Package org.biojava.bio.seq.db

Class TabIndexStore

java.lang.Object

org.biojava.bio.seq.db.TabIndexStore

All Implemented Interfaces:

Serializable, IndexStore

public class TabIndexStore
extends Object
implements IndexStore, Serializable

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

Use the constructor to create a new index store. Use the static factory method open() to load an existing store.

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

Constructors

Constructor	Description
TabIndexStore(File storeFile, File indexFile, String name, SequenceFormat format, SequenceBuilderFactory sbFactory, SymbolTokenization symbolParser)	Create a new TabIndexStore.

Method Summary

Modifier and Type	Method	Description
protected void	addFile(File f)
void	commit()	Commit the stored indices to permanent storage.
protected void	commitStore()
Index	fetch(String id)	Fetch an Index based upon an ID.
protected int	getFileIndex(File file)
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.
protected void	initialize()
static TabIndexStore	open(File storeFile)	Open an existing index store.
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(File storeFile,
                     File indexFile,
                     String name,
                     SequenceFormat format,
                     SequenceBuilderFactory sbFactory,
                     SymbolTokenization symbolParser)
              throws IOException,
                     BioException

Create a new TabIndexStore.

The store file and index file must not exist. This is to prevent you from accidentally destroying an existing index.

Parameters:

storeFile - the file that will be used to persist this index store

indexFile - the file that will hold the actual indecies

name - the name that will be used by the database backed by this index

format - the SequenceFormat for files being indexed

sbFactory - the SequenceBuilderFactory used in building sequences

symbolParser - the SymbolTokenization to use

Throws:

IOException - if there was a problem writing the files

BioException - if any of the parameters were not acceptable

Method Detail

open

public static TabIndexStore open(File storeFile)
                          throws IOException

Open an existing index store.

Parameters:

storeFile - the File encapsulating the store

Returns:

a new TabIndexStore for that file

Throws:

IOException - if the storeFile could not be processed

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(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

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 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 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

commitStore

protected void commitStore()
                    throws IOException

Throws:

IOException

addFile

protected void addFile(File f)

getFileIndex

protected int getFileIndex(File file)

initialize

protected void initialize()
                   throws IOException

Throws:

IOException