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 java.lang.Object
implements UserArgumentProcessor

Field Summary

static java.util.List<java.lang.String>	mandatoryArgs
static java.lang.String	newline
protected StartupParameters	params
static java.lang.String	PDB_DIR the system property PDB_DIR can be used to configure the default location for PDB files.

Constructor Summary

protected

AbstractUserArgumentProcessor()

Method Summary

abstract StructureAlignment	getAlgorithm()
abstract java.lang.String	getDbSearchLegend()
java.lang.String	getDbSearchResult(AFPChain afpChain)
java.util.List<java.lang.String>	getMandatoryArgs()
abstract java.lang.Object	getParameters()
static void	printAboutMe()
void	process(java.lang.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 java.lang.String newline

params

protected StartupParameters params

mandatoryArgs

public static final java.util.List<java.lang.String> mandatoryArgs

PDB_DIR

public static final java.lang.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 java.lang.Object getParameters()

getDbSearchLegend

public abstract java.lang.String getDbSearchLegend()

process

public void process(java.lang.String[] argv)

Description copied from interface: UserArgumentProcessor

Process user arguments that have been provided from the command line

Specified by:

process in interface UserArgumentProcessor

printAboutMe

public static void printAboutMe()

getMandatoryArgs

public java.util.List<java.lang.String> getMandatoryArgs()

getDbSearchResult

public java.lang.String getDbSearchResult(AFPChain afpChain)