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 Summary

Fields

Modifier and Type	Field	Description
static final List<String>	mandatoryArgs
static String	newline
protected StartupParameters	params

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractUserArgumentProcessor()

Method Summary

Modifier and Type	Method	Description
abstract StructureAlignment	getAlgorithm()
abstract String	getDbSearchLegend()
String	getDbSearchResult(AFPChain afpChain)
abstract Object	getParameters()
protected abstract StartupParameters	getStartupParametersInstance()	StartupParameters is a bean to store all the possible command line parameters.
static void	printAboutMe()
String	printHelp()	Print help about the arguments
void	process(String[] argv)	Process user arguments that have been provided from the command line

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

newline

public static String newline

params

protected StartupParameters params

mandatoryArgs

public static final List<String> mandatoryArgs

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

Parameters:

argv -

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: