Class StartupParameters

Method Details

• 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