Package org.biojava.bio.program.ssaha

Class CompactedDataStoreFactory

java.lang.Object

org.biojava.bio.program.ssaha.CompactedDataStoreFactory

All Implemented Interfaces:

DataStoreFactory

public class CompactedDataStoreFactory
extends 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] nameRecord // byte offset into nameTable

  nameRecord:
    int nameTableOffset
    int sequenceStartOffset
 
  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 offset    // offset into the sequence
 

Author:

Matthew Pocock, Thomas Down

Constructor Summary

Constructors

Constructor	Description
CompactedDataStoreFactory()

Method Summary

Modifier and Type	Method	Description
DataStore	buildDataStore(File storeFile, SequenceStreamer streamer, Packing packing, int wordLength, int stepSize, int threshold)
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

CompactedDataStoreFactory

public CompactedDataStoreFactory()

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

buildDataStore

public DataStore buildDataStore(File storeFile,
                                SequenceStreamer streamer,
                                Packing packing,
                                int wordLength,
                                int stepSize,
                                int threshold)
                         throws IllegalAlphabetException,
                                IOException,
                                BioException

Throws:

IllegalAlphabetException

IOException

BioException