/* * 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 org.biojava.bio.symbol.IllegalAlphabetException; import org.biojava.bio.symbol.SymbolList; /** * * * @author Matthew Pocock */ public interface BioPattern { /** * Get a matcher that will use these parameters to search a SymbolList. * *
* The resulting BioMatcher is independant of this BioPattern. * In particular, calling any mutator methods on this pattern will not affect * the matcher. *
* * @param symList the SymbolList to match against * @return a BioMatcher that will perform the search * @throws IllegalAlphabetException if symList is not over the right alphabet */ BioMatcher matcher(SymbolList symList) throws IllegalAlphabetException; }