org.biojava.nbio.structure.align.ce

Class CeUserArgumentProcessor.CeStartupParams

java.lang.Object

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

org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

Direct Known Subclasses:

CeCPUserArgumentProcessor.CeCPStartupParams

Enclosing class:

CeUserArgumentProcessor

protected static class CeUserArgumentProcessor.CeStartupParams
extends StartupParameters

Field Summary

Fields

Modifier and Type	Field and Description
protected double	gapExtension
protected double	gapOpen
protected int	maxGapSize
protected double	maxOptRMSD
protected CeParameters.ScoringStrategy	scoringStrategy
protected boolean	showAFPRanges
protected int	winSize

Constructor Summary

Constructors

Constructor and Description
CeUserArgumentProcessor.CeStartupParams()

Method Summary

Methods

Modifier and Type	Method and Description
double	getGapExtension()
double	getGapOpen()
int	getMaxGapSize() CE specific parameter: set the Max gap size parameter G (during AFP extension).
Double	getMaxOptRMSD() (jCE specific): maximum RMSD that shall be calculated for the alignment.
CeParameters.ScoringStrategy	getScoringStrategy()
int	getWinSize()
boolean	isShowAFPRanges()
void	setGapExtension(double gapExtension)
void	setGapOpen(double gapOpen)
void	setMaxGapSize(int maxGapSize) CE specific parameter: set the Max gap size parameter G (during AFP extension).
void	setMaxOptRMSD(Double maxOptRMSD) (jCE specific): maximum RMSD that shall be calculated for the alignment.
void	setScoringStrategy(CeParameters.ScoringStrategy scoringStrategy)
void	setShowAFPRanges(boolean showAFP)
void	setWinSize(int winSize)
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, isPdbDirSplit, isPrintCE, isPrintFatCat, isPrintXML, isShow3d, isShowMenu, setAlignPairs, setAutoFetch, setCacheFilePath, setDomainSplit, setFile1, setFile2, setNrCPU, setOutFile, setOutputPDB, setPdb1, setPdb2, setPdbDirSplit, 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

Field Detail

maxGapSize

protected int maxGapSize

winSize

protected int winSize

scoringStrategy

protected CeParameters.ScoringStrategy scoringStrategy

maxOptRMSD

protected double maxOptRMSD

gapOpen

protected double gapOpen

gapExtension

protected double gapExtension

showAFPRanges

protected boolean showAFPRanges

Constructor Detail

CeUserArgumentProcessor.CeStartupParams

public CeUserArgumentProcessor.CeStartupParams()

Method Detail

getWinSize

public int getWinSize()

setWinSize

public void setWinSize(int winSize)

getScoringStrategy

public CeParameters.ScoringStrategy getScoringStrategy()

setScoringStrategy

public void setScoringStrategy(CeParameters.ScoringStrategy scoringStrategy)

getGapOpen

public double getGapOpen()

setGapOpen

public void setGapOpen(double gapOpen)

getGapExtension

public double getGapExtension()

setGapExtension

public void setGapExtension(double gapExtension)

getMaxGapSize

public int getMaxGapSize()

CE specific parameter: set the Max gap size parameter G (during AFP extension). Default: 30

Returns:

the maximum gap size G parameter.

setMaxGapSize

public void setMaxGapSize(int maxGapSize)

CE specific parameter: set the Max gap size parameter G (during AFP extension). Default: 30

Parameters:

maxGapSize -

isShowAFPRanges

public boolean isShowAFPRanges()

setShowAFPRanges

public void setShowAFPRanges(boolean showAFP)

getMaxOptRMSD

public Double getMaxOptRMSD()

(jCE specific): maximum RMSD that shall be calculated for the alignment.

Returns:

maxOptRMSD parameter

setMaxOptRMSD

public void setMaxOptRMSD(Double maxOptRMSD)

(jCE specific): maximum RMSD that shall be calculated for the alignment.

Parameters:

maxOptRMSD - max RMSD to calculate

toString

public String toString()

Overrides:

toString in class StartupParameters