Class GenomeChecker

  • All Implemented Interfaces:
    Checker

    public class GenomeChecker
    extends Object
    implements Checker
    This class define a Checker on genome FASTA files.
    Since:
    1.0
    Author:
    Laurent Jourdren
    • Constructor Detail

      • GenomeChecker

        public GenomeChecker()
    • Method Detail

      • getName

        public String getName()
        Description copied from interface: Checker
        Get the name of the checker.
        Specified by:
        getName in interface Checker
        Returns:
        the name of the checker
      • isDesignChecker

        public boolean isDesignChecker()
        Description copied from interface: Checker
        Test if the Checker is a design checker
        Specified by:
        isDesignChecker in interface Checker
      • getFormat

        public DataFormat getFormat()
        Description copied from interface: Checker
        Get format related to the checker.
        Specified by:
        getFormat in interface Checker
        Returns:
        a DataFormat object
      • getCheckersRequired

        public Set<DataFormat> getCheckersRequired()
        Description copied from interface: Checker
        Get the list of Checker required to run before this checker.
        Specified by:
        getCheckersRequired in interface Checker
        Returns:
        a list of DataFormat that are checked by the required checkers
      • configure

        public void configure​(Set<Parameter> stepParameters)
                       throws EoulsanException
        Description copied from interface: Checker
        Set the parameters of the checker to configure the checker.
        Specified by:
        configure in interface Checker
        Parameters:
        stepParameters - parameters of the step
        Throws:
        EoulsanException - if a parameter is invalid
      • check

        public boolean check​(Data data,
                             CheckStore checkInfo)
                      throws EoulsanException
        Description copied from interface: Checker
        Launch the check.
        Specified by:
        check in interface Checker
        Parameters:
        data - data to check
        checkInfo - object that contains data shared between the checkers
        Throws:
        EoulsanException - if an error occurs while executing step