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java.lang.Objectorg.biojava.bio.program.ssaha.CompactedDataStoreFactory
public class CompactedDataStoreFactory
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
Constructor Summary | |
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CompactedDataStoreFactory()
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Method Summary | |
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DataStore |
buildDataStore(File storeFile,
SequenceDB seqDB,
Packing packing,
int wordLength,
int threshold)
Build a new DataStore. |
DataStore |
buildDataStore(File storeFile,
SequenceStreamer streamer,
Packing packing,
int wordLength,
int stepSize,
int threshold)
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DataStore |
getDataStore(File storeFile)
Get a pre-built data store associated with a file. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public CompactedDataStoreFactory()
Method Detail |
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public DataStore getDataStore(File storeFile) throws IOException
DataStoreFactory
getDataStore
in interface DataStoreFactory
storeFile
- the File to map in as a data store
IOException
- if the file could not be mappedpublic DataStore buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) throws IllegalAlphabetException, IOException, BioException
DataStoreFactory
buildDataStore
in interface DataStoreFactory
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
IllegalAlphabetException
- if the packing does not agree with
the sequences
BioException
- if there is a problem building the data store
IOException
public DataStore buildDataStore(File storeFile, SequenceStreamer streamer, Packing packing, int wordLength, int stepSize, int threshold) throws IllegalAlphabetException, IOException, BioException
IllegalAlphabetException
IOException
BioException
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