Package ubic.gemma.apps

Class ArrayDesignAnnotationFileCli

java.lang.Object
ubic.gemma.cli.util.AbstractCLI
ubic.gemma.cli.util.AbstractAuthenticatedCLI
ubic.gemma.cli.util.AbstractAutoSeekingCLI<ArrayDesign>
ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
ubic.gemma.apps.ArrayDesignAnnotationFileCli
All Implemented Interfaces:
org.springframework.beans.factory.Aware, org.springframework.beans.factory.InitializingBean, org.springframework.context.ApplicationContextAware, org.springframework.context.EnvironmentAware, CLI
public class ArrayDesignAnnotationFileCli extends ArrayDesignSequenceManipulatingCli
Given an array design creates a Gene Ontology Annotation file Given a batch file creates all the Annotation files for the AD's specified in the batch file Given nothing creates annotation files for every AD that isn't subsumed or merged into another AD.
Author:
klc, paul

  • Constructor Details

    • ArrayDesignAnnotationFileCli

      public ArrayDesignAnnotationFileCli()

  • Method Details

    • 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

    • 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().

      Overrides:
      processOptions in class ArrayDesignSequenceManipulatingCli
      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.

    • 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

    • 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.

    • doAuthenticatedWork

      protected void doAuthenticatedWork() throws Exception
      Specified by:
      doAuthenticatedWork in class AbstractAuthenticatedCLI
      Throws:
      Exception