org.biojava.bio.seq.db

Class BioIndex

java.lang.Object

org.biojava.bio.seq.db.BioIndex

All Implemented Interfaces:

IndexStore

public class BioIndex
extends Object
implements IndexStore

The original object for indexing sequence files.

This class may not be thread-safe.

Author:

Matthew Pocock, Thomas Down

Constructor Summary

Constructors

Constructor and Description
BioIndex(File indexDirectory) Load an existing index file.
BioIndex(File indexDirectory, String namespace, int idLength)

Method Summary

Methods

Modifier and Type	Method and Description
void	commit() Commit the stored indices to permanent storage.
Index	fetch(String id) Fetch an Index based upon an ID.
Set	getFiles() Retrieve the Set of files that are currently indexed.
SequenceFormat	getFormat() Retrieve the format of the index file.
Set	getIDs() Retrieve the set of all current IDs.
String	getName() Retrieve the name of this store.
SequenceBuilderFactory	getSBFactory() Retrieve the SequenceBuilderFactory used to build Sequence instances.
SymbolTokenization	getSymbolParser() Retrieve the symbol parser used to turn the sequence characters into Symobl objects.
int	guessRecLen(RandomAccessFile file)
void	rollback() Discard all uncommited changes.
void	store(Index indx) Add the Index to the store.

Methods inherited from class java.lang.Object

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

Constructor Detail

BioIndex

public BioIndex(File indexDirectory,
        String namespace,
        int idLength)
         throws IOException,
                BioException

Throws:

IOException

BioException

BioIndex

public BioIndex(File indexDirectory)
         throws IOException,
                BioException

Load an existing index file. If indexDirectory does not exist, or is not a bioindex stoore, this will barf.

Throws:

IOException

BioException

Method Detail

getName

public String getName()

Description copied from interface: IndexStore

Retrieve the name of this store. This will be reflected as the name of the IndexedSequenceDB.

Specified by:

getName in interface IndexStore

Returns:

the String name of the index

guessRecLen

public int guessRecLen(RandomAccessFile file)
                throws IOException

Throws:

IOException

fetch

public Index fetch(String id)
            throws IllegalIDException,
                   BioException

Description copied from interface: IndexStore

Fetch an Index based upon an ID.

Specified by:

fetch in interface IndexStore

Parameters:

id - The ID of the sequence Index to retrieve

Throws:

IllegalIDException - if the ID couldn't be found

BioException - if the fetch fails in the underlying storage mechanism

store

public void store(Index indx)

Description copied from interface: IndexStore

Add the Index to the store.

This method should be transactional. If the store fails, the IndexStore should be left in its original state.

If the file of the Index is not known yet, it is the responsibility of the IndexStore to add it to the set returned by getFiles.

Specified by:

store in interface IndexStore

Parameters:

indx - the Index to add

commit

public void commit()
            throws BioException

Description copied from interface: IndexStore

Commit the stored indices to permanent storage.

Specified by:

commit in interface IndexStore

Throws:

BioException - if for any reason the commit fails

rollback

public void rollback()

Description copied from interface: IndexStore

Discard all uncommited changes.

Specified by:

rollback in interface IndexStore

getIDs

public Set getIDs()

Description copied from interface: IndexStore

Retrieve the set of all current IDs.

This set should either be immutable, or modifiable totally separately from the IndexStore.

Specified by:

getIDs in interface IndexStore

Returns:

a Set of all legal IDs

getFiles

public Set getFiles()

Description copied from interface: IndexStore

Retrieve the Set of files that are currently indexed.

Specified by:

getFiles in interface IndexStore

getFormat

public SequenceFormat getFormat()

Description copied from interface: IndexStore

Retrieve the format of the index file.

This set should either be immutable, or modifiable totally separately from the IndexStore.

Specified by:

getFormat in interface IndexStore

Returns:

a Set of all indexed files

getSBFactory

public SequenceBuilderFactory getSBFactory()

Description copied from interface: IndexStore

Retrieve the SequenceBuilderFactory used to build Sequence instances.

Specified by:

getSBFactory in interface IndexStore

Returns:

the associated SequenceBuilderFactory

getSymbolParser

public SymbolTokenization getSymbolParser()

Description copied from interface: IndexStore

Retrieve the symbol parser used to turn the sequence characters into Symobl objects.

Specified by:

getSymbolParser in interface IndexStore

Returns:

the associated SymbolParser