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## org.biojava.bio.seq.db
Class BioIndex

    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
`BioIndex(File indexDirectory)` Load an existing index file.
`BioIndex(File indexDirectory, String namespace, int idLength)`

Method Summary
`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 Detail

### 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 Detail

### 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

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