Package org.biojava.bio.program.ssaha
Class CompactedDataStoreFactory
java.lang.Object
org.biojava.bio.program.ssaha.CompactedDataStoreFactory
- All Implemented Interfaces:
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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionbuildDataStore
(File storeFile, SequenceStreamer streamer, Packing packing, int wordLength, int stepSize, int threshold) buildDataStore
(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) Build a new DataStore.getDataStore
(File storeFile) Get a pre-built data store associated with a file.
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Constructor Details
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CompactedDataStoreFactory
public CompactedDataStoreFactory()
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Method Details
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getDataStore
Description copied from interface:DataStoreFactory
Get a pre-built data store associated with a file.- Specified by:
getDataStore
in interfaceDataStoreFactory
- 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
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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 interfaceDataStoreFactory
- Parameters:
storeFile
- the file to store the data storeseqDB
- the SequenceDB to store in the data storepacking
- the Packing used to bit-encode the sequenceswordLength
- the number of symbols per wordthreshold
- the number of times a word must appear to be ignored- Throws:
IllegalAlphabetException
- if the packing does not agree with the sequencesBioException
- if there is a problem building the data storeIOException
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buildDataStore
public DataStore buildDataStore(File storeFile, SequenceStreamer streamer, Packing packing, int wordLength, int stepSize, int threshold) throws IllegalAlphabetException, IOException, BioException
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