Package org.biojava.bio.program.ssaha
Interface DataStoreFactory
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- All Known Implementing Classes:
CompactedDataStoreFactory
,MappedDataStoreFactory
,NIODataStoreFactory
public interface DataStoreFactory
Builder for a data store.
- Author:
- Matthew Pocock
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description 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.
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Method Detail
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getDataStore
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
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buildDataStore
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 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 storejava.io.IOException
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