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