Package 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
Modifier and TypeMethodDescriptionbuildDataStore(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.
-
Method Details
-
getDataStore
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:
IOException- if the file could not be mapped
-
buildDataStore
DataStore buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) throws IllegalAlphabetException, IOException, BioException Build a new DataStore.- 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
-