Package chemaxon.standardizer.runner

Class BasicStandardizerRunner

java.lang.Object

chemaxon.standardizer.runner.BasicStandardizerRunner

All Implemented Interfaces:

StandardizerActionRunner, Cloneable

@PublicApi
public class BasicStandardizerRunner
extends Object
implements StandardizerActionRunner

This is the default implementation of StandardizerActionRunner interface.

If the provided molecule is null or contains errors IllegalArgumentException should be thrown during the standardization procedure.

Logs are generated to a System.Logger, that can be collected by using StandardizerLogger.getLogger() method.

Since:

5.11

Field Summary

Fields

Modifier and Type	Field	Description
protected Thread	backgroundThread
protected Molecule	molecule	The Molecule instance to standardize

Constructor Summary

Constructors

Constructor	Description
BasicStandardizerRunner(StandardizerConfigurationReader configurationReader)	Initialize a BasicStandardizerRunner instance with the StandardizerConfiguration read from the provided configuration reader.
BasicStandardizerRunner(StandardizerConfiguration configuration)	Initialize a BasicStandardizerRunner instance with specified StandardizerConfiguration.

Method Summary

Modifier and Type	Method	Description
void	addPropertyChangeListener(PropertyChangeListener changeListener)	Adds a PropertyChangeListener that will receive all the PropertyChangeEvent fired by this class
void	addPropertyChangeListener(String propertyName, PropertyChangeListener listener)	Adds a PropertyChangeListener that will receive the PropertyChangeEvent fired when the property with the given name is changed
void	cancel()	Stops the background thread
BasicStandardizerRunner	clone()
List<StandardizerAction>	getAppliedActions()	Gets the list of actions applied in the configuration at the last execution
List<Changes>	getChanges()	Gets the list of changes applied on the molecule.
protected PropertyChangeSupport	getChangeSupport()	Returns the changeSupport
StandardizerConfiguration	getConfiguration()	Gets the configuration of the runner
int	getCurrent()	Gets the current progress percent
String	getCurrentActionName()	Gets which StandardizerAction instance run currently
protected int	getIndex()	Returns the index of the actual action of the configuration
Molecule	getMolecule()	Returns the target molecule
int	getProgessLength()	Gets the length of the standardization process
protected Runnable	getStrategy()	Returns the strategy to use.
String[]	getTargetGroups()	Gets the target action groups of the standardizer
protected boolean	isCanceled()	Returns whether the process is cancelled
boolean	isRunning()	This function identifies the state of the standardizer thread
protected void	setCanceled(boolean canceled)	Sets whether the process is cancelled
protected void	setChangeSupport(PropertyChangeSupport changeSupport)	Sets the changeSupport
void	setConfiguration(StandardizerConfiguration configuration)	Sets the configuration of the runner
void	setConfigurationReader(StandardizerConfigurationReader configurationReader)	Sets a new configuration for the runner.
void	setIgnoreConfigurationErrors(boolean ignore)	Sets whether configuration errors should be ignored
protected void	setIndex(int index)	Sets the index of the actual action of the configuration
void	setLicenseEnvironment(String env)	Sets the license environment of the runner
void	setMolecule(Molecule molecule)	Sets the molecule to be standardized by the standardizer actions
void	setTargetGroup(String groupName)	Sets the target group of standardizer action of the runner
void	setTargetGroups(String... groupNames)	Sets the target groups of standardizer action of the runner
void	standardize()	Invoke a background thread which will run all standardizer actions on the given molecule
List<Changes>	standardizeAndWait()	Executes all standardizer actions contained by the pre-set configuration on the given molecule and returns the list of applied changes.

Methods inherited from class java.lang.Object

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

Field Details

molecule

protected Molecule molecule

The Molecule instance to standardize

backgroundThread

protected Thread backgroundThread

Constructor Details

BasicStandardizerRunner

public BasicStandardizerRunner(StandardizerConfigurationReader configurationReader)

Initialize a BasicStandardizerRunner instance with the StandardizerConfiguration read from the provided configuration reader.

Parameters:

configurationReader - a StandardizerConfigurationReader instance, containing the configuration of the standardization process

BasicStandardizerRunner

public BasicStandardizerRunner(StandardizerConfiguration configuration)

Initialize a BasicStandardizerRunner instance with specified StandardizerConfiguration.

Parameters:

configuration - the configuration of the standardization procedure

Method Details

setConfigurationReader

public void setConfigurationReader(StandardizerConfigurationReader configurationReader)

Description copied from interface: StandardizerActionRunner

Sets a new configuration for the runner.

Specified by:

setConfigurationReader in interface StandardizerActionRunner

Parameters:

configurationReader - is the StandardizerConfigurationReader instance which provides the current configuration

setMolecule

public void setMolecule(Molecule molecule)

Description copied from interface: StandardizerActionRunner

Sets the molecule to be standardized by the standardizer actions

Specified by:

setMolecule in interface StandardizerActionRunner

Parameters:

molecule - a Molecule instance to be standardized

standardize

public void standardize()
                 throws IllegalArgumentException

Description copied from interface: StandardizerActionRunner

Invoke a background thread which will run all standardizer actions on the given molecule

Specified by:

standardize in interface StandardizerActionRunner

Throws:

IllegalArgumentException - if the configuration or the molecule contains errors

cancel

public void cancel()

Description copied from interface: StandardizerActionRunner

Stops the background thread

Specified by:

cancel in interface StandardizerActionRunner

getCurrent

public int getCurrent()

Description copied from interface: StandardizerActionRunner

Gets the current progress percent

Specified by:

getCurrent in interface StandardizerActionRunner

Returns:

the current progress percent

getCurrentActionName

public String getCurrentActionName()

