Package chemaxon.standardizer.actions

Class RemoveFragmentAction

java.lang.Object

chemaxon.standardizer.AbstractStandardizerAction

chemaxon.standardizer.actions.RemoveFragmentAction

All Implemented Interfaces:

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

@PublicAPI
public final class RemoveFragmentAction
extends AbstractStandardizerAction

Removal standardizer action

Since:

5.11

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	RemoveFragmentAction.Measurement	Type of measurement
static class	RemoveFragmentAction.Method	Type of removal methods

Field Summary

Fields

Modifier and Type	Field	Description
static String	MEASUREMENT_KEY	Key of measurement for parsing and property change
static String	METHOD_KEY	Key of method for parsing and property change

Fields inherited from class chemaxon.standardizer.AbstractStandardizerAction

CONFIG_PATH_KEY, FORMAT_KEY, ID_KEY, support

Constructor Summary

Constructors

Constructor	Description
RemoveFragmentAction(Map<String,String> params)	Initializes the action with parameters

Method Summary

Modifier and Type	Method	Description
RemoveFragmentAction	clone()
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.
RemoveFragmentAction.Measurement	getMeasure()	Gets the measure of the action
RemoveFragmentAction.Method	getMethod()	Gets the method of the action
void	setMeasure(RemoveFragmentAction.Measurement measurement)	Sets the measurement of the action
void	setMethod(RemoveFragmentAction.Method method)	Sets the method of the action
protected Changes	standardize1(Molecule molecule)	This method contains the current standardization mechanism.
String	toString()

Methods inherited from class chemaxon.standardizer.AbstractStandardizerAction

addPropertyChangeListener, addPropertyChangeListener, cloneItem, getDescriptor, getID, isActive, isAvailable, isLicensed, isValid, propertyChange, removePropertyChangeListener, removePropertyChangeListener, setActive, setID, setLicenseEnvironment, setValid, standardize

Methods inherited from class java.lang.Object

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

Field Detail

MEASUREMENT_KEY

public static final String MEASUREMENT_KEY

Key of measurement for parsing and property change

See Also:

Constant Field Values

METHOD_KEY

public static final String METHOD_KEY

Key of method for parsing and property change

See Also:

Constant Field Values

Constructor Detail

RemoveFragmentAction

public RemoveFragmentAction(Map<String,String> params)

Initializes the action with parameters

Parameters:

params - the parameters of the action

Method Detail

getComponents

protected List<Molecule> getComponents(Molecule molecule)

Description copied from class: AbstractStandardizerAction

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.

Overrides:

getComponents in class AbstractStandardizerAction

Parameters:

molecule - the target molecule

Returns:

the resulted list of components

setMethod

public void setMethod(RemoveFragmentAction.Method method)

Sets the method of the action

Parameters:

method - the method to be set

setMeasure

public void setMeasure(RemoveFragmentAction.Measurement measurement)

Sets the measurement of the action

Parameters:

measurement - the measurement of the action

getMethod

public RemoveFragmentAction.Method getMethod()

Gets the method of the action

Returns:

the method of the action

getMeasure

public RemoveFragmentAction.Measurement getMeasure()

Gets the measure of the action

Returns:

the measure of the action

standardize1

protected Changes standardize1(Molecule molecule)

Description copied from class: AbstractStandardizerAction

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 AbstractStandardizerAction.getComponents(Molecule), and AbstractStandardizerAction.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.

Specified by:

standardize1 in class AbstractStandardizerAction

Parameters:

molecule - the Molecule instance to be standardized

Returns:

the changes applied on the molecule during the standardization process

clone

public RemoveFragmentAction clone()
                           throws CloneNotSupportedException

Overrides:

clone in class AbstractStandardizerAction

Throws:

CloneNotSupportedException

toString

public String toString()

Overrides:

toString in class AbstractStandardizerAction