Package org.biojava.nbio.structure.align.ce

Class AbstractUserArgumentProcessor

java.lang.Object
org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
All Implemented Interfaces:
UserArgumentProcessor
Direct Known Subclasses:
CeUserArgumentProcessor, FatCatUserArgumentProcessor, SmithWatermanUserArgumentProcessor
public abstract class AbstractUserArgumentProcessor extends Object implements UserArgumentProcessor
Base class for a new structure alignment CLI.

To add a new StructureAlignment with a CLI similar to CE or FATCAT,

  1. Implement StructureAlignment with the main algorithm
  2. Implement ConfigStrucAligParams. This provides the parameters for the GUI.
  3. Subclass StartupParameters (can be an inner class) with the same parameters described in the ConfigStrucAligParams.
  4. Subclass AbstractUserArgumentProcessor, with the getStartupParams() method returning a fresh instance of the custom StartupParameters
  5. Implement the getParameters() method to copy values from the StartupParameters to the ConfigStrucAligParams.

Note that reflection is used in a number of places, so the CLI argument names must match the get/set functions in both parameter beans.

  • AlignmentGUI automatically takes parameter names and types from the ConfigStrucAligParams
  • AbstractUserArgumentProcessor also takes parameter names and help descriptions from ConfigStrucAligParams, but it saves arguments to the StartupParameter bean.
This means that both beans should be kept in sync.
Author:
Andreas, Spencer

  • Field Details

  • Constructor Details

    • AbstractUserArgumentProcessor

      protected AbstractUserArgumentProcessor()

  • Method Details

    • getStartupParametersInstance

      protected abstract StartupParameters getStartupParametersInstance()
      StartupParameters is a bean to store all the possible command line parameters. The `StartupParameter` class contains the basic set of CLI parameters common to all `StructureAligmnent`s. This method should return a subclass of StartupParameters which has been extended to store values for all additional parameters.
      Returns:
      A new instance of the correct StartupParameters subclass

    • getAlgorithm

      public abstract StructureAlignment getAlgorithm()

    • getParameters

      public abstract Object getParameters()

    • getDbSearchLegend

      public abstract String getDbSearchLegend()

    • process

      public void process(String[] argv)
      Description copied from interface: UserArgumentProcessor
      Process user arguments that have been provided from the command line
      Specified by:
      process in interface UserArgumentProcessor

    • printAboutMe

      public static void printAboutMe()

    • getDbSearchResult

      public String getDbSearchResult(AFPChain afpChain)

    • printHelp

      public String printHelp()
      Description copied from interface: UserArgumentProcessor
      Print help about the arguments
      Specified by:
      printHelp in interface UserArgumentProcessor
      Returns: