CompactedDataStoreFactory (biojava-legacy 1.9.5 API)
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