Package chemaxon.standardizer.actions

Class AliasToGroupAction

java.lang.Object

chemaxon.standardizer.AbstractStandardizerAction

chemaxon.standardizer.actions.AliasToGroupAction

All Implemented Interfaces:

Licensable, StandardizerAction, PropertyChangeListener, Cloneable, EventListener

@PublicApi
public final class AliasToGroupAction
extends AbstractStandardizerAction

Standardizer action that converts atom aliases to abbreviated groups.

Since:

5.11

Field Summary

Fields

Modifier and Type	Field	Description
static final String	ABBREV_GROUPS_KEY	Property Key of the abbreviated group modification

Fields inherited from class chemaxon.standardizer.AbstractStandardizerAction

CONFIG_PATH_KEY, FORMAT_KEY, ID_KEY, support

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
AliasToGroupAction	clone()
Map<String,Molecule>	getGroups()	Gets the abbreviated groups of the action
void	setGroups(Map<String,Molecule> groups)	Sets the abbreviated groups 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, anyBooleanPropertyTrue, cloneItem, getComponents, 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 Details

ABBREV_GROUPS_KEY

public static final String ABBREV_GROUPS_KEY

Property Key of the abbreviated group modification

See Also:

• Constant Field Values

Constructor Details

AliasToGroupAction

public AliasToGroupAction(Map<String,String> params)

Initializes the action with parameters

Parameters:

params - the parameters of the action

Method Details

setGroups

public void setGroups(Map<String,Molecule> groups)

Sets the abbreviated groups of the action

Parameters:

groups - the abbreviated groups of the action

getGroups

public Map<String,Molecule> getGroups()

Gets the abbreviated groups of the action

Returns:

the abbreviated groups 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 AliasToGroupAction clone()
                         throws CloneNotSupportedException

Overrides:

clone in class AbstractStandardizerAction

Throws:

CloneNotSupportedException

toString

public String toString()

Overrides:

toString in class AbstractStandardizerAction