protected static class CeUserArgumentProcessor.CeStartupParams extends StartupParameters
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 and Description |
---|
CeStartupParams() |
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() |
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
protected int maxGapSize
protected int winSize
protected CeParameters.ScoringStrategy scoringStrategy
protected double maxOptRMSD
protected double gapOpen
protected double gapExtension
protected boolean showAFPRanges
public CeStartupParams()
public int getWinSize()
public void setWinSize(int winSize)
public CeParameters.ScoringStrategy getScoringStrategy()
public void setScoringStrategy(CeParameters.ScoringStrategy scoringStrategy)
public double getGapOpen()
public void setGapOpen(double gapOpen)
public double getGapExtension()
public void setGapExtension(double gapExtension)
public int getMaxGapSize()
public void setMaxGapSize(int maxGapSize)
maxGapSize
- public boolean isShowAFPRanges()
public void setShowAFPRanges(boolean showAFP)
public Double getMaxOptRMSD()
public void setMaxOptRMSD(Double maxOptRMSD)
maxOptRMSD
- max RMSD to calculatepublic String toString()
toString
in class StartupParameters
Copyright © 2000–2018 BioJava. All rights reserved.