequence at position number in the container.
int	getChemSequenceCount()	Returns the number of ChemSequences in this Container.
protected void	growChemSequenceArray()	Grows the ChemSequence array by a given size.
void	removeChemSequence(int pos)	Removes a ChemSequence from this container.
void	stateChanged(IChemObjectChangeEvent event)	Called by objects to which this object has registered as a listener.
String	toString()	Returns a String representation of this class.

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

chemSequences

protected IChemSequence[] chemSequences

Array of ChemSquences.

chemSequenceCount

protected int chemSequenceCount

Number of ChemSequences contained by this container.

growArraySize

protected int growArraySize

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

Constructor Details

ChemFile

public ChemFile()

Constructs an empty ChemFile.

Method Details

addChemSequence

public void addChemSequence(IChemSequence chemSequence)

Adds a ChemSequence to this container.

Specified by:

addChemSequence in interface IChemFile

Parameters:

chemSequence - The chemSequence to be added to this container

See Also:

• chemSequences

removeChemSequence

public void removeChemSequence(int pos)

Removes a ChemSequence from this container.

Specified by:

removeChemSequence in interface IChemFile

Parameters:

pos - The position from which to remove

See Also:

• chemSequences
• addChemSequence(org.openscience.cdk.interfaces.IChemSequence)

chemSequences

public Iterable<IChemSequence> chemSequences()

Returns the Iterable to ChemSequences of this container.

Specified by:

chemSequences in interface IChemFile

Returns:

The Iterable to ChemSequences of this container

See Also:

• addChemSequence(org.openscience.cdk.interfaces.IChemSequence)

getChemSequence

public IChemSequence getChemSequence(int number)

Returns the ChemSequence at position number in the container.

Specified by:

getChemSequence in interface IChemFile

Parameters:

number - The position of the ChemSequence to be returned.

Returns:

The ChemSequence at position number.

See Also:

• addChemSequence(org.openscience.cdk.interfaces.IChemSequence)

growChemSequenceArray

protected void growChemSequenceArray()

Grows the ChemSequence array by a given size.

See Also:

• growArraySize

getChemSequenceCount

public int getChemSequenceCount()

Returns the number of ChemSequences in this Container.

Specified by:

getChemSequenceCount in interface IChemFile

Returns:

The number of ChemSequences in this Container

toString

public String toString()

Returns a String representation of this class. It implements RFC #9.

Specified by:

toString in interface IChemObject

Overrides:

toString in class Object

Returns:

String representation of the Object

clone

public Object clone()
             throws CloneNotSupportedException

Allows for getting an clone of this object.

Specified by:

clone in interface IChemObject

Overrides:

clone in class ChemObject

Returns:

a clone of this object

Throws:

CloneNotSupportedException

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