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

void	addExtension(String ext) add a known File extension.
void	clearExtensions() clear all file extensions
FileParsingParameters	getFileParsingParameters() Get the parameters that should be used for file parsing
String	getPath() get the directory path to the files
Structure	getStructure(File file) read file from File and returns a Structure object.
Structure	getStructure(String filename) open filename and returns a Structure object.
Structure	getStructureById(String pdbId) Get a Structure based on its PDB id.
boolean	isAutoFetch() Fetch files automatically from FTP server.
boolean	isPdbDirectorySplit() The PDB files are organized hierarchically (as on the PDB - FTP server.
void	setAutoFetch(boolean autoFetch) Tell the parser to fetch missing PDB files from the FTP server automatically.
void	setFileParsingParameters(FileParsingParameters params) Set the parameters that should be used for file parsing
void	setPath(String path) Set path to file / connection string to db.
void	setPdbDirectorySplit(boolean isSplit) The PDB files are organized hierarchically (as on the PDB - FTP server.

Method Detail

setPath

void setPath(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

String getPath()

get the directory path to the files

Returns:

path

addExtension

void addExtension(String ext)

add a known File extension.

Parameters:

ext - a String ...

clearExtensions

void clearExtensions()

clear all file extensions

getStructure

Structure getStructure(String filename)
                       throws IOException

open filename and returns a Structure object.

Parameters:

filename - a String

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 a PDB or mmcif file

Returns:

a Structure object

Throws:

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.

setPdbDirectorySplit

void setPdbDirectorySplit(boolean isSplit)

The PDB files are organized hierarchically (as on the PDB - FTP server. Directories are split based on the two middle characters of the files).

Parameters:

isSplit -

isPdbDirectorySplit

boolean isPdbDirectorySplit()

The PDB files are organized hierarchically (as on the PDB - FTP server. Directories are split based on the two middle characters of the files).

Returns:

flag

getStructureById

Structure getStructureById(String pdbId)
                           throws IOException

Get a Structure based on its PDB id. The reader takes care of finding the correct file in the PATH configured in get/setPath.

Specified by:

getStructureById in interface StructureIO

Parameters:

pdbId - a String specifying the id value (PDB code)

Returns:

a Structure object

Throws:

IOException - ...

setFileParsingParameters

void setFileParsingParameters(FileParsingParameters params)

Set the parameters that should be used for file parsing

Parameters:

params - FileParsingParameters

getFileParsingParameters

FileParsingParameters getFileParsingParameters()

Get the parameters that should be used for file parsing

Returns:

the FileParsingParameters that are configuring the behavior of the parser