org.biojava.bio.program.ssaha
Class MappedDataStoreFactory

java.lang.Object
  |
  +--org.biojava.bio.program.ssaha.MappedDataStoreFactory

All Implemented Interfaces:

DataStoreFactory

public class MappedDataStoreFactory

extends java.lang.Object

implements DataStoreFactory

Builder for a data store that is backed by a java.nio.MappedByteBuffer. This has a limitation that the total size of the mapped buffer and therefore the hash table can not exceed 2 gigs.

The data store file has the following structure.

 file: header, hash table, nameArray, nameTable, hitTable

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

   hash table:
     int hashTableLength,
     int[hashTableLength] hits // index into hitTable

  nameArray:
    int nameArrayLength,
    int[nameArrayLength] nameArray // byte offset into nameTable

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

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

  hitTableRecord:
    int hitCount,
    hitRecord[hitCount] hit

  hit:
    int seqIndex, // index into nameArray
    int offset    // offset into the sequence
 

Author:

Matthew Pocock

Constructor Summary

MappedDataStoreFactory()

Method Summary

DataStore	buildDataStore(java.io.File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) Build a new DataStore.
DataStore	getDataStore(java.io.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

MappedDataStoreFactory

public MappedDataStoreFactory()

Method Detail

getDataStore

public DataStore getDataStore(java.io.File storeFile)
                       throws java.io.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:

java.io.IOException - if the file could not be mapped

buildDataStore

public DataStore buildDataStore(java.io.File storeFile,
                                SequenceDB seqDB,
                                Packing packing,
                                int wordLength,
                                int threshold)
                         throws IllegalAlphabetException,
                                java.io.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:

BioException - if there is a problem building the data store

IllegalAlphabetException - if the packing does not agree with the sequences

java.io.IOException