/* * BioJava development code * * This code may be freely distributed and modified under the * terms of the GNU Lesser General Public Licence. This should * be distributed with the code. If you do not have a copy, * see: * * http://www.gnu.org/copyleft/lesser.html * * Copyright for this code is held jointly by the individual * authors. These should be listed in @author doc comments. * * For more information on the BioJava project and its aims, * or to join the biojava-l mailing list, visit the home page * at: * * http://www.biojava.org/ * */ package org.biojava.bio.search; import java.util.Map; import java.util.Set; import org.biojava.bio.BioException; import org.biojava.bio.seq.db.SequenceDB; import org.biojava.bio.symbol.SymbolList; /** * 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 * */ public interface SeqSimilaritySearcher { /** * 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. * * @return an unmodifiable Set of SequenceDB objects. Never * returns null but may return an empty set. */ Set getSearchableDBs(); /** * 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. * * @param querySeq the sequence with which to search. May not be * null otherwise an IllegalArgumentException is thrown. * @param 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(). * @param 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. * * @return the sequence similarity search result that encapsulates * the result of the search. Never returns null. * * @exception 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. */ SeqSimilaritySearchResult search(SymbolList querySeq, SequenceDB db, Map searchParameters) throws BioException; }