org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor

Direct Known Subclasses:: CeCPUserArgumentProcessor, CeSideChainUserArgumentProcessor

public class CeUserArgumentProcessor extends AbstractUserArgumentProcessor

process the arguments from command line

Nested Class Summary

Nested Classes

Modifier and Type

Class

Description

protected static class

CeUserArgumentProcessor.CeStartupParams
Field Summary

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

Constructors

Constructor

Description

CeUserArgumentProcessor()
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
- CeUserArgumentProcessor
  
  public CeUserArgumentProcessor()
Method Details
- 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
- 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

Class CeUserArgumentProcessor

Nested Class Summary