001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021package org.biojava.nbio.ws.alignment;
022
023import java.io.Serializable;
024import java.util.Set;
025
026/**
027 * RemotePairwiseAlignmentProperties is a interface that contains the barest of
028 * methods for setting and getting Alignment properties.
029 *
030 * Ideally, one would extend this class if creating a service by creating
031 * wrapper methods that actually call either getAlignementOption or setAlignementOption
032 * with specific values for parameter names and checking values for options.
033 *
034 * For an example, go see NCBIQBlastProperties
035 *
036 * @author Sylvain Foisy, Diploide BioIT
037 * @since Biojava 3
038 *
039 */
040public interface RemotePairwiseAlignmentProperties extends Serializable{
041
042        public static final long serialVersionUID = 1L;
043
044        /**
045         * Method that returns the value associated with the key given in parameter.
046         *
047         * @param key :a String with the required key for this map.
048         * @return a String with the value associated with this key
049         * @throws Exception if key is not in the map of output options.
050         */
051        public String getAlignmentOption(String key) throws Exception;
052
053        /**
054         * Method to set the value for a specific alignment parameter using a key to store in a map.
055         *
056         * @param key :the key use to designate the value to be stored
057         * @param val :the actual value matched to key
058         */
059        public void setAlignementOption(String key,String val);
060
061        /**
062         * Method to get all keys to the information stored in this object.
063         *
064         * @return a <code>Set</code> with all keys held in this instance of the object
065         */
066        public Set<String> getAlignmentOptions();
067}