org.biojava.nbio.structure.align.seq

Class SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

java.lang.Object

org.biojava.nbio.structure.align.ce.StartupParameters

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

Enclosing class:

SmithWatermanUserArgumentProcessor

protected static class SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
extends StartupParameters

Constructor Summary

Constructors

Constructor and Description
SmithWatermanStartupParams()

Method Summary

Modifier and Type	Method and Description
short	getGapExtend()
short	getGapOpen()
double	getMaxRmsd()
int	getMinLen()
void	setGapExtend(short gapExtend)
void	setGapOpen(short gapOpen)
void	setMaxRmsd(double maxRmsd)
void	setMinLen(int minLen)
String	toString()

Methods inherited from class org.biojava.nbio.structure.align.ce.StartupParameters

getAlignPairs, getCacheFilePath, getFile1, getFile2, getNrCPU, getOutFile, getPdb1, getPdb2, getPdbFilePath, getSaveOutputDir, getSearchFile, getShowDBresult, isAutoFetch, isDomainSplit, isOutputPDB, isPrintCE, isPrintFatCat, isPrintXML, isShow3d, isShowMenu, setAlignPairs, setAutoFetch, setCacheFilePath, setDomainSplit, setFile1, setFile2, setNrCPU, setOutFile, setOutputPDB, setPdb1, setPdb2, setPdbFilePath, setPrintCE, setPrintFatCat, setPrintXML, setSaveOutputDir, setSearchFile, setShow3d, setShowDBresult, setShowMenu

Methods inherited from class java.lang.Object

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

Constructor Detail

SmithWatermanStartupParams

public SmithWatermanStartupParams()

Method Detail

getGapOpen

public short getGapOpen()

setGapOpen

public void setGapOpen(short gapOpen)

getGapExtend

public short getGapExtend()

setGapExtend

public void setGapExtend(short gapExtend)

getMaxRmsd

public double getMaxRmsd()

setMaxRmsd

public void setMaxRmsd(double maxRmsd)

getMinLen

public int getMinLen()

setMinLen

public void setMinLen(int minLen)

toString

public String toString()

Overrides:

toString in class StartupParameters