org.openscience.cdk

Class ChemObject

java.lang.Object

org.openscience.cdk.ChemObject

All Implemented Interfaces:

Serializable, Cloneable, ICDKObject, IChemObject

Direct Known Subclasses:

AtomContainer, AtomContainerSet, ChemFile, ChemModel, ChemSequence, DebugChemObject, ElectronContainer, Element, Mapping, PDBStructure, Reaction, ReactionSet

public class ChemObject
extends Object
implements Serializable, IChemObject, Cloneable

The base class for all chemical objects in this cdk. It provides methods for adding listeners and for their notification of events, as well a a hash table for administration of physical or chemical properties

Author:

steinbeck

See Also:

Serialized Form

Source code:

master

Belongs to CDK module:

data

Constructor Summary

Constructors

Constructor and Description
ChemObject() Constructs a new IChemObject.
ChemObject(IChemObject chemObject) Constructs a new IChemObject by copying the flags, and the identifier.

Method Summary

Methods

Modifier and Type	Method and Description
void	addListener(IChemObjectListener col) Use this to add yourself to this IChemObject as a listener.
void	addProperties(Map<Object,Object> properties) Sets the properties of this object.
Object	clone() Clones this IChemObject.
boolean	compare(Object object) Compares a IChemObject with this IChemObject.
IChemObjectBuilder	getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
boolean	getFlag(int mask) Returns the value of a given flag.
boolean[]	getFlags() Returns the whole set of flags.
Short	getFlagValue() Access the internal value used to store the flags.
String	getID() Returns the identifier (ID) of this object.
int	getListenerCount() Returns the number of ChemObjectListeners registered with this object.
boolean	getNotification() Returns the flag that indicates whether notification messages are sent around.
Map<Object,Object>	getProperties() Returns a Map with the IChemObject's properties.
<T> T	getProperty(Object description) Returns a property for the IChemObject.
<T> T	getProperty(Object description, Class<T> c) Access a property of the given description and cast the specified class.
void	notifyChanged() This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
void	notifyChanged(IChemObjectChangeEvent evt) This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
void	removeListener(IChemObjectListener col) Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
void	removeProperty(Object description) Removes a property for a IChemObject.
void	setFlag(int mask, boolean value) Sets the value of some flag.
void	setFlags(boolean[] flagsNew) Sets the whole set of flags.
void	setID(String identifier) Sets the identifier (ID) of this object.
void	setNotification(boolean bool) Set a flag to use or not use notification.
void	setProperties(Map<Object,Object> properties) Set the properties of this object to the provided map (shallow copy).
void	setProperty(Object description, Object property) Sets a property for a IChemObject.
Object	shallowCopy() Clones this IChemObject, but preserves references to Objects.

Methods inherited from class java.lang.Object

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

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

toString

Constructor Detail

ChemObject

public ChemObject()

Constructs a new IChemObject.

ChemObject

public ChemObject(IChemObject chemObject)

Constructs a new IChemObject by copying the flags, and the identifier. It does not copy the listeners and properties.

Parameters:

chemObject - the object to copy

Method Detail

addListener

public void addListener(IChemObjectListener col)

Use this to add yourself to this IChemObject as a listener. In order to do so, you must implement the ChemObjectListener Interface.

Specified by:

addListener in interface IChemObject

Parameters:

col - the ChemObjectListener

See Also:

removeListener(org.openscience.cdk.interfaces.IChemObjectListener)

getListenerCount

public int getListenerCount()

Returns the number of ChemObjectListeners registered with this object.

Specified by:

getListenerCount in interface IChemObject

Returns:

the number of registered listeners.

removeListener

public void removeListener(IChemObjectListener col)

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject. It will then not be notified of change in this object anymore.

Specified by:

removeListener in interface IChemObject

Parameters:

col - The ChemObjectListener to be removed

See Also:

addListener(org.openscience.cdk.interfaces.IChemObjectListener)

notifyChanged

public void notifyChanged()

This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.

Specified by:

notifyChanged in interface IChemObject

notifyChanged

public void notifyChanged(IChemObjectChangeEvent evt)

This should be triggered by an method that changes the content of an object to that the registered listeners can react to it. This is a version of notifyChanged() which allows to propagate a change event while preserving the original origin.

Specified by:

notifyChanged in interface IChemObject

Parameters:

evt - A ChemObjectChangeEvent pointing to the source of where the change happened

setProperty

public void setProperty(Object description,
               Object property)

Sets a property for a IChemObject.

Specified by:

setProperty in interface IChemObject

Parameters:

description - An object description of the property (most likely a unique string)

property - An object with the property itself

See Also:

getProperty(java.lang.Object), removeProperty(java.lang.Object)

removeProperty

public void removeProperty(Object description)

Removes a property for a IChemObject.

Specified by:

removeProperty in interface IChemObject

Parameters:

description - The object description of the property (most likely a unique string)

See Also:

setProperty(java.lang.Object, java.lang.Object), getProperty(java.lang.Object)

getProperty

public <T> T getProperty(Object description)

Returns a property for the IChemObject.

Specified by:

getProperty in interface IChemObject

Type Parameters:

T - generic return type

Parameters:

description - An object description of the property (most likely a unique string)

Returns:

The object containing the property. Returns null if propert is not set.

