Package org.biojava.bio.seq.db

Interface IndexStore

All Known Implementing Classes:

BioIndex, EmblCDROMIndexStore, TabIndexStore

public interface IndexStore

This defines the objects that IndexedSequenceDB uses to store all of the database state, such as name, format, sequence builder and the actual file offsets. You should only ever have to instantiate an implementation of this. Don't call any of the inerface methods directly. They are intended for IndexedSequenceDB, not you. In general, these objects should be transactional. Calls to store should add the index to temporary storage. When commit is invoked, these indices should all be added to the permanent storage. When rollback is invoked, these indexes should be discarded. If commit fails for any reason, it should leave the permanent storage in the pre-commit status.

Author:

Matthew Pocock

Method Summary

Modifier and Type	Method	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.
void	rollback()	Discard all uncommited changes.
void	store(Index indx)	Add the Index to the store.

Method Detail

store

void store(Index indx)
    throws IllegalIDException,
           BioException

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.

Parameters:

indx - the Index to add

Throws:

IllegalIDException - if the index has an invalid ID field

BioException - if the store failed

commit

void commit()
     throws BioException

Commit the stored indices to permanent storage.

Throws:

BioException - if for any reason the commit fails

rollback

void rollback()

Discard all uncommited changes.

fetch

Index fetch(String id)
     throws IllegalIDException,
            BioException

Fetch an Index based upon an ID.

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

getName

String getName()

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

Returns:

the String name of the index

getIDs

Set getIDs()

Retrieve the set of all current IDs.

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

Returns:

a Set of all legal IDs

getFiles

Set getFiles()

Retrieve the Set of files that are currently indexed.

getFormat

SequenceFormat getFormat()

Retrieve the format of the index file.

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

Returns:

a Set of all indexed files

getSBFactory

SequenceBuilderFactory getSBFactory()

Retrieve the SequenceBuilderFactory used to build Sequence instances.

Returns:

the associated SequenceBuilderFactory

getSymbolParser

SymbolTokenization getSymbolParser()

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

Returns:

the associated SymbolParser