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

Modifier and Type	Method and Description
FiniteAlphabet	getAlphabet() The alphabet of symbol lists that can be searched against this DataStore.
void	search(java.lang.String id, SymbolList symList, SearchListener listener) Search the DataStore with a symbol list.
java.lang.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(java.lang.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

java.lang.String seqNameForID(int id)
                       throws java.lang.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:

java.lang.IndexOutOfBoundsException - if id is negative or too large

SearchException