Description copied from interface: StandardizerActionRunner

Gets which StandardizerAction instance run currently

Specified by:

getCurrentActionName in interface StandardizerActionRunner

Returns:

which StandardizerAction instance run currently

getProgessLength

public int getProgessLength()

Description copied from interface: StandardizerActionRunner

Gets the length of the standardization process

Specified by:

getProgessLength in interface StandardizerActionRunner

Returns:

the length of the standardization process

isRunning

public boolean isRunning()

Description copied from interface: StandardizerActionRunner

This function identifies the state of the standardizer thread

Specified by:

isRunning in interface StandardizerActionRunner

Returns:

true if the background thread runs false otherwise

addPropertyChangeListener

public void addPropertyChangeListener(PropertyChangeListener changeListener)

Description copied from interface: StandardizerActionRunner

Adds a PropertyChangeListener that will receive all the PropertyChangeEvent fired by this class

Specified by:

addPropertyChangeListener in interface StandardizerActionRunner

Parameters:

changeListener - a PropertyChangeListener instance

addPropertyChangeListener

public void addPropertyChangeListener(String propertyName,
 PropertyChangeListener listener)

Description copied from interface: StandardizerActionRunner

Adds a PropertyChangeListener that will receive the PropertyChangeEvent fired when the property with the given name is changed

Specified by:

addPropertyChangeListener in interface StandardizerActionRunner

Parameters:

propertyName - the name of the property to be listened

listener - a PropertyChangeListener instance

standardizeAndWait

public List<Changes> standardizeAndWait()
                                 throws IllegalArgumentException

Description copied from interface: StandardizerActionRunner

Executes all standardizer actions contained by the pre-set configuration on the given molecule and returns the list of applied changes. For each action of the configuration there is a change object (or null) in the list.

Specified by:

standardizeAndWait in interface StandardizerActionRunner

Returns:

the list of changes applied on the molecule

Throws:

IllegalArgumentException - if the configuration or the molecule contains errors

getStrategy

protected Runnable getStrategy()

Returns the strategy to use.

Returns:

the strategy

setCanceled

protected void setCanceled(boolean canceled)

Sets whether the process is cancelled

Parameters:

canceled - whether the process should be cancelled

isCanceled

protected boolean isCanceled()

Returns whether the process is cancelled

Returns:

whether the process is cancelled

setIndex

protected void setIndex(int index)

Sets the index of the actual action of the configuration

Parameters:

index - the index of the actual action of the configuration

getIndex

protected int getIndex()

Returns the index of the actual action of the configuration

Returns:

the index of the actual action of the configuration

setConfiguration

public void setConfiguration(StandardizerConfiguration configuration)

Description copied from interface: StandardizerActionRunner

Sets the configuration of the runner

Specified by:

setConfiguration in interface StandardizerActionRunner

Parameters:

configuration - the configuration to be set to the runner

getMolecule

public Molecule getMolecule()

Returns the target molecule

Returns:

the target molecule

setChangeSupport

protected void setChangeSupport(PropertyChangeSupport changeSupport)

Sets the changeSupport

Parameters:

changeSupport - the changeSupport to be set

getChangeSupport

protected PropertyChangeSupport getChangeSupport()

Returns the changeSupport

Returns:

the changeSupport

getConfiguration

public StandardizerConfiguration getConfiguration()

Description copied from interface: StandardizerActionRunner

Gets the configuration of the runner

Specified by:

getConfiguration in interface StandardizerActionRunner

Returns:

the configuration of the runner

getAppliedActions

public List<StandardizerAction> getAppliedActions()

Description copied from interface: StandardizerActionRunner

Gets the list of actions applied in the configuration at the last execution

Specified by:

getAppliedActions in interface StandardizerActionRunner

Returns:

the list of applied actions at the last execution

setTargetGroup

public void setTargetGroup(String groupName)

Description copied from interface: StandardizerActionRunner

Sets the target group of standardizer action of the runner

Specified by:

setTargetGroup in interface StandardizerActionRunner

Parameters:

groupName - the name of the group of standardizer actions

setTargetGroups

public void setTargetGroups(String... groupNames)

Description copied from interface: StandardizerActionRunner

Sets the target groups of standardizer action of the runner

Specified by:

setTargetGroups in interface StandardizerActionRunner

Parameters:

groupNames - the names of the groups of standardizer actions

getTargetGroups

public String[] getTargetGroups()

Gets the target action groups of the standardizer

Returns:

the target action groups of the standardizer

clone

public BasicStandardizerRunner clone()
                              throws CloneNotSupportedException

Overrides:

clone in class Object

Throws:

CloneNotSupportedException

setLicenseEnvironment

public void setLicenseEnvironment(String env)

Description copied from interface: StandardizerActionRunner

Sets the license environment of the runner

Specified by:

setLicenseEnvironment in interface StandardizerActionRunner

Parameters:

env - the license environment of the runner

getChanges

public List<Changes> getChanges()

Description copied from interface: StandardizerActionRunner

Gets the list of changes applied on the molecule. For each action of the configuration there is a change object (or null) in the list.

Specified by:

getChanges in interface StandardizerActionRunner

Returns:

the list of changes applied on the molecule

setIgnoreConfigurationErrors

public void setIgnoreConfigurationErrors(boolean ignore)

Description copied from interface: StandardizerActionRunner

Sets whether configuration errors should be ignored

Specified by:

setIgnoreConfigurationErrors in interface StandardizerActionRunner

Parameters:

ignore - whether configuration errors should be ignored