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 Details
- 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 Details
- 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

Class TabIndexStore

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

TabIndexStore

Method Details

open

store

fetch

commit

rollback

getName

getIDs

getFiles

getFormat

getSBFactory

getSymbolParser

commitStore

addFile

getFileIndex

initialize