chemaxon.standardizer.advancedactions

Class TransformAction

java.lang.Object

chemaxon.standardizer.AbstractStandardizerAction

chemaxon.standardizer.advancedactions.TransformAction

All Implemented Interfaces:

chemaxon.license.Licensable, StandardizerAction, java.beans.PropertyChangeListener, java.lang.Cloneable, java.util.EventListener

@PublicAPI
public final class TransformAction
extends AbstractStandardizerAction

Transformation standardizer action

Since:

5.11

Author:

Imre Barna

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	EXACT_KEY Key of exact for parsing and property change
protected static java.lang.String	LINE_SEP Line separator.
static java.lang.String	SEARCH_OPTIONS_KEY Key of search options for parsing and property change
static java.lang.String	STRUCTURE_KEY Key of query molecule for parsing and property change

Fields inherited from class chemaxon.standardizer.AbstractStandardizerAction

CONFIG_PATH_KEY, FORMAT_KEY, ID_KEY, support

Constructor Summary

Constructors

Constructor and Description
TransformAction(java.util.Map<java.lang.String,java.lang.String> params) Initializes the action with parameters

Method Summary

Modifier and Type	Method and Description
TransformAction	clone()
protected java.util.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.
java.lang.String	getSearchOptions() Gets the search options of the action
java.lang.String	getStructure() Deprecated.
RxnMolecule	getTransform() Gets the transformation molecule of the action
java.lang.String	getType() Gets the type of transformation
boolean	isEditable() Returns if this action is editable.
boolean	isExact() Gets the exact value of the action
void	setEditable(boolean editable) Sets if this action is editable.
void	setExact(boolean exact) Sets the exact value of the action
void	setSearchOptions(java.lang.String optionString) Sets the search options of the action
void	setStructure(java.lang.String structure) Deprecated. use setTransform(RxnMolecule) method instead
void	setTransform(RxnMolecule structure) Sets the transformation
protected Changes	standardize1(Molecule molecule) This method contains the current standardization mechanism.
java.lang.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

EXACT_KEY

public static final java.lang.String EXACT_KEY

Key of exact for parsing and property change

See Also:

Constant Field Values

SEARCH_OPTIONS_KEY

public static final java.lang.String SEARCH_OPTIONS_KEY

Key of search options for parsing and property change

See Also:

Constant Field Values

STRUCTURE_KEY

public static final java.lang.String STRUCTURE_KEY

Key of query molecule for parsing and property change

See Also:

Constant Field Values

LINE_SEP

protected static final java.lang.String LINE_SEP

Line separator.

Constructor Detail

TransformAction

public TransformAction(java.util.Map<java.lang.String,java.lang.String> params)

Initializes the action with parameters

Parameters:

params - the parameters of the action

Method Detail

setSearchOptions

public void setSearchOptions(java.lang.String optionString)

Sets the search options of the action

Parameters:

optionString - the search options of the action

getSearchOptions

public java.lang.String getSearchOptions()

Gets the search options of the action

Returns:

the search options of the action

setEditable

public void setEditable(boolean editable)

Sets if this action is editable.

Parameters:

editable - the new editable flag

isEditable

public boolean isEditable()

Returns if this action is editable.

Returns:

true if the action is editable

setExact

public void setExact(boolean exact)

Sets the exact value of the action

Parameters:

exact - the exact value of the action

isExact

public boolean isExact()

Gets the exact value of the action

Returns:

the exact value of the action

setStructure

@Deprecated
public void setStructure(java.lang.String structure)

Deprecated. use setTransform(RxnMolecule) method instead

Sets the transformation

Parameters:

structure - the molecule defining the transformation

setTransform

public void setTransform(RxnMolecule structure)

Sets the transformation

Parameters:

structure - the molecule defining the transformation

getStructure

@Deprecated
public java.lang.String getStructure()

Deprecated.

Gets the transformation

Returns:

the string representation of the molecule defining the transformation

getTransform

public RxnMolecule getTransform()

Gets the transformation molecule of the action

Returns:

the transformation molecule of the action

getType

public java.lang.String getType()

Gets the type of transformation

Returns:

the type of the transformation

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

getComponents

protected java.util.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

clone

public TransformAction clone()
                      throws java.lang.CloneNotSupportedException

Overrides:

clone in class AbstractStandardizerAction

Throws:

java.lang.CloneNotSupportedException

toString

public java.lang.String toString()

Overrides:

toString in class AbstractStandardizerAction