See Also:

setProperty(java.lang.Object, java.lang.Object), removeProperty(java.lang.Object)

getProperty

public <T> T getProperty(Object description,
                Class<T> c)

Access a property of the given description and cast the specified class.

IAtom atom = new Atom("C");
     atom.setProperty("number", 1); // set an integer property

     // access the property and automatically cast to an int
     Integer number = atom.getProperty("number");

     // if the method is in a chain or needs to be nested the type
     // can be provided
     methodAcceptingInt(atom.getProperty("number", Integer.class));

     // the type cannot be checked and so...
     String number = atom.getProperty("number"); // ClassCastException

     // if the type is provided a more meaningful error is thrown
     atom.getProperty("number", String.class); // IllegalArgumentException

 

Specified by:

getProperty in interface IChemObject

Type Parameters:

T - generic type (of provided class)

Parameters:

description - description of a property (normally a string)

c - type of the value to be returned

Returns:

the value stored for the specified description.

See Also:

IChemObject.getProperty(Object), IChemObject.addProperties(java.util.Map)

getProperties

public Map<Object,Object> getProperties()

Returns a Map with the IChemObject's properties.

Specified by:

getProperties in interface IChemObject

Returns:

The object's properties as an Hashtable

See Also:

addProperties(java.util.Map<java.lang.Object, java.lang.Object>)

clone

public Object clone()
             throws CloneNotSupportedException

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 Object

Returns:

The cloned object

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned

compare

public boolean compare(Object object)

Compares a IChemObject with this IChemObject.

Parameters:

object - Object of type AtomType

Returns:

true if the atom types are equal

getID

public String getID()

Returns the identifier (ID) of this object.

Specified by:

getID in interface IChemObject

Returns:

a String representing the ID value

See Also:

setID(java.lang.String)

setID

public void setID(String identifier)

Sets the identifier (ID) of this object.

Specified by:

setID in interface IChemObject

Parameters:

identifier - a String representing the ID value

See Also:

getID()

setFlag

public void setFlag(int mask,
           boolean value)

Sets the value of some flag. The flag is a mask from a given CDKConstant (e.g. CDKConstants.ISAROMATIC or CDKConstants.VISITED). The flags are intrinsic internal properties and should not be used to store custom values, please use IChemObject.setProperty(Object, Object).

// set this chem object to be aromatic
 chemObject.setFlag(CDKConstants.ISAROMATIC, Boolean.TRUE);
 // ...
 // indicate we have visited this chem object
 chemObject.setFlag(CDKConstants.VISITED, Boolean.TRUE);
 

Specified by:

setFlag in interface IChemObject

Parameters:

mask - flag to set the value for

value - value to assign to flag

See Also:

IChemObject.getFlag(int), CDKConstants

getFlag

public boolean getFlag(int mask)

Returns the value of a given flag. The flag is a mask from a given CDKConstant (e.g. CDKConstants.ISAROMATIC).

if(chemObject.getFlag(CDKConstants.ISAROMATIC)){
     // handle aromatic flag on this chem object
 }
 

Specified by:

getFlag in interface IChemObject

Parameters:

mask - flag to retrieve the value of

Returns:

true if the flag flag_type is set

See Also:

IChemObject.setFlag(int, boolean), CDKConstants

getFlagValue

public Short getFlagValue()

Access the internal value used to store the flags. The flags are stored on a single numeric value and are set/cleared.

Specified by:

getFlagValue in interface IChemObject

Returns:

numeric representation of the flags

setProperties

public void setProperties(Map<Object,Object> properties)

Set the properties of this object to the provided map (shallow copy). Any existing properties are removed.

Specified by:

setProperties in interface IChemObject

Parameters:

properties - map key-value pairs

addProperties

public void addProperties(Map<Object,Object> properties)

Sets the properties of this object.

Specified by:

addProperties in interface IChemObject

Parameters:

properties - a Hashtable specifying the property values

See Also:

getProperties()

setFlags

public void setFlags(boolean[] flagsNew)

Sets the whole set of flags.

Specified by:

setFlags in interface IChemObject

Parameters:

flagsNew - the new flags.

See Also:

getFlags()

getFlags

public boolean[] getFlags()

Returns the whole set of flags.

Specified by:

getFlags in interface IChemObject

Returns:

the flags.

See Also:

setFlags(boolean[])

shallowCopy

public Object shallowCopy()

Clones this IChemObject, but preserves references to Objects.

Returns:

Shallow copy of this IChemObject

See Also:

clone()

getBuilder

public IChemObjectBuilder getBuilder()

Description copied from interface: ICDKObject

Returns a IChemObjectBuilder for the data classes that extend this class.

Specified by:

getBuilder in interface ICDKObject

Returns:

The IChemObjectBuilder matching this ICDKObject

setNotification

public void setNotification(boolean bool)

Description copied from interface: IChemObject

Set a flag to use or not use notification. By default it should be set to true.

Specified by:

setNotification in interface IChemObject

Parameters:

bool - if true, then notification messages are sent.

See Also:

IChemObject.getNotification()

getNotification

public boolean getNotification()

Description copied from interface: IChemObject

Returns the flag that indicates whether notification messages are sent around.

Specified by:

getNotification in interface IChemObject

Returns:

true if messages are sent.

See Also:

IChemObject.setNotification(boolean)