chemaxon.checkers.runner

Class BasicCheckerRunner

java.lang.Object

chemaxon.checkers.runner.BasicCheckerRunner

All Implemented Interfaces:

CheckerRunner

Direct Known Subclasses:

AdvancedCheckerRunner, SketchCheckerRunner

public class BasicCheckerRunner
extends Object
implements CheckerRunner

This is the default basic implementation of CheckerRunner interface/

Since:

Marvin 5.7

Version:

5.9

Author:

Attila Szabo

Field Summary

Fields

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

Constructor Summary

Constructors

Constructor and Description
BasicCheckerRunner(ConfigurationReader configurationReader) Initiate a BasicCheckerRunner instance which will can execute StructureChecker instances read from configurationReader
BasicCheckerRunner(ConfigurationReader configurationReader, chemaxon.structurechecker.factory.CheckerFixerFactory checkerFixerFactory) Initiate a BasicCheckerRunner instance which will can execute StructureChecker instances read from configurationReader
BasicCheckerRunner(ConfigurationReader configurationReader, StructureFixerFactory fixerFactory) Deprecated. use BasicCheckerRunner(ConfigurationReader, CheckerFixerFactory) instead
BasicCheckerRunner(List<StructureChecker> checkerList) Initiate a BasicCheckerRunner instance with specified StructureChecker list.
BasicCheckerRunner(List<StructureChecker> checkerList, boolean addFixers) Initiate a BasicCheckerRunner instance with specified StructureChecker list.

Method Summary

Methods

Modifier and Type	Method and 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
void	check() Invoke a background thread which will run all checkers on the given molecule
List<StructureCheckerResult>	checkAndWait() Execute all the checker instances on the given molecule and return a List of StructureCheckerResult which contains all the identified problems
protected void	convertResult(StructureCheckerResult result) This method provides the possibility to convert back the affected properties of the result if there was any convert in the molecule structure before check.
boolean	fix() Runs all StructureChecker on the given molecule and after that fixes all identified problems with the first StructureFixer which is associated with the current problem.
boolean	fix(StructureCheckerResult result) Fixes the problem identified by result with the first StructureFixer which is associated with the StructureCheckerErrorType of the result.
protected PropertyChangeSupport	getChangeSupport() Returns the changeSupport
List<StructureChecker>	getCheckerConfiguration() Gets the list of available checkers
protected List<StructureChecker>	getCheckerList() Returns the checkerList
int	getCurrent()
String	getCurrentCheckerName()
List<StructureFixer>	getFixers(StructureCheckerResult result) Returns all the StructureFixer instances which associated with the StructureCheckerErrorType of the result
protected int	getIndex() Returns the index
protected Molecule	getMolecule() Returns the molecule
int	getProgessLength()
List<StructureCheckerResult>	getResultList()
protected Runnable	getStrategy() Returns the strategy to use.
protected boolean	isCanceled() Returns the canceled
boolean	isChecking() This function identifies the state of the checker thread
protected boolean	isDoodle() Returns the isDoodle
protected void	setCanceled(boolean canceled) Sets the canceled
protected void	setChangeSupport(PropertyChangeSupport changeSupport) Sets the changeSupport
protected void	setCheckerList(List<StructureChecker> checkerList) Sets the checkerList
void	setConfigurationReader(ConfigurationReader configurationReader) Sets a new configuration for the Runner.
protected void	setDoodle(boolean isDoodle) Sets the isDoodle
void	setIgnoreConfigurationErrors(boolean ignore) Sets whether configuration errors should be ignored on execution.
protected void	setIndex(int index) Sets the index
void	setMolecule(Molecule molecule) Sets the molecule to be checked by the checkers
protected void	setResultList(List<StructureCheckerResult> resultList) Sets the resultList

Methods inherited from class java.lang.Object

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

Field Detail

molecule

protected Molecule molecule

The Molecule instance to check

backgroundThread

protected Thread backgroundThread

Constructor Detail

BasicCheckerRunner

public BasicCheckerRunner(ConfigurationReader configurationReader)

Initiate a BasicCheckerRunner instance which will can execute StructureChecker instances read from configurationReader

Parameters:

configurationReader - a ConfigurationReader instance

BasicCheckerRunner

@Deprecated
public BasicCheckerRunner(ConfigurationReader configurationReader,
                             StructureFixerFactory fixerFactory)

Deprecated. use BasicCheckerRunner(ConfigurationReader, CheckerFixerFactory) instead

Initiate a BasicCheckerRunner instance which will can execute StructureChecker instances read from configurationReader

Parameters:

configurationReader - a ConfigurationReader instance

fixerFactory - the fixer factory

BasicCheckerRunner

public BasicCheckerRunner(ConfigurationReader configurationReader,
                  chemaxon.structurechecker.factory.CheckerFixerFactory checkerFixerFactory)

Initiate a BasicCheckerRunner instance which will can execute StructureChecker instances read from configurationReader

Parameters:

configurationReader - a ConfigurationReader instance

checkerFixerFactory - the factory for fixers

BasicCheckerRunner

public BasicCheckerRunner(List<StructureChecker> checkerList)

Initiate a BasicCheckerRunner instance with specified StructureChecker list.

Parameters:

checkerList - the checker list

Since:

5.9

BasicCheckerRunner

public BasicCheckerRunner(List<StructureChecker> checkerList,
                  boolean addFixers)

Initiate a BasicCheckerRunner instance with specified StructureChecker list.

Parameters:

checkerList - the checker list

addFixers - whether the default set of fixers should be associated to the provided checkers

Since:

6.1

Method Detail

setConfigurationReader

public void setConfigurationReader(ConfigurationReader configurationReader)

Description copied from interface: CheckerRunner

Sets a new configuration for the Runner.

Specified by:

setConfigurationReader in interface CheckerRunner

Parameters:

configurationReader - is the ConfigurationReader instance which provides the current configuraiton

fix

public boolean fix()

Description copied from interface: CheckerRunner

Runs all StructureChecker on the given molecule and after that fixes all identified problems with the first StructureFixer which is associated with the current problem.

Specified by:

fix in interface CheckerRunner

Returns:

true if the fix ended correctly false otherwise

fix

public boolean fix(StructureCheckerResult result)

Description copied from interface: CheckerRunner

Fixes the problem identified by result with the first StructureFixer which is associated with the StructureCheckerErrorType of the result.

Specified by:

fix in interface CheckerRunner

Parameters:

result - a StructureCheckerResult instance which identifies the problem

Returns:

true if the fix ended correctly false otherwise

getFixers

public List<StructureFixer> getFixers(StructureCheckerResult result)

Description copied from interface: CheckerRunner

Returns all the StructureFixer instances which associated with the StructureCheckerErrorType of the result

Specified by:

getFixers in interface CheckerRunner

Parameters:

result - a StructureCheckerResult instance which identifies the current problem

Returns:

a List of StructureFixer

setMolecule

public void setMolecule(Molecule molecule)

Description copied from interface: CheckerRunner

Sets the molecule to be checked by the checkers

Specified by:

setMolecule in interface CheckerRunner

Parameters:

molecule - a Molecule instance to be checked

check

public void check()

Description copied from interface: CheckerRunner

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

Specified by:

check in interface CheckerRunner

cancel

public void cancel()

Description copied from interface: CheckerRunner

Stops the background thread

Specified by:

cancel in interface CheckerRunner

getCurrent

public int getCurrent()

Specified by:

getCurrent in interface CheckerRunner

Returns:

the current progress percent

getCurrentCheckerName

public String getCurrentCheckerName()

Specified by:

getCurrentCheckerName in interface CheckerRunner

Returns:

which StructureChecker instance run currently

getProgessLength

public int getProgessLength()

Specified by:

getProgessLength in interface CheckerRunner

Returns:

the length of the checking process

getResultList

public List<StructureCheckerResult> getResultList()

Specified by:

getResultList in interface CheckerRunner

Returns:

a List of StructureCheckerResult which contains all the dentified problem about the given molecule

isChecking

public boolean isChecking()

Description copied from interface: CheckerRunner

This function identifies the state of the checker thread

Specified by:

isChecking in interface CheckerRunner

Returns:

true if the background thread runs false otherwise

addPropertyChangeListener

public void addPropertyChangeListener(PropertyChangeListener changeListener)

Description copied from interface: CheckerRunner

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

Specified by:

addPropertyChangeListener in interface CheckerRunner

Parameters:

changeListener - a PropertyChangeListener instance

addPropertyChangeListener

public void addPropertyChangeListener(String propertyName,
                             PropertyChangeListener listener)

Description copied from interface: CheckerRunner

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

Specified by:

addPropertyChangeListener in interface CheckerRunner

Parameters:

propertyName - the name of the property to be listened

listener - a PropertyChangeListener instance

checkAndWait

public List<StructureCheckerResult> checkAndWait()

Description copied from interface: CheckerRunner

Execute all the checker instances on the given molecule and return a List of StructureCheckerResult which contains all the identified problems

Specified by:

checkAndWait in interface CheckerRunner

Returns:

a List of StructureCheckerResult which contains all the identified problem about the given molecule

convertResult

protected void convertResult(StructureCheckerResult result)

This method provides the possibility to convert back the affected properties of the result if there was any convert in the molecule structure before check. By default this implementation is empty and isn't needed to override!

Parameters:

result - the StructureCheckerResult instance

getStrategy

protected Runnable getStrategy()

Returns the strategy to use.

Returns:

the strategy

setCanceled

protected void setCanceled(boolean canceled)

Sets the canceled

Parameters:

canceled - the canceled to set

isCanceled

protected boolean isCanceled()

Returns the canceled

Returns:

the canceled

setDoodle

protected void setDoodle(boolean isDoodle)

Sets the isDoodle

Parameters:

isDoodle - the isDoodle to set

isDoodle

protected boolean isDoodle()

Returns the isDoodle

Returns:

the isDoodle

setIndex

protected void setIndex(int index)

Sets the index

Parameters:

index - the index to set

getIndex

protected int getIndex()

Returns the index

Returns:

the index

setResultList

protected void setResultList(List<StructureCheckerResult> resultList)

Sets the resultList

Parameters:

resultList - the resultList to set

setCheckerList

protected void setCheckerList(List<StructureChecker> checkerList)

Sets the checkerList

Parameters:

checkerList - the checkerList to set

getCheckerList

protected List<StructureChecker> getCheckerList()

Returns the checkerList

Returns:

the checkerList

getMolecule

protected Molecule getMolecule()

Returns the molecule

Returns:

the molecule

setChangeSupport

protected void setChangeSupport(PropertyChangeSupport changeSupport)

Sets the changeSupport

Parameters:

changeSupport - the changeSupport to set

getChangeSupport

protected PropertyChangeSupport getChangeSupport()

Returns the changeSupport

Returns:

the changeSupport

getCheckerConfiguration

public List<StructureChecker> getCheckerConfiguration()

Description copied from interface: CheckerRunner

Gets the list of available checkers

Specified by:

getCheckerConfiguration in interface CheckerRunner

Returns:

the list of available checkers

setIgnoreConfigurationErrors

public void setIgnoreConfigurationErrors(boolean ignore)

Description copied from interface: CheckerRunner

Sets whether configuration errors should be ignored on execution.

Specified by:

setIgnoreConfigurationErrors in interface CheckerRunner

Parameters:

ignore - true if configuration errors should be ignored on execution