Package org.biojava.nbio.structure.io

Interface StructureIOFile

All Superinterfaces:
StructureProvider
All Known Implementing Classes:
BcifFileReader, CifFileReader, LocalPDBDirectory, MMTFFileReader, PDBFileReader
public interface StructureIOFile extends StructureProvider
StructureIOFile extends StructureProvider with methods specific to parsing files from the filesystem.
Author:
Andreas Prlic

  • Method Details

    • addExtension

      void addExtension(String ext)
      Associates a file extension with this particular StructureIOFile, indicating that files of that type can be parsed. This is generally called only in the constructor of the implementing class.
      Parameters:
      ext - a String ...

    • getExtensions

      List<String> getExtensions()
      Returns a list of extensions supported by this class
      Returns:
      a (potentially empty) list of strings

    • getStructure

      Structure getStructure(String filename) throws IOException
      Open filename and return a Structure object. Not to be confused with StructureProvider.getStructureById(String)
      Parameters:
      filename - The path to the file. Must be the correct format for the implementing class.
      Returns:
      a Structure object
      Throws:
      IOException - ...

    • getStructure

      Structure getStructure(File file) throws IOException
      Read file from File and returns a Structure object.
      Parameters:
      file - file containing the structure. Must be the correct format for the implementing class
      Returns:
      a Structure object
      Throws:
      IOException - ...