Package org.openscience.cdk.debug

Class DebugChemFile

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.ChemFile

org.openscience.cdk.debug.DebugChemFile

All Implemented Interfaces:

Serializable, Cloneable, ICDKObject, IChemFile, IChemObject, IChemObjectListener

public class DebugChemFile
extends ChemFile
implements IChemFile

Debugging data class.

Author:

egonw

See Also:

• Serialized Form

Field Summary

Fields inherited from class org.openscience.cdk.ChemFile

chemSequenceCount, chemSequences, growArraySize

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
DebugChemFile()

Method Summary

Modifier and Type	Method	Description
void	addChemSequence(IChemSequence chemSequence)	Adds a ChemSequence to this container.
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.
Iterable<IChemSequence>	chemSequences()	Returns the Iterable to ChemSequences of this container.
Object	clone()	Allows for getting an clone of this object.
IChemObjectBuilder	getBuilder()	Returns a IChemObjectBuilder for the data classes that extend this class.
IChemSequence	getChemSequence(int number)	Returns the ChemSequence at position number in the container.
int	getChemSequenceCount()	Returns the number of ChemSequences in this Container.
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.
Map<Object,Object>	getProperties()	Returns a Map with the IChemObject's properties.
<T> T	getProperty(Object description)	Returns a property for the IChemObject.
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	removeChemSequence(int pos)	Removes a ChemSequence from this container.
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 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	setProperty(Object description, Object property)	Sets a property for a IChemObject.

Methods inherited from class org.openscience.cdk.ChemFile

growChemSequenceArray, stateChanged, toString

Methods inherited from class org.openscience.cdk.ChemObject

clear, compare, flags, getFlagValue, getNotification, getProperty, is, set, 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

clear, flags, getFlagValue, getNotification, getProperty, is, set, setNotification, setProperties, toString

Constructor Details

DebugChemFile

public DebugChemFile()

Method Details

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. IChemObject.AROMATIC or IChemObject.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)

getFlag

public boolean getFlag(int flagType)

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

 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)

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

Allows for getting an clone of this object.

Specified by:

clone in interface IChemObject

Overrides:

clone in class ChemFile

Returns:

a clone of this 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

addChemSequence

public void addChemSequence(IChemSequence chemSequence)

Adds a ChemSequence to this container.

Specified by:

addChemSequence in interface IChemFile

Overrides:

addChemSequence in class ChemFile

Parameters:

chemSequence - The chemSequence to be added to this container

See Also:

• ChemFile.chemSequences

removeChemSequence

public void removeChemSequence(int pos)

Removes a ChemSequence from this container.

Specified by:

removeChemSequence in interface IChemFile

Overrides:

removeChemSequence in class ChemFile

Parameters:

pos - The position from which to remove

See Also:

• ChemFile.chemSequences
• ChemFile.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

Overrides:

chemSequences in class ChemFile

Returns:

The Iterable to ChemSequences of this container

See Also:

• ChemFile.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

Overrides:

getChemSequence in class ChemFile

Parameters:

number - The position of the ChemSequence to be returned.

Returns:

The ChemSequence at position number.

See Also:

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

getChemSequenceCount

public int getChemSequenceCount()

Returns the number of ChemSequences in this Container.

Specified by:

getChemSequenceCount in interface IChemFile

Overrides:

getChemSequenceCount in class ChemFile

Returns:

The number of ChemSequences in this Container