Package org.biojava.bio.structure.io

Interface StructureIOFile

  • All Superinterfaces:
    StructureIO
    All Known Implementing Classes:
    MMCIFFileReader, PDBFileReader
    public interface StructureIOFile
extends StructureIO
    interface StructureIOFile extends the StructureIO interface and adds a few File specific methods.
    Author:
    Andreas Prlic

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      void addExtension​(java.lang.String ext)
      add a known File extension.
      void clearExtensions()
      clear all file extensions
      java.lang.String getPath()
      get the directory path to the files
      Structure getStructure​(java.io.File file)
      read file from File and returns a Structure object.
      Structure getStructure​(java.lang.String filename)
      open filename and returns a Structure object.
      boolean isAutoFetch()
      Fetch files automatically from FTP server.
      void setAutoFetch​(boolean autoFetch)
      Tell the parser to fetch missing PDB files from the FTP server automatically.
      void setPath​(java.lang.String path)
      Set path to file / connection string to db.

    • Method Detail

      • setPath

        void setPath​(java.lang.String path)
        Set path to file / connection string to db. This is for installations of PDB/mmCif where all files are located in one directory.
        Parameters:
        path - a String specifying the path value

      • getPath

        java.lang.String getPath()
        get the directory path to the files
        Returns:
        path

      • addExtension

        void addExtension​(java.lang.String ext)
        add a known File extension.
        Parameters:
        ext - a String ...

      • clearExtensions

        void clearExtensions()
        clear all file extensions

      • getStructure

        Structure getStructure​(java.lang.String filename)
                throws java.io.IOException
        open filename and returns a Structure object.
        Parameters:
        filename - a String
        Returns:
        a Structure object
        Throws:
        java.io.IOException - ...

      • getStructure

        Structure getStructure​(java.io.File file)
                throws java.io.IOException
        read file from File and returns a Structure object.
        Parameters:
        file - file containing a PDB or mmcif file
        Returns:
        a Structure object
        Throws:
        java.io.IOException - ...

      • isAutoFetch

        boolean isAutoFetch()
        Fetch files automatically from FTP server. Default: false
        Returns:
        flag is true or false.

      • setAutoFetch

        void setAutoFetch​(boolean autoFetch)
        Tell the parser to fetch missing PDB files from the FTP server automatically. default is false. If true, new PDB files will be automatically stored in the Path and gzip compressed.
        Parameters:
        autoFetch - flag.