Class StartupParameters

    • Constructor Detail

      • StartupParameters

        public StartupParameters()
    • Method Detail

      • getSearchFile

        public java.lang.String getSearchFile()
        An input file to be used for the DB search
        Returns:
      • setSearchFile

        public void setSearchFile​(java.lang.String searchFile)
      • getAlignPairs

        public java.lang.String getAlignPairs()
        The file that contains a list of PDB pairs to be aligned
        Returns:
      • setAlignPairs

        public void setAlignPairs​(java.lang.String alignPairs)
      • getSaveOutputDir

        public java.lang.String getSaveOutputDir()
      • setSaveOutputDir

        public void setSaveOutputDir​(java.lang.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 java.lang.String getPdb1()
      • setPdb1

        public void setPdb1​(java.lang.String pdb1)
        mandatory argument to set the first PDB (and optionally chain ID) to be aligned.
        Parameters:
        pdb1 -
      • getPdb2

        public java.lang.String getPdb2()
      • setPdb2

        public void setPdb2​(java.lang.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 java.lang.String getPdbFilePath()
      • setPdbFilePath

        public void setPdbFilePath​(java.lang.String pdbFilePath)
        mandatory argument to set the location of PDB files.
        Parameters:
        pdbFilePath -
      • getCacheFilePath

        public java.lang.String getCacheFilePath()
      • setCacheFilePath

        public void setCacheFilePath​(java.lang.String cacheFilePath)
      • isShow3d

        public boolean isShow3d()
      • setShow3d

        public void setShow3d​(boolean show3d)
      • getOutFile

        public java.lang.String getOutFile()
      • setOutFile

        public void setOutFile​(java.lang.String outFile)
      • isAutoFetch

        public boolean isAutoFetch()
      • setAutoFetch

        public void setAutoFetch​(boolean autoFetch)
      • getShowDBresult

        public java.lang.String getShowDBresult()
      • setShowDBresult

        public void setShowDBresult​(java.lang.String showDBresult)
      • getNrCPU

        public int getNrCPU()
      • setNrCPU

        public void setNrCPU​(int nrCPU)
      • getFile1

        public java.lang.String getFile1()
      • setFile1

        public void setFile1​(java.lang.String file1)
      • getFile2

        public java.lang.String getFile2()
      • setFile2

        public void setFile2​(java.lang.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 java.lang.String toString()
        Overrides:
        toString in class java.lang.Object