Package ubic.gemma.apps

Class ArrayDesignBioSequenceDetachCli

  • All Implemented Interfaces:
    org.springframework.beans.factory.Aware, org.springframework.beans.factory.InitializingBean, org.springframework.context.ApplicationContextAware, org.springframework.context.EnvironmentAware, CLI
    public class ArrayDesignBioSequenceDetachCli
extends ArrayDesignSequenceManipulatingCli
    Remove all associations that this array design has with BioSequences. This is needed for cases where the original import has associated the probes with the wrong sequences. A common case is for GEO data sets where the actual oligonucleotide is not given. Instead the submitter provides Genbank accessions, which are misleading. This method can be used to clear those until the "right" sequences can be identified and filled in. Note that this does not remove the BioSequences, it just nulls the BiologicalCharacteristics of the CompositeSequences.
    Author:
    pavlidis

    • Constructor Detail

      • ArrayDesignBioSequenceDetachCli

        public ArrayDesignBioSequenceDetachCli()

    • 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.

      • getShortDesc

        public String getShortDesc()
        Description copied from interface: CLI
        Obtain a short description for this command explaining what it does.
        Specified by:
        getShortDesc in interface CLI
        Overrides:
        getShortDesc in class AbstractCLI

      • 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