SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams (biojava-structure 7.1.4 API)

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

Description

SmithWatermanStartupParams()
Method Summary

Modifier and Type

Method

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, 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, setShow3d, setShowDBresult, setShowMenu

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details
- SmithWatermanStartupParams
  
  public SmithWatermanStartupParams()
Method Details
- 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