Package org.biojava.nbio.structure.io

Class BcifFileReader

java.lang.Object

org.biojava.nbio.structure.io.LocalPDBDirectory

org.biojava.nbio.structure.io.BcifFileReader

All Implemented Interfaces:

StructureIOFile, StructureProvider

public class BcifFileReader
extends LocalPDBDirectory

Parse binary Cif files and provide capabilities to store them locally.

Since:

5.3.0

Author:

Sebastian Bittrich

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory

LocalPDBDirectory.FetchBehavior, LocalPDBDirectory.ObsoleteBehavior

Field Summary

Fields

Modifier and Type	Field	Description
static final String[]	CIF_OBSOLETE_DIR
static final String[]	CIF_SPLIT_DIR

Fields inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory

DEFAULT_BCIF_FILE_SERVER, DEFAULT_PDB_FILE_SERVER, LAST_REMEDIATION_DATE, MIN_PDB_FILE_SIZE, PDB_FILE_SERVER_PROPERTY

Constructor Summary

Constructors

Constructor	Description
BcifFileReader()	Constructs a new BcifFileReader, initializing the extensions member variable.
BcifFileReader(String path)	Constructs a new BcifFileReader, initializing the extensions member variable.

Method Summary

Modifier and Type	Method	Description
protected String	getFilename(String pdbId)	Converts a PDB ID into a filename with the proper extension
protected String[]	getObsoleteDirPath()	Location of obsolete files within the directory, as an array of paths.
protected String[]	getSplitDirPath()	Location of split files within the directory, as an array of paths.
Structure	getStructure(InputStream inStream)	Handles the actual parsing of the file into a Structure object.

Methods inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory

addExtension, checkFileExists, checkFileExists, clearExtensions, deleteStructure, deleteStructure, downloadStructure, getDir, getExtensions, getFetchBehavior, getFileParsingParameters, getInputStream, getLocalFile, getLocalFile, getObsoleteBehavior, getPath, getServerName, getStructure, getStructure, getStructure, getStructureById, getStructureById, initPaths, prefetchStructure, setFetchBehavior, setFileParsingParameters, setObsoleteBehavior, setPath

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

CIF_SPLIT_DIR

public static final String[] CIF_SPLIT_DIR

CIF_OBSOLETE_DIR

public static final String[] CIF_OBSOLETE_DIR

Constructor Details

BcifFileReader

public BcifFileReader()

Constructs a new BcifFileReader, initializing the extensions member variable. The path is initialized in the same way as UserConfiguration, i.e. to system property/environment variable UserConfiguration.PDB_DIR. Both autoFetch and splitDir are initialized to false

BcifFileReader

public BcifFileReader(String path)

Constructs a new BcifFileReader, initializing the extensions member variable. The path is initialized to the given path, both autoFetch and splitDir are initialized to false.

Method Details

getStructure

public Structure getStructure(InputStream inStream)
                       throws IOException

Description copied from class: LocalPDBDirectory

Handles the actual parsing of the file into a Structure object.

Specified by:

getStructure in class LocalPDBDirectory

Parameters:

inStream -

Returns:

Throws:

IOException

getFilename

protected String getFilename(String pdbId)

Description copied from class: LocalPDBDirectory

Converts a PDB ID into a filename with the proper extension

Specified by:

getFilename in class LocalPDBDirectory

Parameters:

pdbId -

Returns:

The filename, e.g. "4hhb.pdb.gz"

getSplitDirPath

protected String[] getSplitDirPath()

Description copied from class: LocalPDBDirectory

Location of split files within the directory, as an array of paths. These will be joined with either slashes (for the URL) or the file separator (for directories). The returned results should be constant, to allow for caching.

Specified by:

getSplitDirPath in class LocalPDBDirectory

Returns:

A list of directories, relative to the /pub/pdb directory on the server

getObsoleteDirPath

protected String[] getObsoleteDirPath()

Description copied from class: LocalPDBDirectory

Location of obsolete files within the directory, as an array of paths. These will be joined with either slashes (for the URL) or the file separator (for directories). The returned results should be constant, to allow for caching.

Specified by:

getObsoleteDirPath in class LocalPDBDirectory

Returns:

A list of directories, relative to the /pub/pdb directory on the server