SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams (biojava 6.1.0 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

All Methods Instance Methods Concrete Methods
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, 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

Constructor Detail
- SmithWatermanStartupParams
```
public SmithWatermanStartupParams()
```

Method Detail

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