org.biojava.bio.structure.server
Class FlatFileInstallation

java.lang.Object
  org.biojava.bio.structure.server.FlatFileInstallation

All Implemented Interfaces:

PDBInstallation

public class FlatFileInstallation
extends Object
implements PDBInstallation

a PDB installation that reads all files from one directory in the file system. and keeps several files with the information parsed from the PDB headers for easier data access.
In particular these files are:

• pdbinfo.txt - contains resolution, experimetnal technique, deposition and modification date, biological description of the structure
• chaininfo.txt - contains information about every chain, like the compound information from the header, the nr of amino acids in chain, The alignment to the SEQRES residues

In order to create these index files for this PDB installation, please see the PrepareIndexFile class.

Author:

Andreas Prlic

See Also:

PrepareIndexFile

Field Summary

static SimpleDateFormat	dateFormat
static String	DEFAUL_CHAIN_FILE
static String	DEFAULT_INDEX_FILE
static Logger	logger

Constructor Summary

FlatFileInstallation(File filePath)
create a new FlatFile Installation and point it to the directory that contains all PDB files

Method Summary

void	addPDBFilter(PDBFilter filter) add a filter for PDB files.
void	applyFilters()
void	clearFilters() remove all filters, next time getAll is called, it will return all available PDBs
List<PDBHeader>	getAll() get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBs
File	getChainInfoFile()
File	getFilePath()
PDBHeader	getPDBHeader(String pdbId) get the PDB header for a single protein structure
File	getPDBInfoFile()
Structure	getStructure(String pdbId) request a structure by its PDB identifier
boolean	hasNext() return if the iteration over all structures will return another structure
Structure	next() iterate over all structures in this Installation that pass the provided filters and return the next one in the list.
void	setChainInfoFile(File chainInfoFile)
void	setFilePath(File filePath)
void	setPDBInfoFile(File indexFile)

Methods inherited from class java.lang.Object

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

Field Detail

logger

public static final Logger logger

DEFAULT_INDEX_FILE

public static final String DEFAULT_INDEX_FILE

See Also:

Constant Field Values

DEFAUL_CHAIN_FILE

public static final String DEFAUL_CHAIN_FILE

See Also:

Constant Field Values

dateFormat

public static SimpleDateFormat dateFormat

Constructor Detail

FlatFileInstallation

public FlatFileInstallation(File filePath)

create a new FlatFile Installation and point it to the directory that contains all PDB files

Parameters:

filePath -

Method Detail

getPDBInfoFile

public File getPDBInfoFile()

setPDBInfoFile

public void setPDBInfoFile(File indexFile)

getChainInfoFile

public File getChainInfoFile()

setChainInfoFile

public void setChainInfoFile(File chainInfoFile)

getFilePath

public File getFilePath()

setFilePath

public void setFilePath(File filePath)

addPDBFilter

public void addPDBFilter(PDBFilter filter)

Description copied from interface: PDBInstallation

add a filter for PDB files. THis can be used to request, e.g. all X-ray structures, or all structures with a given resolution, all proteins with a certain function, etc.

Specified by:

addPDBFilter in interface PDBInstallation

Parameters:

filter - the filter to apply when getAll is being called.

See Also:

PDBInstallation.getAll()

clearFilters

public void clearFilters()

Description copied from interface: PDBInstallation

remove all filters, next time getAll is called, it will return all available PDBs

Specified by:

clearFilters in interface PDBInstallation

applyFilters

public void applyFilters()

getAll

public List<PDBHeader> getAll()

Description copied from interface: PDBInstallation

get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBs

Specified by:

getAll in interface PDBInstallation

Returns:

a list of PDBHeader objects

getPDBHeader

public PDBHeader getPDBHeader(String pdbId)

Description copied from interface: PDBInstallation

get the PDB header for a single protein structure

Specified by:

getPDBHeader in interface PDBInstallation

Returns:

the PDB header object

getStructure

public Structure getStructure(String pdbId)

Description copied from interface: PDBInstallation

request a structure by its PDB identifier

Specified by:

getStructure in interface PDBInstallation

Returns:

the structure for the pdbId

hasNext

public boolean hasNext()

Description copied from interface: PDBInstallation

return if the iteration over all structures will return another structure

Specified by:

hasNext in interface PDBInstallation

Returns:

true if there is another structure that has not been iterated over yet

next

public Structure next()

Description copied from interface: PDBInstallation

iterate over all structures in this Installation that pass the provided filters and return the next one in the list.

Specified by:

next in interface PDBInstallation

Returns:

the next structure