org.biojava.nbio.structure.align.ce

Class StartupParameters

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 and Description
StartupParameters()

Method Summary

Methods

Modifier and Type	Method and 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	isPdbDirSplit() Deprecated. Always returns true (4.0.0)
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	setPdbDirSplit(boolean pdbDirSplit) Deprecated. Ignored (4.0.0)
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 -

isPdbDirSplit

@Deprecated
public boolean isPdbDirSplit()

Deprecated. Always returns true (4.0.0)

Returns:

true

setPdbDirSplit

@Deprecated
public void setPdbDirSplit(boolean pdbDirSplit)

Deprecated. Ignored (4.0.0)

Parameters:

pdbDirSplit - Ignored

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