org.biojava.bio.program.ssaha

Class NIODataStoreFactory

java.lang.Object

org.biojava.bio.program.ssaha.NIODataStoreFactory

All Implemented Interfaces:

DataStoreFactory

public class NIODataStoreFactory
extends Object
implements DataStoreFactory

Builder for a datastore that has no practical file size limit.

This implementation of the data store factory uses longs as indecies internaly, so can be used with files exceeding 2 gigs in size.

The data store file has the following structure.

 file: header, hash table, nameTable, hitTable

 header:
   long hashTablePos, // byte offset in file
   long hitTablePos,  // byte offset in file
   long nameTablePos, // byte offset in file
   int wordLength,
   int serializedPackingLength,
   byte[] serializedPacking

 hashTable:
   long hashTableLength,
   long[hashTableLength] hits // byte offset into hitTable

 nameTable:
   int nameTableSize, // size in bytes
   (short nameLength, char[nameLength] name)[nameTableSize] names

 hitTable:
   long hitTableSize, // size in bytes
   hitTableRecord[hitTableSize] hits

 hitTableRecord:
   int hitCount,
   hitRecord[hitCount] hit

 hit:
   long seqOffset, // byte offset into sequence names table
   int pos         // biological position in sequence
 

Author:

Matthew Pocock

Constructor Summary

Constructors

Constructor and Description
NIODataStoreFactory()

Method Summary

Methods

Modifier and Type	Method and Description
DataStore	buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) Build a new DataStore.
DataStore	getDataStore(File storeFile) Get a pre-built data store associated with a file.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

NIODataStoreFactory

public NIODataStoreFactory()

Method Detail

getDataStore

public DataStore getDataStore(File storeFile)
                       throws IOException

Description copied from interface: DataStoreFactory

Get a pre-built data store associated with a file.

Specified by:

getDataStore in interface DataStoreFactory

Parameters:

storeFile - the File to map in as a data store

Returns:

the DataStore made by mapping the file

Throws:

IOException - if the file could not be mapped

buildDataStore

public DataStore buildDataStore(File storeFile,
                       SequenceDB seqDB,
                       Packing packing,
                       int wordLength,
                       int threshold)
                         throws IllegalAlphabetException,
                                IOException,
                                BioException

Description copied from interface: DataStoreFactory

Build a new DataStore.

Specified by:

buildDataStore in interface DataStoreFactory

Parameters:

storeFile - the file to store the data store

seqDB - the SequenceDB to store in the data store

packing - the Packing used to bit-encode the sequences

wordLength - the number of symbols per word

threshold - the number of times a word must appear to be ignored

Throws:

IllegalAlphabetException - if the packing does not agree with the sequences

BioException - if there is a problem building the data store

IOException