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

Class CeCPUserArgumentProcessor

java.lang.Object

org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor

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

org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor

All Implemented Interfaces:

UserArgumentProcessor

public class CeCPUserArgumentProcessor
extends CeUserArgumentProcessor

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
protected class	CeCPUserArgumentProcessor.CeCPStartupParams

Nested classes/interfaces inherited from class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor

CeUserArgumentProcessor.CeStartupParams

Field Summary

Fields inherited from class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor

mandatoryArgs, newline, params

Constructor Summary

Constructors

Constructor	Description
CeCPUserArgumentProcessor()

Method Summary

Modifier and Type	Method	Description
StructureAlignment	getAlgorithm()
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.CeUserArgumentProcessor

getDbSearchLegend

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

CeCPUserArgumentProcessor

public CeCPUserArgumentProcessor()

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.

Overrides:

getStartupParametersInstance in class CeUserArgumentProcessor

Returns:

A new instance of the correct StartupParameters subclass

getAlgorithm

public StructureAlignment getAlgorithm()

Overrides:

getAlgorithm in class CeUserArgumentProcessor

getParameters

public Object getParameters()

Overrides:

getParameters in class CeUserArgumentProcessor