public void TestAddGetAnnotations () {
			Sequence seq = new Sequence( AlphabetType.DNA, "ACTG" );
			AnnotationList a1 = seq.Annotations;
			Assert.AreEqual( 0, a1.Count );

			AnnotationList a2 = new AnnotationList();
			a2.Add( new Annotation( "name1", "value1" ) );
			a2.Add( new Annotation( "name2", "value2" ) );
			seq.Annotations.AddRange( a2 );
			Assert.AreEqual( "name1", seq.Annotations[0].Name );
			Assert.AreEqual( "value2", seq.Annotations[1].Value );
			Assert.AreEqual( "name1", seq.Annotations[ "name1" ].Name );
			Assert.AreEqual( "value2", seq.Annotations.Value( "name2" ) );
			Assert.AreEqual( null, seq.Annotations.Value( "name3" ) );
			Assert.AreEqual( null, seq.Annotations[ "name3" ] );
		}
        /// <summary>
        /// This method takes in a MBF sequence and converts it to BioPatML sequence.
        /// </summary>
        /// <param name="mbfseq">The MBF sequence one is interested in.</param>
        /// <returns>Returns the converted BioPatML sequence.</returns>
        public QUT.Bio.BioPatML.Sequences.Sequence ParseMBFSequence
                                                            (Sequence mbfseq)
        {
            GenBankMetadata metaData;

            #region If sequence is complex type e.g. Genbank file with features 
            if (mbfseq.Metadata.ContainsKey(Helper.GenBankMetadataKey))
            {
                //Retrieves our meta data out
                metaData = (GenBankMetadata)mbfseq.Metadata[Helper.GenBankMetadataKey];

                //Create our BioPatML sequence
                QUT.Bio.BioPatML.Sequences.Sequence bioSequence = new QUT.Bio.BioPatML.Sequences.Sequence
                                            (ParseAlphabet(mbfseq), mbfseq.ToString(),
                                                        IsCircularStrand(metaData.Locus));

                #region Top the BioPatML Sequence with Feature data and sequence name

                //Add features to sequence
                bioSequence.AddFeatures(ExtractFeatures(metaData));

                //Add mbf sequence name to BioPatML sequence
                //Create annotation to put in our sequence data like name
                AnnotationList jacobiMeta = new AnnotationList();
                jacobiMeta.Add("SequenceName", metaData.Locus.Name);
                bioSequence.AddAnnotations(jacobiMeta);

                #endregion

                return bioSequence;

            }
            #endregion
            #region Else we assume it is a simple type e.g. Fasta files
            else
            {
                QUT.Bio.BioPatML.Sequences.Sequence bioSequence = new QUT.Bio.BioPatML.Sequences.Sequence
                                            (ParseAlphabet(mbfseq), mbfseq.ToString(),
                                                        false);

                AnnotationList jacobiMeta = new AnnotationList();
                jacobiMeta.Add("SequenceName", mbfseq.DisplayID);
                bioSequence.AddAnnotations(jacobiMeta);
                return bioSequence;
            }
            #endregion
        }
        /// <summary>
        /// Gets all annotations which name matches the given regular expression.
        /// </summary>
        /// <param name="regExp">
        /// Regular expression, <see> Pattern package </see>
        /// </param>
        /// <returns> 
        /// Returns an annotation list with all annotations matching the given name.
        /// </returns>
        public AnnotationList GetAll(Regex regExp)
        {
            AnnotationList aList = new AnnotationList();

            foreach (Annotation a in ListAnnotation)

                if (regExp.IsMatch(a.Name))
                    aList.Add(a);


            return (aList);
        }
        /// <summary>
        /// This method transfers all available features from the MBF sequence and 
        /// populate them into biopatml features data type.
        /// In this version only its name, start and end location is populated.
        /// </summary>
        /// <param name="metadata"></param>
        /// <returns></returns>
        private FeatureList ExtractFeatures(GenBankMetadata metadata)
        {
            List<FeatureItem> mbfFeatures = metadata.Features.All;
            FeatureList bioFeatureList = new FeatureList();

            foreach (FeatureItem item in mbfFeatures)
            {
                #region Constructs the feature outline first

                //Strand is always assumed to be forward +1
                QUT.Bio.BioPatML.Sequences.Feature bioFeature = new QUT.Bio.BioPatML.Sequences.Feature
                                        (item.Key, item.Location.Start, item.Location.End, 1);

                bioFeatureList.Add(bioFeature);

                #endregion

                #region Adds the qualifier key and values to Feature using AnnotationList

                AnnotationList annList = new AnnotationList();

                foreach (KeyValuePair<string, List<string>> qualitfier in item.Qualifiers)
                    annList.Add(qualitfier.Key, qualitfier.Value[0]);

                bioFeature.AddAnnotations(annList);

                #endregion
            }

            return bioFeatureList;
        }
        /// <summary>
        ///  Get all annotations with a given name.
        /// </summary>
        /// <param name="name"> Name of the annotations to retrieve. </param>
        /// <returns> 
        /// Returns a of list annotations that matches the
        /// specified name. 
        /// </returns>
        public AnnotationList GetAll(String name)
        {
            AnnotationList aList = new AnnotationList();

            foreach (Annotation a in ListAnnotation)
            
                if(a.Name.Equals(name))
                    aList.Add(a);


            return aList;
        }