Package org.biojava.bio.program.indexdb

Class BioStoreFactory

java.lang.Object

org.biojava.bio.program.indexdb.BioStoreFactory

public class BioStoreFactory
extends Object

BioStoreFactory creates BioStore instances. These are directory and file structures which index flat files according to the OBDA specification.

Author:

Matthew Pocock, Keith James, Greg Cox

Field Summary

Fields

Modifier and Type	Field	Description
static String	KEYS	KEYS is the key used to identify the secondary namespaces in the OBDA config.dat files.
static AnnotationType	META_DATA_TYPE	AnnotationType that all meta-data files should fit.
static String	PRIMARY_KEY_NAME	PRIMARY_KEY_NAME is the key used to identify the primary namespace in the OBDA config.dat files.
static String	SEQUENCE_FORMAT	SEQUENCE_FORMAT is the key used to identify the format of the indexed sequence files represented by the store in the OBDA config.dat files.
static String	STORE_NAME	STORE_NAME is the key used to identify the arbitrary name of the store in the OBDA config.dat files.

Constructor Summary

Constructors

Constructor	Description
BioStoreFactory()	Creates a new BioStoreFactory.

Method Summary

Modifier and Type	Method	Description
void	addKey(String keyName, int length)	addKey adds a new identifier namespace.
static int	calculatePrimRecLen(int idLen)	calculatePrimRecLen calculates the byte length of primary namespace records.
static int	calculateSecRecLen(int idLen, String primaryKey, Map keys)	calculateSecRecLen calculates the byte length of secondary namespace records.
BioStore	createBioStore()	createBioStore creates a BioStore reflecting the current state of the factory and returns a reference to it.
Set	getKeys()
String	getPrimaryKey()	getPrimaryKey returns the primary identifier namespace.
LifeScienceIdentifier	getSequenceFormat()	getSequenceFormat returns the current sequence format name.
File	getStoreLocation()	getStoreLocation returns the directory of the bew index.
String	getStoreName()	getStoreName returns the name to be given to the new index.
static File	makeConfigFile(File storeLoc)	makeConfigFile returns a file which represents an OBDA "config.dat" in the specified index directory.
static File	makePrimaryKeyFile(File storeLoc, String key)	makePrimaryKeyFile returns a file which represents an OBDA "key_<primary namespace>.key" primary key file on the specified index directory.
static File	makeSecondaryFile(File storeLoc, String key)	makeSecondaryFile returns a file which represents an OBDA "id_<secondary namespace>.index" secondary key file on the specified.
void	removeKey(String keyName)	removeKey removes the specified key.
void	setPrimaryKey(String primaryKey)	setPrimaryKey sets the primary identifier namespace.
void	setSequenceFormat(LifeScienceIdentifier format)	setSequenceFormat sets the sequence format name which will be indicated in the index.
void	setStoreLocation(File storeLoc)	setStoreLocation sets the directory of the new index.
void	setStoreName(String name)	setStoreName sets the name to be given to the new index.

Methods inherited from class java.lang.Object

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

Field Detail

STORE_NAME

public static final String STORE_NAME

STORE_NAME is the key used to identify the arbitrary name of the store in the OBDA config.dat files.

See Also:

Constant Field Values

SEQUENCE_FORMAT

public static final String SEQUENCE_FORMAT

SEQUENCE_FORMAT is the key used to identify the format of the indexed sequence files represented by the store in the OBDA config.dat files.

See Also:

Constant Field Values

PRIMARY_KEY_NAME

public static final String PRIMARY_KEY_NAME

PRIMARY_KEY_NAME is the key used to identify the primary namespace in the OBDA config.dat files.

See Also:

Constant Field Values

KEYS

public static final String KEYS

KEYS is the key used to identify the secondary namespaces in the OBDA config.dat files.

See Also:

Constant Field Values

META_DATA_TYPE

public static final AnnotationType META_DATA_TYPE

AnnotationType that all meta-data files should fit.

Constructor Detail

BioStoreFactory

public BioStoreFactory()

Creates a new BioStoreFactory.

Method Detail

setStoreName

public void setStoreName(String name)

setStoreName sets the name to be given to the new index.

Parameters:

name - a String.

getStoreName

public String getStoreName()

getStoreName returns the name to be given to the new index.

Returns:

a String.

setStoreLocation

public void setStoreLocation(File storeLoc)

setStoreLocation sets the directory of the new index.

Parameters:

storeLoc - a File.

getStoreLocation

public File getStoreLocation()

getStoreLocation returns the directory of the bew index.

Returns:

a File.

setSequenceFormat

public void setSequenceFormat(LifeScienceIdentifier format)

setSequenceFormat sets the sequence format name which will be indicated in the index.

Parameters:

format - a LifeScienceIdentifier which must be one of those mandated by the OBDA flatfile indexing specification.

getSequenceFormat

public LifeScienceIdentifier getSequenceFormat()

getSequenceFormat returns the current sequence format name.

Returns:

a LifeScienceIdentifier.

setPrimaryKey

public void setPrimaryKey(String primaryKey)

setPrimaryKey sets the primary identifier namespace.

Parameters:

primaryKey - a String.

getPrimaryKey

public String getPrimaryKey()

getPrimaryKey returns the primary identifier namespace.

Returns:

a String.

addKey

public void addKey(String keyName,
                   int length)

addKey adds a new identifier namespace.

Parameters:

keyName - a String.

length - an int indicating the byte length of the key records.

getKeys

public Set getKeys()

removeKey

public void removeKey(String keyName)

removeKey removes the specified key.

Parameters:

keyName - a String.

createBioStore

public BioStore createBioStore()
                        throws BioException

createBioStore creates a BioStore reflecting the current state of the factory and returns a reference to it.

Returns:

a BioStore.

Throws:

BioException - if an error occurs.

makeConfigFile

public static File makeConfigFile(File storeLoc)
                           throws IOException

makeConfigFile returns a file which represents an OBDA "config.dat" in the specified index directory.

Parameters:

storeLoc - a File indicating the index directory.

Returns:

a File representing "config.dat".

Throws:

IOException - if an error occurs.

makePrimaryKeyFile

public static File makePrimaryKeyFile(File storeLoc,
                                      String key)
                               throws IOException

makePrimaryKeyFile returns a file which represents an OBDA "key_<primary namespace>.key" primary key file on the specified index directory.

Parameters:

storeLoc - a File indicating the parent path.

key - a String primary key namespace.

Returns:

a File representing a "key_<primary namespace>.key".

Throws:

IOException - if an error occurs.

makeSecondaryFile

public static File makeSecondaryFile(File storeLoc,
                                     String key)
                              throws IOException

makeSecondaryFile returns a file which represents an OBDA "id_<secondary namespace>.index" secondary key file on the specified.

Parameters:

storeLoc - a File indicating the parent path.

key - a String secondary key namespace.

Returns:

a File representing an "id_<secondary namespace>.index" file.

Throws:

IOException - if an error occurs.

calculatePrimRecLen

public static int calculatePrimRecLen(int idLen)

calculatePrimRecLen calculates the byte length of primary namespace records.

Parameters:

idLen - an int the number of bytes required to hold the primary namespace ID.

Returns:

an int record length in bytes.

calculateSecRecLen

public static int calculateSecRecLen(int idLen,
                                     String primaryKey,
                                     Map keys)

calculateSecRecLen calculates the byte length of secondary namespace records.

Parameters:

idLen - an int the number of bytes required to hold the secondary namespace ID.

primaryKey - a String the primary namespace ID.

keys - a Map of secondary keys to their byte lengths.

Returns:

an int record length in bytes.