org.biojava.bio.structure.align.ce

Class AbstractUserArgumentProcessor

java.lang.Object

org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor

All Implemented Interfaces:

UserArgumentProcessor

Direct Known Subclasses:

CeSideChainUserArgumentProcessor, CeUserArgumentProcessor, FatCatUserArgumentProcessor, SmithWatermanUserArgumentProcessor

public abstract class AbstractUserArgumentProcessor
extends Object
implements UserArgumentProcessor

Field Summary

Fields

Modifier and Type	Field and Description
static List<String>	mandatoryArgs
static String	newline
protected StartupParameters	params
static String	PDB_DIR the system property PDB_DIR can be used to configure the default location for PDB files.

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractUserArgumentProcessor()

Method Summary

Methods

Modifier and Type	Method and Description
abstract StructureAlignment	getAlgorithm()
abstract String	getDbSearchLegend()
String	getDbSearchResult(AFPChain afpChain)
List<String>	getMandatoryArgs()
abstract Object	getParameters()
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 Detail

newline

public static String newline

params

protected StartupParameters params

mandatoryArgs

public static final List<String> mandatoryArgs

PDB_DIR

public static final String PDB_DIR

the system property PDB_DIR can be used to configure the default location for PDB files.

See Also:

Constant Field Values

Constructor Detail

AbstractUserArgumentProcessor

protected AbstractUserArgumentProcessor()

Method Detail

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

getMandatoryArgs

public List<String> getMandatoryArgs()

getDbSearchResult

public String getDbSearchResult(AFPChain afpChain)