Package chemaxon.standardizer

Class AbstractStandardizerAction

java.lang.Object

chemaxon.standardizer.AbstractStandardizerAction

All Implemented Interfaces:

chemaxon.license.Licensable, StandardizerAction, PropertyChangeListener, Cloneable, EventListener

Direct Known Subclasses:

AbsoluteStereoAction, chemaxon.standardizer.actions.AbstractSgroupAction, AddExplicitHydrogensAction, AliasToAtomAction, AliasToGroupAction, AromatizeAction, Clean2DAction, Clean3DAction, ClearIsotopesAction, ClearStereoAction, ConvertDoubleBondsAction, ConvertPiMetalBondsAction, ConvertToEnhancedStereoAction, CreateGroupAction, DearomatizeAction, DisconnectMetalAtomsAction, ExpandAction, MapAction, MapReactionAction, MesomerizeAction, NeutralizeAction, RemoveAbsoluteStereoAction, RemoveAtomValuesAction, RemoveAttachedDataAction, RemoveExplicitHydrogensAction, RemoveFragmentAction, RemoveRGroupDefinitionsAction, RemoveSolventsAction, RemoveStereoCareBoxAction, ReplaceAtomsAction, SetAbsoluteStereoAction, SetHydrogenIsotopeSymbolAction, StripSaltsAction, TautomerizeAction, TransformAction, UnmapAction, WedgeCleanAction

@PublicAPI
public abstract class AbstractStandardizerAction
extends Object
implements StandardizerAction, chemaxon.license.Licensable, Cloneable, PropertyChangeListener

Abstract implementation of the StandardizerAction.

The abstract implementation manages license checking, availability, validity of the action, manages the Changes, and collecting information for mapping.

The standardization process of the target molecule must be implemented by the method standardize1(Molecule)

Special molecules containing more components (e.g. RgMolecule, RxnMolecule) are decomponented by the method getComponents(Molecule), and standardize1(Molecule) method is called on each component, before applied on the original molecule. If a descendant does not want this to occur, this method must be overridden.

Since:

5.11

Field Summary

Fields

Modifier and Type	Field	Description
static String	CONFIG_PATH_KEY	The key of configuration path parameter of the abstract action.
static String	FORMAT_KEY	The key of the molecule format parameter of the abstract action.
static String	ID_KEY	The key of the ID parameter of the abstract action.
protected PropertyChangeSupport	support

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractStandardizerAction(Map<String,String> params)	Initializes the functionality of the abstract implementation.

Method Summary

Modifier and Type	Method	Description
void	addPropertyChangeListener(PropertyChangeListener listener)	Add a PropertyChangeListener to the listener list.
void	addPropertyChangeListener(String propertyName, PropertyChangeListener listener)	Add a PropertyChangeListener for a specific property.
protected boolean	anyBooleanPropertyTrue(Map<String,String> params, String... keys)	Check the given map, whether there is a String 'true' (case in-sensitive) value for any of the given keys
AbstractStandardizerAction	clone()
StandardizerAction	cloneItem()	Returns a clone of this StandardizerAction instance
protected List<Molecule>	getComponents(Molecule molecule)	A recursive algorithm getting all components (reactants, agents and products of reaction molecules, R-group definitions of Rg-Molecules) of the molecule.
StandardizerActionDescriptor	getDescriptor()	Gets the descriptor of the standardizer action.
String	getID()	Gets the identifier string of the standardizer action.
boolean	isActive()	Returns true if the action is active, and can be used
boolean	isAvailable()	Returns true if the action is available, and can be used
boolean	isLicensed()
boolean	isValid()	Returns true if the action's parameters are valid, false otherwise
void	propertyChange(PropertyChangeEvent evt)
void	removePropertyChangeListener(PropertyChangeListener listener)	Remove a PropertyChangeListener from the listener list.
void	removePropertyChangeListener(String propertyName, PropertyChangeListener listener)	Remove a PropertyChangeListener for a specific property.
void	setActive(boolean active)	Sets whether the action is active, and can be used
void	setID(String id)	Sets the identifier string of the standardizer action
void	setLicenseEnvironment(String env)	Sets the license environment of the action
void	setValid(boolean valid)	Sets the validity of the standardizer action.
Changes	standardize(Molecule molecule)	Calls standardize1(Molecule) If molecule has more components standardize1(Molecule) is invoked on all components instead of the molecule itself. If standardize1(Molecule) doesn't return a not null Change object for the molecule or for any of the components the value of the returned changes object's Changes.isModified() property is set based on whether molecule's MoleculeGraph.getGrinvCC() property value has changed during the standardization action.
protected abstract Changes	standardize1(Molecule molecule)	This method contains the current standardization mechanism.
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

CONFIG_PATH_KEY

public static final String CONFIG_PATH_KEY

The key of configuration path parameter of the abstract action. The map provided in the constructor AbstractStandardizerAction(Map) may contain the value of the path of the configuration defined by this key.

