org.biojava.bio.program.ssaha
Interface DataStoreFactory

All Known Implementing Classes:
CompactedDataStoreFactory, MappedDataStoreFactory, NIODataStoreFactory

public interface DataStoreFactory

Builder for a data store.

Author:
Matthew Pocock

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.
 

Method Detail

getDataStore

public DataStore getDataStore(java.io.File storeFile)
                       throws java.io.IOException
Get a pre-built data store associated with a file.

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
Build a new DataStore.

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
java.io.IOException