org.biojava.nbio.structure.io

Interface StructureIOFile

All Superinterfaces:

StructureProvider

All Known Implementing Classes:

BcifFileReader, CifFileReader, LocalPDBDirectory, MMCIFFileReader, MMTFFileReader, PDBFileReader

public interface StructureIOFile
extends StructureProvider

StructureIOFile extends StructureProvider with methods specific to parsing files from the filesystem.

Author:

Andreas Prlic

Method Summary

Modifier and Type	Method and Description
void	addExtension(String ext) Associates a file extension with this particular StructureIOFile, indicating that files of that type can be parsed.
List<String>	getExtensions() Returns a list of extensions supported by this class
Structure	getStructure(File file) Read file from File and returns a Structure object.
Structure	getStructure(String filename) Open filename and return a Structure object.

Methods inherited from interface org.biojava.nbio.structure.io.StructureProvider

getFileParsingParameters, getStructureById, setFileParsingParameters

Method Detail

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 - ...