Class ArrayDesignSequenceManipulatingCli

    • Constructor Detail

      • ArrayDesignSequenceManipulatingCli

        public ArrayDesignSequenceManipulatingCli()
    • Method Detail

      • getCommandGroup

        public GemmaCLI.CommandGroup getCommandGroup()
        Description copied from interface: CLI
        Obtain the command group for this CLI.
      • buildOptions

        protected void buildOptions​(org.apache.commons.cli.Options options)
        Description copied from class: AbstractCLI
        Build option implementation.

        Implement this method to add options to your command line, using the OptionBuilder.

        This is called right after AbstractCLI.buildStandardOptions(Options) so the options will be added after standard options.

        Specified by:
        buildOptions in class AbstractCLI
      • processOptions

        protected void processOptions​(org.apache.commons.cli.CommandLine commandLine)
                               throws org.apache.commons.cli.ParseException
        Description copied from class: AbstractCLI
        Process command line options.

        Implement this to provide processing of options. It is called after AbstractCLI.buildOptions(Options) and right before AbstractCLI.doWork().

        Specified by:
        processOptions in class AbstractCLI
        Throws:
        org.apache.commons.cli.ParseException - in case of unrecoverable failure (i.e. missing option or invalid value), an exception can be raised and will result in an exit code of AbstractCLI.FAILURE.
      • isSubsumedOrMerged

        protected boolean isSubsumedOrMerged​(ArrayDesign arrayDesign)
        Parameters:
        arrayDesign - the array design to check
        Returns:
        true if the sequences on the given array design would be equivalently treated by analyzing another array design. In the case of subsumption, this only works if the array design has been either analyzed for subsuming status. (the analysis is not done as part of this call).
      • locateArrayDesign

        protected ArrayDesign locateArrayDesign​(String name)
        Parameters:
        name - of the array design to find.
        Returns:
        an array design, if found. Bails otherwise with an error exit code