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.biojavax.bio.alignment;
022
023import java.io.Serializable;
024import java.util.Properties;
025import java.util.Set;
026
027import org.biojava.bio.BioException;
028
029/**
030 * RemotePairwiseAlignmentProperties is a interface that contains the barest of 
031 * methods for setting and getting Alignment properties.
032 * 
033 * Ideally, one would extend this class if creating a service by creating 
034 * wrapper methods that actually call either getAlignementOption or setAlignementOption
035 * with specific values for parameter names and checking values for options.
036 * 
037 * For an example, go see RemoteQBlastProperties
038 * 
039 * @author Sylvain Foisy, Diploide BioIT
040 * @since 1.8
041 *
042 */
043public interface RemotePairwiseAlignmentProperties extends Serializable{
044
045        public static final long serialVersionUID = 1L;
046        
047    /**
048     * Method that returns the value associated with the key given in parameter.
049     * 
050     * @param key :a String with the required key for this map.
051     * @return a String with the value associated with this key
052     * @throws BioException if key is not in the map of output options.
053     */
054        public String getAlignmentOption(String key) throws BioException;
055        
056        /**
057         * Method to set the value for a specific alignment parameter using a key to store in a map.
058         * 
059         * @param key :the key use to designate the value to be stored
060         * @param val :the actual value matched to key
061         */
062        public void setAlignementOption(String key,String val);
063        
064        /**
065         * Method to get all keys to the information stored in this object.
066         * 
067         * @return a <code>Set</code> with all keys held in this instance of the object 
068         */
069        public Set<String> getAlignmentOptions();
070}