org.openscience.cdk.debug

Class DebugIsotope

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.Element

org.openscience.cdk.Isotope

org.openscience.cdk.debug.DebugIsotope

All Implemented Interfaces:

Serializable, Cloneable, ICDKObject, IChemObject, IElement, IIsotope

public class DebugIsotope
extends Isotope
implements IIsotope

Debugging data class.

Author:

egonw

See Also:

Serialized Form

Source code:

master

Belongs to CDK module:

datadebug

Field Summary

Fields inherited from class org.openscience.cdk.Isotope

exactMass, naturalAbundance

Fields inherited from class org.openscience.cdk.Element

atomicNumber, symbol

Constructor Summary

Constructors

Constructor and Description
DebugIsotope(IElement element)
DebugIsotope(int atomicNumber, String elementSymbol, double exactMass, double abundance)
DebugIsotope(int atomicNumber, String elementSymbol, int massNumber, double exactMass, double abundance)
DebugIsotope(String elementSymbol)
DebugIsotope(String elementSymbol, int massNumber)

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.
Integer	getAtomicNumber() Returns the atomic number of this element.
IChemObjectBuilder	getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
Double	getExactMass() Gets the ExactMass attribute of the Isotope object.
boolean	getFlag(int flagType) Returns the value of a given flag.
boolean[]	getFlags() Returns the whole set of flags.
String	getID() Returns the identifier (ID) of this object.
int	getListenerCount() Returns the number of ChemObjectListeners registered with this object.
Integer	getMassNumber() Returns the atomic mass of this element.
Double	getNaturalAbundance() Gets the NaturalAbundance attribute of the Isotope object.
Map<Object,Object>	getProperties() Returns a Map with the IChemObject's properties.
<T> T	getProperty(Object description) Returns a property for the IChemObject.
String	getSymbol() Returns the element symbol of this element.
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	setAtomicNumber(Integer atomicNumber) Sets the atomic number of this element.
void	setExactMass(Double exactMass) Sets the ExactMass attribute of the Isotope object.
void	setFlag(int flagType, boolean flagValue) 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	setMassNumber(Integer massNumber) Sets the atomic mass of this element.
void	setNaturalAbundance(Double naturalAbundance) Sets the NaturalAbundance attribute of the Isotope object.
void	setProperty(Object description, Object property) Sets a property for a IChemObject.
void	setSymbol(String symbol) Sets the element symbol of this element.

Methods inherited from class org.openscience.cdk.Isotope

compare, toString

Methods inherited from class org.openscience.cdk.ChemObject

getFlagValue, getNotification, getProperty, setNotification, setProperties, 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.IChemObject

getFlagValue, getNotification, getProperty, setNotification, setProperties, toString

Constructor Detail

DebugIsotope

public DebugIsotope(String elementSymbol)

DebugIsotope

public DebugIsotope(int atomicNumber,
            String elementSymbol,
            int massNumber,
            double exactMass,
            double abundance)

DebugIsotope

public DebugIsotope(int atomicNumber,
            String elementSymbol,
            double exactMass,
            double abundance)

DebugIsotope

public DebugIsotope(String elementSymbol,
            int massNumber)

DebugIsotope

public DebugIsotope(IElement element)

Method Detail

getAtomicNumber

public Integer getAtomicNumber()

Returns the atomic number of this element.

Once instantiated all field not filled by passing parameters to the constructor are null. Elements can be configured by using the IsotopeFactory.configure() method:

   Element element = new Element("C");
   IsotopeFactory if = IsotopeFactory.getInstance(element.getNewBuilder());
   if.configure(element);
 

Specified by:

getAtomicNumber in interface IElement

Overrides:

getAtomicNumber in class Element

Returns:

The atomic number of this element

See Also:

Element.setAtomicNumber(java.lang.Integer)

setAtomicNumber

public void setAtomicNumber(Integer atomicNumber)

Sets the atomic number of this element.

Specified by:

setAtomicNumber in interface IElement

Overrides:

setAtomicNumber in class Element

Parameters:

atomicNumber - The atomic mass to be assigned to this element

See Also:

Element.getAtomicNumber()

getSymbol

public String getSymbol()

Returns the element symbol of this element.

Specified by:

getSymbol in interface IElement

Overrides:

getSymbol in class Element

Returns:

The element symbol of this element. Null if unset.

See Also:

Element.setSymbol(java.lang.String)

setSymbol

public void setSymbol(String symbol)

Sets the element symbol of this element.

Specified by:

setSymbol in interface IElement

Overrides:

setSymbol in class Element

Parameters:

symbol - The element symbol to be assigned to this atom

See Also:

Element.getSymbol()

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

Overrides:

addListener in class ChemObject

Parameters:

col - the ChemObjectListener

See Also:

ChemObject.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

Overrides:

getListenerCount in class ChemObject

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

Overrides:

removeListener in class ChemObject

Parameters:

col - The ChemObjectListener to be removed

See Also:

ChemObject.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

Overrides:

notifyChanged in class ChemObject

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

Overrides:

notifyChanged in class ChemObject

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

Overrides:

setProperty in class ChemObject

Parameters:

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

property - An object with the property itself

See Also:

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

removeProperty

public void removeProperty(Object description)

Removes a property for a IChemObject.

