Class StartupParameters
- java.lang.Object
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- org.biojava.nbio.structure.align.ce.StartupParameters
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- Direct Known Subclasses:
CeUserArgumentProcessor.CeStartupParams
,FatCatUserArgumentProcessor.FatCatStartupParams
,SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
public class StartupParameters extends java.lang.Object
a simple bean that contains the parameters that can get set at startup- Author:
- Andreas Prlic
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Constructor Summary
Constructors Constructor Description StartupParameters()
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Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description java.lang.String
getAlignPairs()
The file that contains a list of PDB pairs to be alignedjava.lang.String
getCacheFilePath()
java.lang.String
getFile1()
java.lang.String
getFile2()
int
getNrCPU()
java.lang.String
getOutFile()
java.lang.String
getPdb1()
java.lang.String
getPdb2()
java.lang.String
getPdbFilePath()
java.lang.String
getSaveOutputDir()
java.lang.String
getSearchFile()
An input file to be used for the DB searchjava.lang.String
getShowDBresult()
boolean
isAutoFetch()
boolean
isDomainSplit()
boolean
isOutputPDB()
When writing the results to a file, don;t write as XML but write aligned PDB fileboolean
isPdbDirSplit()
Deprecated.Always returns true (4.0.0)boolean
isPrintCE()
Display the output string in CE styleboolean
isPrintFatCat()
boolean
isPrintXML()
boolean
isShow3d()
boolean
isShowMenu()
void
setAlignPairs(java.lang.String alignPairs)
void
setAutoFetch(boolean autoFetch)
void
setCacheFilePath(java.lang.String cacheFilePath)
void
setDomainSplit(boolean isDomainSplit)
void
setFile1(java.lang.String file1)
void
setFile2(java.lang.String file2)
void
setNrCPU(int nrCPU)
void
setOutFile(java.lang.String outFile)
void
setOutputPDB(boolean printPDB)
When writing the results to a file, don;t write as XML but write aligned PDB filevoid
setPdb1(java.lang.String pdb1)
mandatory argument to set the first PDB (and optionally chain ID) to be aligned.void
setPdb2(java.lang.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(java.lang.String pdbFilePath)
mandatory argument to set the location of PDB files.void
setPrintCE(boolean printCE)
Display the output string in CE stylevoid
setPrintFatCat(boolean printFatCat)
void
setPrintXML(boolean printXML)
void
setSaveOutputDir(java.lang.String saveOutputDir)
void
setSearchFile(java.lang.String searchFile)
void
setShow3d(boolean show3d)
void
setShowDBresult(java.lang.String showDBresult)
void
setShowMenu(boolean showMenu)
java.lang.String
toString()
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Method Detail
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getSearchFile
public java.lang.String getSearchFile()
An input file to be used for the DB search- Returns:
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setSearchFile
public void setSearchFile(java.lang.String searchFile)
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getAlignPairs
public java.lang.String getAlignPairs()
The file that contains a list of PDB pairs to be aligned- Returns:
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setAlignPairs
public void setAlignPairs(java.lang.String alignPairs)
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getSaveOutputDir
public java.lang.String getSaveOutputDir()
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setSaveOutputDir
public void setSaveOutputDir(java.lang.String saveOutputDir)
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isShowMenu
public boolean isShowMenu()
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setShowMenu
public void setShowMenu(boolean showMenu)
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isPrintCE
public boolean isPrintCE()
Display the output string in CE style- Returns:
- flag
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setPrintCE
public void setPrintCE(boolean printCE)
Display the output string in CE style- Parameters:
printCE
- a flag
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getPdb1
public java.lang.String getPdb1()
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setPdb1
public void setPdb1(java.lang.String pdb1)
mandatory argument to set the first PDB (and optionally chain ID) to be aligned.- Parameters:
pdb1
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getPdb2
public java.lang.String getPdb2()
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setPdb2
public void setPdb2(java.lang.String pdb2)
mandatory argument to set the second PDB (and optionally chain ID) to be aligned.- Parameters:
pdb2
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isPdbDirSplit
@Deprecated public boolean isPdbDirSplit()
Deprecated.Always returns true (4.0.0)- Returns:
- true
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setPdbDirSplit
@Deprecated public void setPdbDirSplit(boolean pdbDirSplit)
Deprecated.Ignored (4.0.0)- Parameters:
pdbDirSplit
- Ignored
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isPrintXML
public boolean isPrintXML()
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setPrintXML
public void setPrintXML(boolean printXML)
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isPrintFatCat
public boolean isPrintFatCat()
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setPrintFatCat
public void setPrintFatCat(boolean printFatCat)
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getPdbFilePath
public java.lang.String getPdbFilePath()
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setPdbFilePath
public void setPdbFilePath(java.lang.String pdbFilePath)
mandatory argument to set the location of PDB files.- Parameters:
pdbFilePath
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getCacheFilePath
public java.lang.String getCacheFilePath()
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setCacheFilePath
public void setCacheFilePath(java.lang.String cacheFilePath)
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isShow3d
public boolean isShow3d()
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setShow3d
public void setShow3d(boolean show3d)
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getOutFile
public java.lang.String getOutFile()
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setOutFile
public void setOutFile(java.lang.String outFile)
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isAutoFetch
public boolean isAutoFetch()
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setAutoFetch
public void setAutoFetch(boolean autoFetch)
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getShowDBresult
public java.lang.String getShowDBresult()
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setShowDBresult
public void setShowDBresult(java.lang.String showDBresult)
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getNrCPU
public int getNrCPU()
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setNrCPU
public void setNrCPU(int nrCPU)
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getFile1
public java.lang.String getFile1()
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setFile1
public void setFile1(java.lang.String file1)
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getFile2
public java.lang.String getFile2()
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setFile2
public void setFile2(java.lang.String file2)
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isOutputPDB
public boolean isOutputPDB()
When writing the results to a file, don;t write as XML but write aligned PDB file- Returns:
- flag
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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
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isDomainSplit
public boolean isDomainSplit()
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setDomainSplit
public void setDomainSplit(boolean isDomainSplit)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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