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
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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.
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Method Details
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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
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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
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