Package org.biojava.nbio.structure.align.seq

Class SmithWatermanUserArgumentProcessor

java.lang.Object

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

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

All Implemented Interfaces:

UserArgumentProcessor

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