org.biojava.bio.structure.align.ce
Class StartupParameters

java.lang.Object
  extended by org.biojava.bio.structure.align.ce.StartupParameters

public class StartupParameters
extends Object

a simple bean that contains the parameters that can get set at startup

Author:
Andreas Prlic

Constructor Summary
StartupParameters()
           
 
Method Summary
 String getAlignPairs()
           
 String getFile1()
           
 String getFile2()
           
 int getMaxGapSize()
          CE specific parameter: set the Max gap size parameter G (during AFP extension).
 Double getMaxOptRMSD()
          (jCE specific): maximum RMSD that shall be calculated for the alignment.
 String getOutFile()
           
 String getPdb1()
           
 String getPdb2()
           
 String getPdbFilePath()
           
 String getSaveOutputDir()
           
 String getShowDBresult()
           
 boolean isAutoFetch()
           
 boolean isFlexible()
           
 boolean isOutputPDB()
          When writing the results to a file, don;t write as XML but write aligned PDB file
 boolean isPdbDirSplit()
           
 boolean isPrintCE()
          Display the output string in CE style
 boolean isPrintFatCat()
           
 boolean isPrintXML()
           
 boolean isShow3d()
           
 boolean isShowAFPRanges()
           
 boolean isShowMenu()
           
 void setAlignPairs(String alignPairs)
           
 void setAutoFetch(boolean autoFetch)
           
 void setFile1(String file1)
           
 void setFile2(String file2)
           
 void setFlexible(boolean flexible)
           
 void setMaxGapSize(int maxGapSize)
          CE specific parameter: set the Max gap size parameter G (during AFP extension).
 void setMaxOptRMSD(Double maxOptRMSD)
          (jCE specific): maximum RMSD that shall be calculated for the alignment.
 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)
           
 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 setShow3d(boolean show3d)
           
 void setShowAFPRanges(boolean showAFP)
           
 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

toString

public String toString()
Overrides:
toString in class Object

getAlignPairs

public String getAlignPairs()

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

isFlexible

public boolean isFlexible()

setFlexible

public void setFlexible(boolean flexible)

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

public boolean isPdbDirSplit()

setPdbDirSplit

public void setPdbDirSplit(boolean pdbDirSplit)

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 -

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)

getMaxGapSize

public int getMaxGapSize()
CE specific parameter: set the Max gap size parameter G (during AFP extension). Default: 30

Returns:
the maximum gap size G parameter.

setMaxGapSize

public void setMaxGapSize(int maxGapSize)
CE specific parameter: set the Max gap size parameter G (during AFP extension). Default: 30

Parameters:
maxGapSize -

getFile1

public String getFile1()

setFile1

public void setFile1(String file1)

getFile2

public String getFile2()

setFile2

public void setFile2(String file2)

isShowAFPRanges

public boolean isShowAFPRanges()

setShowAFPRanges

public void setShowAFPRanges(boolean showAFP)

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

getMaxOptRMSD

public Double getMaxOptRMSD()
(jCE specific): maximum RMSD that shall be calculated for the alignment.

Returns:
maxOptRMSD parameter

setMaxOptRMSD

public void setMaxOptRMSD(Double maxOptRMSD)
(jCE specific): maximum RMSD that shall be calculated for the alignment.

Parameters:
maxOptRMSD - max RMSD to calculate