See Also:

Constant Field Values

ID_KEY

public static final String ID_KEY

The key of the ID parameter of the abstract action. The map provided in the constructor AbstractStandardizerAction(Map) may contain the value of the identifier of the action defined by this key.

See Also:

Constant Field Values

FORMAT_KEY

public static final String FORMAT_KEY

The key of the molecule format parameter of the abstract action. The map provided in the constructor AbstractStandardizerAction(Map) may contain the value of the identifier of the action defined by this key.

See Also:

Constant Field Values

support

protected PropertyChangeSupport support

Constructor Detail

AbstractStandardizerAction

protected AbstractStandardizerAction(Map<String,String> params)

Initializes the functionality of the abstract implementation. Sets the ID of the action, if it is provided, and starts property change observing on the descriptor

Parameters:

params - the parameters of the action in a map representation

Method Detail

getDescriptor

public StandardizerActionDescriptor getDescriptor()

Description copied from interface: StandardizerAction

Gets the descriptor of the standardizer action. Contains all necessary informations of the action for user interfaces.

Specified by:

getDescriptor in interface StandardizerAction

Returns:

the descriptor of the standardizer action.

isValid

public boolean isValid()

Description copied from interface: StandardizerAction

Returns true if the action's parameters are valid, false otherwise

Specified by:

isValid in interface StandardizerAction

Returns:

true if the action's parameters are valid, false otherwise

setValid

public void setValid(boolean valid)

Sets the validity of the standardizer action. The validity of the standardizer action depends on the validity of the provided parameters of the constructor AbstractStandardizerAction(Map)

If a descendant standardizer action has an invalid parameter, the validity should be false.

Parameters:

valid - the validity of the standardizer action

isAvailable

public boolean isAvailable()

Description copied from interface: StandardizerAction

Returns true if the action is available, and can be used

Specified by:

isAvailable in interface StandardizerAction

Returns:

true if the action is available, and can be used

standardize

public final Changes standardize(Molecule molecule)

Calls standardize1(Molecule)
If molecule has more components standardize1(Molecule) is invoked on all components instead of the molecule itself.
If standardize1(Molecule) doesn't return a not null Change object for the molecule or for any of the components the value of the returned changes object's Changes.isModified() property is set based on whether molecule's MoleculeGraph.getGrinvCC() property value has changed during the standardization action.

Specified by:

standardize in interface StandardizerAction

Parameters:

molecule - the target molecule of the standardization process

Returns:

the change set of the molecule

standardize1

protected abstract Changes standardize1(Molecule molecule)
                                 throws IllegalArgumentException

This method contains the current standardization mechanism. Descendants needs to implement this method.
Special molecules containing more components (e.g. RgMolecule, RxnMolecule) are decomponented by the method getComponents(Molecule), and standardize1(Molecule) method is called on each component, before applied on the original molecule. If a descendant does not want this to occur, this method must be overridden.
Logs of standardization should be generated to a Logger, that can be collected by using StandardizerLogger.getLogger() method.

Parameters:

molecule - the Molecule instance to be standardized

Returns:

the changes applied on the molecule during the standardization process

Throws:

IllegalArgumentException - if the provided molecule or the provided parameters of the action are invalid

cloneItem

public StandardizerAction cloneItem()

Description copied from interface: StandardizerAction

Returns a clone of this StandardizerAction instance

Specified by:

cloneItem in interface StandardizerAction

Returns:

a clone of this StandardizerAction instance

clone

public AbstractStandardizerAction clone()
                                 throws CloneNotSupportedException

Overrides:

clone in class Object

Throws:

CloneNotSupportedException

removePropertyChangeListener

public void removePropertyChangeListener(String propertyName,
                                         PropertyChangeListener listener)

Description copied from interface: StandardizerAction

Remove a PropertyChangeListener for a specific property. If listener was added more than once to the same event source for the specified property, it will be notified one less time after being removed. If propertyName is null, no exception is thrown and no action is taken. If listener is null, or was never added for the specified property, no exception is thrown and no action is taken.

