public void TestAddGetPattern () {
			SetBest set = new SetBest();
			Assert.AreEqual( 0, set.Count );

			Motif motif = new Motif( "motif1", AlphabetType.DNA, "ACTG", 0.7 );
			set.Add( motif );
			Assert.AreEqual( 1, set.Count );
			Assert.AreEqual( motif, set[0] );
		}
		/** Tests if the match method finds the best pattern */
		public void TestMatch1 () {
			Sequence seq = new Sequence( AlphabetType.DNA, "taaacc" );
			SetBest set = new SetBest( "set1", 0.5 );
			set.Add( new Motif( "motif1", AlphabetType.DNA, "taa", 0.0 ) );
			set.Add( new Motif( "motif2", AlphabetType.DNA, "aacc", 0.0 ) );
			FeatureList matches;

			matches = seq.Search( 1, seq.Length, set );
			Assert.AreEqual( 3, matches.Count );
			Assert.AreEqual( "taa", matches[ 0 ].Letters() );
			Assert.AreEqual( 1.00, ( (Match) matches[ 0 ] ).Similarity, 1e-2 );
			Assert.AreEqual( "aaac", matches[ 1 ].Letters() );
			Assert.AreEqual( 0.75, ( (Match) matches[ 1 ] ).Similarity, 1e-2 );
			Assert.AreEqual( "aacc", matches[ 2 ].Letters() );
			Assert.AreEqual( 1.00, ( (Match) matches[ 2 ] ).Similarity, 1e-2 );
		}
		/** Tests the matching a pattern set against a sequence */
		public void TestMatch () {
			Sequence seq = new Sequence( AlphabetType.DNA, "atgcatgc" );
			SetBest set = new SetBest( "set1", 0.5 );
			set.Add( new Motif( "motif1", AlphabetType.DNA, "tgca", 0.0 ) );
			set.Add( new Motif( "", AlphabetType.DNA, "tgc", 0.0 ) );

			Match match = set.Match( seq, 2 );
			Assert.AreEqual( 2, match.Start );
			Assert.AreEqual( 4, match.Length );
			Assert.AreEqual( 1, match.Strand );
			Assert.AreEqual( 1, match.Similarity, 1e-2 );

			match = set.Match( seq, 1 );
			Assert.AreEqual( null, match );

			match = set.Match( seq, 6 );
			Assert.AreEqual( 6, match.Start );
			Assert.AreEqual( 3, match.Length );
			Assert.AreEqual( 1, match.Similarity, 1e-2 );
		}
        /// <summary>
        /// 
        /// Reads a pattern from a starting specified node. This method
        /// recursivly calls the reading methods of the different patterns.
        /// </summary>
        /// <param name="node">Node of the pattern the reading starts with.</param>
        /// <param name="definition">Pattern definition which pattern list will be extended 
        /// with the pattern and all its sub-patterns read.
        /// </param>
        /// <returns>The read pattern or null if there is no pattern to read.</returns>
        /// <exception cref="System.SystemException">Thrown when unknown pattern was found</exception>
        public static IPattern ReadPattern
                    (XmlNode node, Definition definition)
        {
            while (node != null
                    && node.NodeType != XmlNodeType.Element)

                node = node.NextSibling; //Iterate thru the list of nodes until it is an element

            IPattern pattern = null;
            String mode = XMLHelper.GetAttrValueString(node, "mode");

            switch (node.Name)
            {
                case "Any":
                    pattern = new Any();
                    break;

                case "Alignment":
                    pattern = new Alignment();
                    break;

                case "Composition" :
                    pattern = new Composition();
                    break;

                case "Constraint":
                    pattern = new Constraint();
                    break;

                case "Iteration":
                    pattern = new Iteration();
                    break;

                case "Logic":
                    pattern = new Logic();
                    break;

                case "Motif":
                    pattern = new Motif();
                    break;

                case "PWM":
                    pattern = new PWM();
                    break;

                case "Regex":
                    pattern = new RegularExp();
                    break;

                case "Prosite":
                    pattern = new Prosite();
                    break;

                case "Block":
                    pattern = new Block();
                    break;

                case "Gap":
                    pattern = new Gap();
                    break;

                case "Repeat":
                    pattern = new Repeat();
                    break;

                case "Series":
                    pattern = mode.Equals("ALL") ? 
                        pattern = new SeriesAll() : pattern = new SeriesBest();
                    break;

                case "Set":
                    pattern = mode.Equals("ALL") ?
                       pattern = new SetAll() : pattern = new SetBest();
                    break;

                case "Void":
                    pattern = new VoidPattern();
                    break;

                case "Use":
                    pattern = new Use();
                    break;

                throw new SystemException
                    ("Unknown pattern found: " + node.Name);
 
            }

 
            pattern.ReadNode(node, definition);      // read the node data and initialize the pattern
            definition.Patterns.Add
                            (0, pattern); //Always adding the element to last index
 
            return pattern;
        }