Package org.biojava.bio.program.ssaha
Class CompactedDataStore
java.lang.Object
org.biojava.bio.program.ssaha.CompactedDataStore
- All Implemented Interfaces:
DataStore
An implementation of DataStore that will map onto a file using the NIO
constructs. You should obtain one of these by using the methods in
MappedDataStoreFactory.
- Author:
- Matthew Pocock, Thomas Down
-
Method Summary
Modifier and TypeMethodDescriptionvoid
fireHits
(int word, int offset, SearchListener listener) The alphabet of symbol lists that can be searched against this DataStore.void
search
(String seqID, SymbolList symList, SearchListener listener) Search the DataStore with a symbol list.seqNameForID
(int id) Resolve an ID to a sequence name.
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Method Details
-
getAlphabet
Description copied from interface:DataStore
The alphabet of symbol lists that can be searched against this DataStore.- Specified by:
getAlphabet
in interfaceDataStore
- Returns:
- a FiniteAlphabet search types of SymbolList
-
search
Description copied from interface:DataStore
Search the DataStore with a symbol list. -
seqNameForID
Description copied from interface:DataStore
Resolve an ID to a sequence name.- Specified by:
seqNameForID
in interfaceDataStore
- Parameters:
id
- the int number of the sequence name to resolve- Returns:
- the name of that sequence as a String
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fireHits
-