Class SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
- java.lang.Object
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- org.biojava.nbio.structure.align.ce.StartupParameters
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- org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
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- Enclosing class:
- SmithWatermanUserArgumentProcessor
protected static class SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams extends StartupParameters
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Constructor Summary
Constructors Constructor Description SmithWatermanStartupParams()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description shortgetGapExtend()shortgetGapOpen()voidsetGapExtend(short gapExtend)voidsetGapOpen(short gapOpen)java.lang.StringtoString()-
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
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Method Detail
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getGapOpen
public short getGapOpen()
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setGapOpen
public void setGapOpen(short gapOpen)
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getGapExtend
public short getGapExtend()
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setGapExtend
public void setGapExtend(short gapExtend)
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toString
public java.lang.String toString()
- Overrides:
toStringin classStartupParameters
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