org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor

public class SmithWatermanUserArgumentProcessor extends AbstractUserArgumentProcessor

Nested Class Summary

Nested Classes

Modifier and Type

Class

Description

protected static class

SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
Field Summary

Fields inherited from class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
mandatoryArgs, newline, params
Constructor Summary

Constructors

Constructor

Description

SmithWatermanUserArgumentProcessor()
Method Summary

Modifier and Type

Method

Description

StructureAlignment

getAlgorithm()

String

getDbSearchLegend()

Object

getParameters()

protected StartupParameters

getStartupParametersInstance()

StartupParameters is a bean to store all the possible command line parameters.

Methods inherited from class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
getDbSearchResult, printAboutMe, printHelp, process

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- SmithWatermanUserArgumentProcessor
  
  public SmithWatermanUserArgumentProcessor()
Method Details
- getAlgorithm
  
  public StructureAlignment getAlgorithm()
  
  Specified by:
  
  getAlgorithm in class AbstractUserArgumentProcessor
- getParameters
  
  public Object getParameters()
  
  Specified by:
  
  getParameters in class AbstractUserArgumentProcessor
- getDbSearchLegend
  
  public String getDbSearchLegend()
  
  Specified by:
  
  getDbSearchLegend in class AbstractUserArgumentProcessor
- getStartupParametersInstance
  
  protected StartupParameters getStartupParametersInstance()
  
  Description copied from class: AbstractUserArgumentProcessor
  
  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.
  
  Specified by:
  
  getStartupParametersInstance in class AbstractUserArgumentProcessor
  
  Returns:
  
  A new instance of the correct StartupParameters subclass

Class SmithWatermanUserArgumentProcessor

Nested Class Summary