Package chemaxon.checkers.runner

Class AdvancedCheckerRunner

java.lang.Object

chemaxon.checkers.runner.BasicCheckerRunner

chemaxon.checkers.runner.AdvancedCheckerRunner

All Implemented Interfaces:

CheckerRunner

@PublicAPI
public class AdvancedCheckerRunner
extends chemaxon.checkers.runner.BasicCheckerRunner

CheckerRunner implementation with advanced fixing capabilities.
StructureFixer selection is based on provided fixer class if available, or falls back to StructureCheckerResult based selection.
Supports multiple iterations of checking and fixing for the best fixing efforts.

Since:

5.7

Field Summary

Fields

Modifier and Type	Field	Description
protected chemaxon.checkers.logger.StructureCheckerLogger	logger

Fields inherited from class chemaxon.checkers.runner.BasicCheckerRunner

backgroundThread, molecule

Constructor Summary

Constructors

Constructor	Description
AdvancedCheckerRunner(ConfigurationReader configurationReader)	Constructs CheckerRunner with more advanced fixing capabilities.
AdvancedCheckerRunner(ConfigurationReader configurationReader, chemaxon.structurechecker.factory.CheckerFixerFactory checkerFixerFactory)	Constructs CheckerRunner with more advanced fixing capabilities.
AdvancedCheckerRunner(List<StructureChecker> checkerList)	Constructs CheckerRunner with more advanced fixing capabilities.

Method Summary

Modifier and Type	Method	Description
void	check()	Invokes a background thread which will run all checkers on the given molecule
List<StructureCheckerResult>	checkAndWait()	Executes all the checker instances on the given molecule and returns a List of StructureCheckerResult containing all the identified problems
boolean	fix()	Checks the structure, then fixes the problems based on configuration. NOTE: FixMode and fixerClassName from configuration is used to choose best fixer.
boolean	fix(StructureCheckerResult result)	Fixes the given result based on the fixer defined for the checker.
protected boolean	fix(StructureChecker checker, StructureCheckerResult result)	Tries to fix the problem detected by the specified checker, or falls back to result based behavior.
chemaxon.checkers.logger.StructureCheckerLogger	getLogger()	Returns the current logger.
protected boolean	isFallBackToBasic()	Returns true if runner should fall back to basic runner when preferred fix failed.
void	setLogger(chemaxon.checkers.logger.StructureCheckerLogger logger)	Sets the logger.
void	setMolecule(Molecule molecule)	Sets the molecule to be checked by the checkers

Methods inherited from class chemaxon.checkers.runner.BasicCheckerRunner

addPropertyChangeListener, addPropertyChangeListener, cancel, convertResult, getChangeSupport, getCheckerConfiguration, getCheckerList, getCurrent, getCurrentCheckerName, getFixers, getIndex, getMolecule, getProgessLength, getResultList, getStrategy, isCanceled, isChecking, isDoodle, setCanceled, setChangeSupport, setCheckerList, setConfigurationReader, setDoodle, setIgnoreConfigurationErrors, setIndex, setResultList

Methods inherited from class java.lang.Object

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

Field Details

logger

protected chemaxon.checkers.logger.StructureCheckerLogger logger

Constructor Details

AdvancedCheckerRunner

public AdvancedCheckerRunner(ConfigurationReader configurationReader)

Constructs CheckerRunner with more advanced fixing capabilities.

Parameters:

configurationReader - the checker configuration

AdvancedCheckerRunner

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

Constructs CheckerRunner with more advanced fixing capabilities.

Parameters:

configurationReader - the checker configuration

checkerFixerFactory - the factory for fixers

AdvancedCheckerRunner

public AdvancedCheckerRunner(List<StructureChecker> checkerList)

Constructs CheckerRunner with more advanced fixing capabilities.

Parameters:

checkerList - the checker list

Method Details

fix

public boolean fix(StructureCheckerResult result)

Fixes the given result based on the fixer defined for the checker. If fixer is not defined, the fixer with the highest priority associated to the error type of the result will be executed.

Specified by:

fix in interface CheckerRunner

Overrides:

fix in class chemaxon.checkers.runner.BasicCheckerRunner

Parameters:

result - the checker result to fix

Returns:

true if the fix ended correctly false otherwise

fix

protected boolean fix(StructureChecker checker,
 StructureCheckerResult result)

Tries to fix the problem detected by the specified checker, or falls back to result based behavior. NOTE: if FixMode is different from FixMode.FIX, no fixing attempt will be performed.

Parameters:

checker - the checker that detected the problem

result - the result of check

Returns:

true if problem is fixed

isFallBackToBasic

protected boolean isFallBackToBasic()

Returns true if runner should fall back to basic runner when preferred fix failed.

Returns:

true if runner should fall back to basic runner when preferred fix failed

Since:

5.12

fix

public boolean fix()

Checks the structure, then fixes the problems based on configuration.
NOTE: FixMode and fixerClassName from configuration is used to choose best fixer. Checkers with FixMode FixMode.ASK will not be fixed. Runs multiple iterations for best fix results.

Specified by:

fix in interface CheckerRunner

Overrides:

fix in class chemaxon.checkers.runner.BasicCheckerRunner

Returns:

true if the fix ended correctly false otherwise

checkAndWait

public List<StructureCheckerResult> checkAndWait()

Description copied from interface: CheckerRunner

Executes all the checker instances on the given molecule and returns a List of StructureCheckerResult containing all the identified problems

Specified by:

checkAndWait in interface CheckerRunner

Overrides:

checkAndWait in class chemaxon.checkers.runner.BasicCheckerRunner

Returns:

a List of StructureCheckerResult containing all the identified problem about the given molecule

check

public void check()

Description copied from interface: CheckerRunner

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

Specified by:

check in interface CheckerRunner

Overrides:

check in class chemaxon.checkers.runner.BasicCheckerRunner

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

Overrides:

setMolecule in class chemaxon.checkers.runner.BasicCheckerRunner

Parameters:

molecule - a Molecule instance to be checked

getLogger

public chemaxon.checkers.logger.StructureCheckerLogger getLogger()

Returns the current logger.

Returns:

the current logger

setLogger

public void setLogger(chemaxon.checkers.logger.StructureCheckerLogger logger)

Sets the logger.

Parameters:

logger - the new logger