java.lang.Object
- org.biojava.nbio.structure.align.ce.StartupParameters

Direct Known Subclasses:

CeUserArgumentProcessor.CeStartupParams, FatCatUserArgumentProcessor.FatCatStartupParams, SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
```
public class StartupParameters
extends Object
```
a simple bean that contains the parameters that can get set at startup

Author:

Andreas Prlic

Constructor Summary

Constructors
Constructor Description

StartupParameters()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`String`	`getAlignPairs()`	The file that contains a list of PDB pairs to be aligned
`String`	`getCacheFilePath()`
`String`	`getFile1()`
`String`	`getFile2()`
`int`	`getNrCPU()`
`String`	`getOutFile()`
`String`	`getPdb1()`
`String`	`getPdb2()`
`String`	`getPdbFilePath()`
`String`	`getSaveOutputDir()`
`String`	`getSearchFile()`	An input file to be used for the DB search
`String`	`getShowDBresult()`
`boolean`	`isAutoFetch()`
`boolean`	`isDomainSplit()`
`boolean`	`isOutputPDB()`	When writing the results to a file, don;t write as XML but write aligned PDB file
`boolean`	`isPrintCE()`	Display the output string in CE style
`boolean`	`isPrintFatCat()`
`boolean`	`isPrintXML()`
`boolean`	`isShow3d()`
`boolean`	`isShowMenu()`
`void`	`setAlignPairs(String alignPairs)`
`void`	`setAutoFetch(boolean autoFetch)`
`void`	`setCacheFilePath(String cacheFilePath)`
`void`	`setDomainSplit(boolean isDomainSplit)`
`void`	`setFile1(String file1)`
`void`	`setFile2(String file2)`
`void`	`setNrCPU(int nrCPU)`
`void`	`setOutFile(String outFile)`
`void`	`setOutputPDB(boolean printPDB)`	When writing the results to a file, don;t write as XML but write aligned PDB file
`void`	`setPdb1(String pdb1)`	mandatory argument to set the first PDB (and optionally chain ID) to be aligned.
`void`	`setPdb2(String pdb2)`	mandatory argument to set the second PDB (and optionally chain ID) to be aligned.
`void`	`setPdbFilePath(String pdbFilePath)`	mandatory argument to set the location of PDB files.
`void`	`setPrintCE(boolean printCE)`	Display the output string in CE style
`void`	`setPrintFatCat(boolean printFatCat)`
`void`	`setPrintXML(boolean printXML)`
`void`	`setSaveOutputDir(String saveOutputDir)`
`void`	`setSearchFile(String searchFile)`
`void`	`setShow3d(boolean show3d)`
`void`	`setShowDBresult(String showDBresult)`
`void`	`setShowMenu(boolean showMenu)`
`String`	`toString()`

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

Constructor Detail
- StartupParameters
```
public StartupParameters()
```

Method Detail

getSearchFile
```
public String getSearchFile()
```
An input file to be used for the DB search

Returns:

setSearchFile

public void setSearchFile(String searchFile)

getAlignPairs
```
public String getAlignPairs()
```
The file that contains a list of PDB pairs to be aligned

Returns:

setAlignPairs

public void setAlignPairs(String alignPairs)

getSaveOutputDir
```
public String getSaveOutputDir()
```

setSaveOutputDir

public void setSaveOutputDir(String saveOutputDir)

isShowMenu
```
public boolean isShowMenu()
```

setShowMenu

public void setShowMenu(boolean showMenu)

isPrintCE
```
public boolean isPrintCE()
```
Display the output string in CE style

Returns:

flag

setPrintCE
```
public void setPrintCE(boolean printCE)
```
Display the output string in CE style

Parameters:

printCE - a flag

getPdb1
```
public String getPdb1()
```

setPdb1
```
public void setPdb1(String pdb1)
```
mandatory argument to set the first PDB (and optionally chain ID) to be aligned.

Parameters:

pdb1 -

getPdb2
```
public String getPdb2()
```

setPdb2
```
public void setPdb2(String pdb2)
```
mandatory argument to set the second PDB (and optionally chain ID) to be aligned.

Parameters:

pdb2 -

isPrintXML
```
public boolean isPrintXML()
```

setPrintXML

public void setPrintXML(boolean printXML)

isPrintFatCat
```
public boolean isPrintFatCat()
```

setPrintFatCat

public void setPrintFatCat(boolean printFatCat)

getPdbFilePath
```
public String getPdbFilePath()
```

setPdbFilePath
```
public void setPdbFilePath(String pdbFilePath)
```
mandatory argument to set the location of PDB files.

Parameters:

pdbFilePath -

getCacheFilePath
```
public String getCacheFilePath()
```

setCacheFilePath

public void setCacheFilePath(String cacheFilePath)

isShow3d
```
public boolean isShow3d()
```

setShow3d

public void setShow3d(boolean show3d)

getOutFile
```
public String getOutFile()
```

setOutFile

public void setOutFile(String outFile)

isAutoFetch
```
public boolean isAutoFetch()
```

setAutoFetch

public void setAutoFetch(boolean autoFetch)

getShowDBresult
```
public String getShowDBresult()
```

setShowDBresult

public void setShowDBresult(String showDBresult)

getNrCPU
```
public int getNrCPU()
```

setNrCPU
```
public void setNrCPU(int nrCPU)
```

getFile1
```
public String getFile1()
```

setFile1

public void setFile1(String file1)

getFile2
```
public String getFile2()
```

setFile2

public void setFile2(String file2)

isOutputPDB
```
public boolean isOutputPDB()
```
When writing the results to a file, don;t write as XML but write aligned PDB file

Returns:

flag

setOutputPDB
```
public void setOutputPDB(boolean printPDB)
```
When writing the results to a file, don;t write as XML but write aligned PDB file

Parameters:

printPDB - flag to print aligned PDB

isDomainSplit
```
public boolean isDomainSplit()
```

setDomainSplit

public void setDomainSplit(boolean isDomainSplit)

toString
```
public String toString()
```
Overrides:

toString in class Object

Class StartupParameters

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

StartupParameters

Method Detail

getSearchFile

setSearchFile

getAlignPairs

setAlignPairs

getSaveOutputDir

setSaveOutputDir

isShowMenu

setShowMenu

isPrintCE

setPrintCE

getPdb1

setPdb1

getPdb2

setPdb2

isPrintXML

setPrintXML

isPrintFatCat

setPrintFatCat

getPdbFilePath

setPdbFilePath

getCacheFilePath

setCacheFilePath

isShow3d

setShow3d

getOutFile

setOutFile

isAutoFetch

setAutoFetch

getShowDBresult

setShowDBresult

getNrCPU

setNrCPU

getFile1

setFile1

getFile2

setFile2

isOutputPDB

setOutputPDB

isDomainSplit

setDomainSplit

toString