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

Method Summary

FiniteAlphabet	getAlphabet() The 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.
String	seqNameForID(int id) Resolve an ID to a sequence name.

Method Detail

getAlphabet

FiniteAlphabet getAlphabet()

The alphabet of symbol lists that can be searched against this DataStore.

Returns:

a FiniteAlphabet search types of SymbolList

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 with

listener - the listener to inform of hits

Throws:

IllegalAlphabetException - if the symbol list is of a type that is not compatible with this data store

SearchException

seqNameForID

String seqNameForID(int id)
                    throws IndexOutOfBoundsException,
                           SearchException

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 large

SearchException