Package org.biojava.nbio.structure.align.ce

Class CeCPUserArgumentProcessor.CeCPStartupParams

java.lang.Object

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

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

org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams

Enclosing class:

CeCPUserArgumentProcessor

protected class CeCPUserArgumentProcessor.CeCPStartupParams
extends CeUserArgumentProcessor.CeStartupParams

Field Summary

Fields

Modifier and Type	Field	Description
protected CECPParameters.DuplicationHint	duplicationHint
protected Integer	minCPLength

Fields inherited from class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

gapExtension, gapOpen, maxGapSize, maxOptRMSD, scoringStrategy, showAFPRanges, winSize

Constructor Summary

Constructors

Constructor	Description
CeCPStartupParams()

Method Summary

Modifier and Type	Method	Description
CECPParameters.DuplicationHint	getDuplicationHint()
Integer	getMinCPLength()
void	setDuplicationHint(CECPParameters.DuplicationHint duplicationHint)
void	setMinCPLength(Integer minCPLength)
String	toString()

Methods inherited from class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

getGapExtension, getGapOpen, getMaxGapSize, getMaxOptRMSD, getScoringStrategy, getWinSize, isShowAFPRanges, setGapExtension, setGapOpen, setMaxGapSize, setMaxOptRMSD, setScoringStrategy, setShowAFPRanges, setWinSize

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

Field Detail

duplicationHint

protected CECPParameters.DuplicationHint duplicationHint

minCPLength

protected Integer minCPLength

Constructor Detail

CeCPStartupParams

public CeCPStartupParams()

Method Detail

getDuplicationHint

public CECPParameters.DuplicationHint getDuplicationHint()

setDuplicationHint

public void setDuplicationHint(CECPParameters.DuplicationHint duplicationHint)

getMinCPLength

public Integer getMinCPLength()

setMinCPLength

public void setMinCPLength(Integer minCPLength)

toString

public String toString()

Overrides:

toString in class CeUserArgumentProcessor.CeStartupParams