Package ubic.gemma.apps

Class ArrayDesignBioSequenceDetachCli

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.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 Details

    • ArrayDesignBioSequenceDetachCli

      public ArrayDesignBioSequenceDetachCli()

  • Method Details

    • 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

    • 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.

    • doAuthenticatedWork

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