Specified by:

removePropertyChangeListener in interface StandardizerAction

Parameters:

propertyName - The name of the property that was listened on.

listener - The PropertyChangeListener to be removed

See Also:

PropertyChangeSupport.removePropertyChangeListener(String, PropertyChangeListener)

addPropertyChangeListener

public void addPropertyChangeListener(String propertyName,
                                      PropertyChangeListener listener)

Description copied from interface: StandardizerAction

Add a PropertyChangeListener for a specific property. The listener will be invoked only when a call on firePropertyChange names that specific property. The same listener object may be added more than once. For each property, the listener will be invoked the number of times it was added for that property. If propertyName or listener is null, no exception is thrown and no action is taken.

Specified by:

addPropertyChangeListener in interface StandardizerAction

Parameters:

propertyName - The name of the property to listen on.

listener - The PropertyChangeListener to be added

See Also:

PropertyChangeSupport.addPropertyChangeListener(String, PropertyChangeListener)

removePropertyChangeListener

public void removePropertyChangeListener(PropertyChangeListener listener)

Description copied from interface: StandardizerAction

Remove a PropertyChangeListener from the listener list. This removes a PropertyChangeListener that was registered for all properties. If listener was added more than once to the same event source, it will be notified one less time after being removed. If listener is null, or was never added, no exception is thrown and no action is taken.

Specified by:

removePropertyChangeListener in interface StandardizerAction

Parameters:

listener - The PropertyChangeListener to be removed

See Also:

PropertyChangeSupport.removePropertyChangeListener(PropertyChangeListener)

addPropertyChangeListener

public void addPropertyChangeListener(PropertyChangeListener listener)

Description copied from interface: StandardizerAction

Add a PropertyChangeListener to the listener list. The listener is registered for all properties. The same listener object may be added more than once, and will be called as many times as it is added. If listener is null, no exception is thrown and no action is taken.

Specified by:

addPropertyChangeListener in interface StandardizerAction

Parameters:

listener - The PropertyChangeListener to be added

See Also:

PropertyChangeSupport.addPropertyChangeListener(PropertyChangeListener)

setLicenseEnvironment

public void setLicenseEnvironment(String env)

Description copied from interface: StandardizerAction

Sets the license environment of the action

Specified by:

setLicenseEnvironment in interface chemaxon.license.Licensable

Specified by:

setLicenseEnvironment in interface StandardizerAction

Parameters:

env - the license environment of the action

isLicensed

public boolean isLicensed()

Specified by:

isLicensed in interface chemaxon.license.Licensable

toString

public String toString()

Overrides:

toString in class Object

propertyChange

public void propertyChange(PropertyChangeEvent evt)

Specified by:

propertyChange in interface PropertyChangeListener

getID

public String getID()

Gets the identifier string of the standardizer action.

Specified by:

getID in interface StandardizerAction

Returns:

the identifier string of the standardizer action

setID

public void setID(String id)

Sets the identifier string of the standardizer action

Parameters:

id - the identifier string of the standardizer action

isActive

public boolean isActive()

Description copied from interface: StandardizerAction

Returns true if the action is active, and can be used

Specified by:

isActive in interface StandardizerAction

Returns:

true if the action is active, and can be used

setActive

public void setActive(boolean active)

Description copied from interface: StandardizerAction

Sets whether the action is active, and can be used

Specified by:

setActive in interface StandardizerAction

Parameters:

active - whether the action should be active, and can be used

anyBooleanPropertyTrue

protected boolean anyBooleanPropertyTrue(Map<String,String> params,
                                         String... keys)

Check the given map, whether there is a String 'true' (case in-sensitive) value for any of the given keys

Parameters:

params - The map in question

keys - array of one or more keys, which values we are interested in

Returns:

true is returned if 'true' (case in-sensitive) is found for any key in the map, 'false' otherwise

getComponents

protected List<Molecule> getComponents(Molecule molecule)

A recursive algorithm getting all components (reactants, agents and products of reaction molecules, R-group definitions of Rg-Molecules) of the molecule. Used to collect all. If components must not be standardized, this method should be overridden.

Parameters:

molecule - the target molecule

Returns:

the resulted list of components