Class CeUserArgumentProcessor.CeStartupParams
- java.lang.Object
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- org.biojava.nbio.structure.align.ce.StartupParameters
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- org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
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- Direct Known Subclasses:
CeCPUserArgumentProcessor.CeCPStartupParams
- Enclosing class:
- CeUserArgumentProcessor
protected static class CeUserArgumentProcessor.CeStartupParams extends StartupParameters
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Field Summary
Fields Modifier and Type Field Description protected double
gapExtension
protected double
gapOpen
protected int
maxGapSize
protected double
maxOptRMSD
protected CeParameters.ScoringStrategy
scoringStrategy
protected boolean
showAFPRanges
protected int
winSize
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Constructor Summary
Constructors Constructor Description CeStartupParams()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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()
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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
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Field Detail
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maxGapSize
protected int maxGapSize
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winSize
protected int winSize
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scoringStrategy
protected CeParameters.ScoringStrategy scoringStrategy
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maxOptRMSD
protected double maxOptRMSD
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gapOpen
protected double gapOpen
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gapExtension
protected double gapExtension
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showAFPRanges
protected boolean showAFPRanges
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Constructor Detail
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CeStartupParams
public CeStartupParams()
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Method Detail
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getWinSize
public int getWinSize()
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setWinSize
public void setWinSize(int winSize)
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getScoringStrategy
public CeParameters.ScoringStrategy getScoringStrategy()
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setScoringStrategy
public void setScoringStrategy(CeParameters.ScoringStrategy scoringStrategy)
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getGapOpen
public double getGapOpen()
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setGapOpen
public void setGapOpen(double gapOpen)
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getGapExtension
public double getGapExtension()
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setGapExtension
public void setGapExtension(double gapExtension)
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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.
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setMaxGapSize
public void setMaxGapSize(int maxGapSize)
CE specific parameter: set the Max gap size parameter G (during AFP extension). Default: 30- Parameters:
maxGapSize
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isShowAFPRanges
public boolean isShowAFPRanges()
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setShowAFPRanges
public void setShowAFPRanges(boolean showAFP)
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getMaxOptRMSD
public Double getMaxOptRMSD()
(jCE specific): maximum RMSD that shall be calculated for the alignment.- Returns:
- maxOptRMSD parameter
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setMaxOptRMSD
public void setMaxOptRMSD(Double maxOptRMSD)
(jCE specific): maximum RMSD that shall be calculated for the alignment.- Parameters:
maxOptRMSD
- max RMSD to calculate
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toString
public String toString()
- Overrides:
toString
in classStartupParameters
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