Package chemaxon.checkers.runner

Class 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

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      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

    • Field Detail

      • logger

        protected chemaxon.checkers.logger.StructureCheckerLogger logger

    • Constructor Detail

      • 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 Detail

      • 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

      • 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