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

Description

BioIndex(File indexDirectory)

Load an existing index file.

BioIndex(File indexDirectory, String namespace, int idLength)
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.

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 Details
- 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 Details
- 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

Class BioIndex

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

BioIndex

BioIndex

Method Details

getName

guessRecLen

fetch

store

commit

rollback

getIDs

getFiles

getFormat

getSBFactory

getSymbolParser