org.biojava.bio.search

Interface SeqSimilaritySearcher

public interface SeqSimilaritySearcher

Objects of this type represent one particular installation (not just implementation) of a sequence similarity searcher such as BLASTP. Objects of this type must be immutable such that all parameters affecting the outcome of a search must be passed as an argument to the search() method.

Author:

Gerald Loeffler for the IMP

Method Summary

Modifier and Type	Method and Description
Set	getSearchableDBs() Return a set of all databases that can be searched with this sequence similarity searcher.
SeqSimilaritySearchResult	search(SymbolList querySeq, SequenceDB db, Map searchParameters) Using this sequence similarity searcher, search with the given sequence against the given sequence database.

Method Detail

getSearchableDBs

Set getSearchableDBs()

Return a set of all databases that can be searched with this sequence similarity searcher. This method reflects the fact that objects of this type represent a particular installation of a searcher which has access to only a limited number of databases.

Returns:

an unmodifiable Set of SequenceDB objects. Never returns null but may return an empty set.

search

SeqSimilaritySearchResult search(SymbolList querySeq,
                                 SequenceDB db,
                                 Map searchParameters)
                          throws BioException

Using this sequence similarity searcher, search with the given sequence against the given sequence database. It is a precondition that the sequence and the sequence database be compatible with each other and with this sequence similarity searcher, otherwise an IllegalArgumentException is thrown.

Particular implementations of a searcher will differ in the number and kind of parameters that can be used to customize a search. All these parameters must be passed as an argument to this method, i.e. these parameters are not part of the state of this searcher.

This method performs a synchronous search, i.e. it will block until the search result becomes available.

Parameters:

querySeq - the sequence with which to search. May not be null otherwise an IllegalArgumentException is thrown.

db - the sequence database against which the similarity search will be performed. May not be null otherwise an IllegalArgumentException is thrown. Must also be an element of the set of searchable dbs returned by getSearchableDBs().

searchParameters - parameters that customize the search. Null must always be a legal value for this argument and results in a default search being performed. If this map contains keys and/or values that are not supported by a particular implementation of this interface, an IllegalArgumentException is thrown.

Returns:

the sequence similarity search result that encapsulates the result of the search. Never returns null.

Throws:

BioException - if the actual search fails for some reason. If, however, the search can not even be started, because a precondition is not met, an IllegalArgumentException is thrown.