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(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