Class AffyProbeCollapseCli

  • All Implemented Interfaces:
    org.springframework.beans.factory.InitializingBean, CLI

    public class AffyProbeCollapseCli
    extends ArrayDesignSequenceManipulatingCli
    Purely a testing tool, to turn Affy individual probes (by probeset) into collapsed sequences. This is what happens internally when we add sequences to a platform, but this makes it possible to see (and check) the sequences first before committing to them.

    Should probably be in GemmaAnalysis but that is badly broken.

    You just run this like

    $GEMMACMD affyCollapse [filename]

    It doesn't handle the regular argument setup, wasn't worth the trouble. Generates FASTA format but easy to change.

    Author:
    paul
    • Constructor Detail

      • AffyProbeCollapseCli

        public AffyProbeCollapseCli()
    • Method Detail

      • getCommandName

        public String getCommandName()
        Description copied from interface: CLI
        A short memorable name for the command that can be used to locate this class.
        Specified by:
        getCommandName in interface CLI
        Overrides:
        getCommandName in class AbstractCLI
        Returns:
        name; if null or blank, this will not be available as a shortcut command.
      • 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.

        Overrides:
        buildOptions in class ArrayDesignSequenceManipulatingCli