chemaxon.checkers.runner
Class AdvancedCheckerRunner

java.lang.Object
  chemaxon.checkers.runner.BasicCheckerRunner
      chemaxon.checkers.runner.AdvancedCheckerRunner

All Implemented Interfaces:

CheckerRunner

public class AdvancedCheckerRunner
extends 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

Version:

5.9

Author:

Istvan Rabel

Field Summary

protected boolean	fallBackToBasic indicates that fix should fall back to super fix, or not
protected chemaxon.checkers.logger.StructureCheckerLogger	logger

Fields inherited from class chemaxon.checkers.runner.BasicCheckerRunner

backgroundThread, molecule

Constructor Summary

AdvancedCheckerRunner(ConfigurationReader configurationReader)
Constructs CheckerRunner with more advanced fixing capabilities.

Method Summary

void	check() Invoke a background thread which will run all checkers on the given molecule
java.util.List<StructureCheckerResult>	checkAndWait() Execute all the checker instances on the given molecule and return a List of StructureCheckerResult which contains all the identified problems
boolean	fix() Checks the structure, then fixes the problems based on configuration.
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.
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, fix, 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 Detail

logger

protected chemaxon.checkers.logger.StructureCheckerLogger logger

fallBackToBasic

protected boolean fallBackToBasic

indicates that fix should fall back to super fix, or not

Constructor Detail

AdvancedCheckerRunner

public AdvancedCheckerRunner(ConfigurationReader configurationReader)

Constructs CheckerRunner with more advanced fixing capabilities.

Parameters:

configurationReader - the checker configuration

Method Detail

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

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 BasicCheckerRunner

Returns:

true if the fix ended correctly false otherwise

checkAndWait

public java.util.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

Overrides:

checkAndWait in class BasicCheckerRunner

Returns:

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

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

Overrides:

check in class 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 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