Package org.biojava.nbio.structure.align.ce

Class StartupParameters

    • 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 -

      • 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)