Specified by:

removeProperty in interface IChemObject

Overrides:

removeProperty in class ChemObject

Parameters:

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

See Also:

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

getProperty

public <T> T getProperty(Object description)

Returns a property for the IChemObject.

Specified by:

getProperty in interface IChemObject

Overrides:

getProperty in class ChemObject

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:

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

getProperties

public Map<Object,Object> getProperties()

Returns a Map with the IChemObject's properties.

Specified by:

getProperties in interface IChemObject

Overrides:

getProperties in class ChemObject

Returns:

The object's properties as an Hashtable

See Also:

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

getID

public String getID()

Returns the identifier (ID) of this object.

Specified by:

getID in interface IChemObject

Overrides:

getID in class ChemObject

Returns:

a String representing the ID value

See Also:

ChemObject.setID(java.lang.String)

setID

public void setID(String identifier)

Sets the identifier (ID) of this object.

Specified by:

setID in interface IChemObject

Overrides:

setID in class ChemObject

Parameters:

identifier - a String representing the ID value

See Also:

ChemObject.getID()

setFlag

public void setFlag(int flagType,
           boolean flagValue)

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

Overrides:

setFlag in class ChemObject

Parameters:

flagType - flag to set the value for

flagValue - value to assign to flag

See Also:

IChemObject.getFlag(int), CDKConstants

getFlag

public boolean getFlag(int flagType)

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

Overrides:

getFlag in class ChemObject

Parameters:

flagType - flag to retrieve the value of

Returns:

true if the flag flag_type is set

See Also:

IChemObject.setFlag(int, boolean), CDKConstants

addProperties

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

Sets the properties of this object.

Specified by:

addProperties in interface IChemObject

Overrides:

addProperties in class ChemObject

Parameters:

properties - a Hashtable specifying the property values

See Also:

ChemObject.getProperties()

setFlags

public void setFlags(boolean[] flagsNew)

Sets the whole set of flags.

Specified by:

setFlags in interface IChemObject

Overrides:

setFlags in class ChemObject

Parameters:

flagsNew - the new flags.

See Also:

ChemObject.getFlags()

getFlags

public boolean[] getFlags()

Returns the whole set of flags.

Specified by:

getFlags in interface IChemObject

Overrides:

getFlags in class ChemObject

Returns:

the flags.

See Also:

ChemObject.setFlags(boolean[])

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 Isotope

Returns:

The cloned object

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned

getBuilder

public IChemObjectBuilder getBuilder()

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

Specified by:

getBuilder in interface ICDKObject

Overrides:

getBuilder in class ChemObject

Returns:

The IChemObjectBuilder matching this ICDKObject

setNaturalAbundance

public void setNaturalAbundance(Double naturalAbundance)

Sets the NaturalAbundance attribute of the Isotope object.

Specified by:

setNaturalAbundance in interface IIsotope

Overrides:

setNaturalAbundance in class Isotope

Parameters:

naturalAbundance - The new NaturalAbundance value

See Also:

Isotope.getNaturalAbundance()

setExactMass

public void setExactMass(Double exactMass)

Sets the ExactMass attribute of the Isotope object.

Specified by:

setExactMass in interface IIsotope

Overrides:

setExactMass in class Isotope

Parameters:

exactMass - The new ExactMass value

See Also:

Isotope.getExactMass()

getNaturalAbundance

public Double getNaturalAbundance()

Gets the NaturalAbundance attribute of the Isotope object.

Once instantiated all field not filled by passing parameters to the constructor are null. Isotopes can be configured by using the IsotopeFactory.configure() method:

   Isotope isotope = new Isotope("C", 13);
   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
   if.configure(isotope);
 

Specified by:

getNaturalAbundance in interface IIsotope

Overrides:

getNaturalAbundance in class Isotope

Returns:

The NaturalAbundance value

See Also:

Isotope.setNaturalAbundance(java.lang.Double)

getExactMass

public Double getExactMass()

Gets the ExactMass attribute of the Isotope object.

Once instantiated all field not filled by passing parameters to the constructor are null. Isotopes can be configured by using the IsotopeFactory.configure() method:

   Isotope isotope = new Isotope("C", 13);
   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
   if.configure(isotope);
 

Specified by:

getExactMass in interface IIsotope

Overrides:

getExactMass in class Isotope

Returns:

The ExactMass value

See Also:

Isotope.setExactMass(java.lang.Double)

getMassNumber

public Integer getMassNumber()

Returns the atomic mass of this element.

Once instantiated all field not filled by passing parameters to the constructor are null. Isotopes can be configured by using the IsotopeFactory.configure() method:

   Isotope isotope = new Isotope("C", 13);
   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
   if.configure(isotope);
 

Specified by:

getMassNumber in interface IIsotope

Overrides:

getMassNumber in class Isotope

Returns:

The atomic mass of this element

See Also:

Isotope.setMassNumber(Integer)

setMassNumber

public void setMassNumber(Integer massNumber)

Sets the atomic mass of this element.

Specified by:

setMassNumber in interface IIsotope

Overrides:

setMassNumber in class Isotope

Parameters:

massNumber - The atomic mass to be assigned to this element

See Also:

Isotope.getMassNumber()