org.biojava.bio.seq.db
Class TabIndexStore

java.lang.Object
  |
  +--org.biojava.bio.seq.db.TabIndexStore

All Implemented Interfaces:

IndexStore, java.io.Serializable

public class TabIndexStore

extends java.lang.Object

implements IndexStore, java.io.Serializable

Implements IndexStore as a serialized file for the java data and a tab-delimited file of offsets.

The tab-delimited file looks like:

 fileNumber \t offset \t id \n
 

Author:

Matthew Pocock, Thomas Down, Keith James, David Huen

See Also:

Serialized Form

Constructor Summary

TabIndexStore(java.io.File storeFile, java.io.File indexFile, java.lang.String name, SequenceFormat format, SequenceBuilderFactory sbFactory, SymbolTokenization symbolParser)

Method Summary

protected void	addFile(java.io.File f)
void	commit() Commit the stored indices to permanent storage.
protected void	commitStore()
Index	fetch(java.lang.String id) Fetch an Index based upon an ID.
protected int	getFileIndex(java.io.File file)
java.util.Set	getFiles() Retrieve the Set of files that are currently indexed.
SequenceFormat	getFormat() Retrieve the format of the index file.
java.util.Set	getIDs() Retrieve the set of all current IDs.
java.lang.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.
protected void	initialize()
static TabIndexStore	open(java.io.File storeFile)
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

TabIndexStore

public TabIndexStore(java.io.File storeFile,
                     java.io.File indexFile,
                     java.lang.String name,
                     SequenceFormat format,
                     SequenceBuilderFactory sbFactory,
                     SymbolTokenization symbolParser)
              throws java.io.IOException,
                     BioException

Method Detail

open

public static TabIndexStore open(java.io.File storeFile)
                          throws java.io.IOException

java.io.IOException

store

public void store(Index indx)
           throws IllegalIDException,
                  BioException

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

Throws:

IllegalIDException - if the index has an invalid ID field

BioException - if the store failed

fetch

public Index fetch(java.lang.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:

BioException - if the fetch fails in the underlying storage mechanism

IllegalIDException - if the ID couldn't be found

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

getName

public java.lang.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

getIDs

public java.util.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 java.util.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

commitStore

protected void commitStore()
                    throws java.io.IOException

java.io.IOException

addFile

protected void addFile(java.io.File f)

getFileIndex

protected int getFileIndex(java.io.File file)

initialize

protected void initialize()
                   throws java.io.IOException

java.io.IOException