Package org.biojava.bio.program.ssaha
Interface DataStore
- All Known Implementing Classes:
CompactedDataStore
public interface DataStore
A repository that can be searched with a sequence.
- Author:
- Matthew Pocock
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Method Summary
Modifier and TypeMethodDescriptionThe alphabet of symbol lists that can be searched against this DataStore.void
search
(String id, 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
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getAlphabet
The alphabet of symbol lists that can be searched against this DataStore.- Returns:
- a FiniteAlphabet search types of SymbolList
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search
void search(String id, SymbolList symList, SearchListener listener) throws IllegalAlphabetException, SearchException Search the DataStore with a symbol list.- Parameters:
id
- the ID to report the symbol list by e.g. 'test' or 'foo1'symList
- the symbol list to search withlistener
- the listener to inform of hits- Throws:
IllegalAlphabetException
- if the symbol list is of a type that is not compatible with this data storeSearchException
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seqNameForID
Resolve an ID to a sequence name.- Parameters:
id
- the int number of the sequence name to resolve- Returns:
- the name of that sequence as a String
- Throws:
IndexOutOfBoundsException
- if id is negative or too largeSearchException
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