public void TestReadSampleGenbankFileAsTextReaderObj () {
			using ( reader = new BioPatMBF_Reader() ) {
				System.Diagnostics.Debug.WriteLine( reader.Read(
					Global.GetResourceReader( _sampleGenBankFile1 )
				) );
			}
		}
		public void TestMotifPattern_Motif () {
			BiopatMLFilePath = "BioPaperTestData/MotifPattern/Motif.xml";

			using ( BioPatMBF_Reader gbReader = new BioPatMBF_Reader() ) {
				BioList = gbReader.Read( Global.GetResourceReader( _singleDnaSeqGenBankFilename ) );
			}

			MyPatterns = DefinitionIO.Read( Global.GetResourceReader( BiopatMLFilePath ) );

			FeatureList Matches = BioList[0].Search( SearchPosition, BioList[0].Length, MyPatterns.Pattern );

			//According to Jacobi library total matches should be 57 
			Assert.AreEqual( 57, Matches.Count );
			Assert.AreEqual( "Pribnow-box", Matches.Name );
			//Perform some random checks from the 57 list

			Match matched = (Match) Matches[10]; //try get the 11th matched

			Assert.AreEqual( 0.66, matched.Similarity, 1e-2 );
			Assert.AreEqual( 6, matched.Length );
			Assert.AreEqual( "ttttat", matched.Letters() );

			//try the first match
			matched = (Match) Matches[0];
			Assert.AreEqual( AlphabetFactory.Instance( AlphabetType.DNA ), matched.Alphabet );
			Assert.AreEqual( 6, matched.Length );
			Assert.AreEqual( 0.5, matched.Similarity, 1e-2 );

			// Check the last match
			matched = (Match) Matches[56];
			Assert.AreEqual( 0.5, matched.Similarity, 1e-2 );
			Assert.AreEqual( "tttctt", matched.Letters() );

		}
        public void TestStructuredPattern_SeriesAll()
        {
            BiopatMLFilePath = "BioPaperTestData/StructuredPattern/SeriesAll.xml";

            using (BioPatMBF_Reader gbReader = new BioPatMBF_Reader())
            {
				BioList = gbReader.Read( Global.GetResourceReader( _singleDnaSeqGenBankFilename ) );
            }

			MyPatterns = DefinitionIO.Read( Global.GetResourceReader(   BiopatMLFilePath ) );

			FeatureList Matches = BioList[0].Search( SearchPosition, BioList[0].Length, MyPatterns.Pattern );

            //expecting 49 matches based on the old jacobi result
            Assert.AreEqual(49, Matches.Count);

            Match matched = (Match)Matches[0]; //Query the 1st matched from the list of matches
            Assert.AreEqual(3, matched.SubMatches.Count); //should have 3 sub matches

            Assert.AreEqual("aattt", matched.SubMatches[0].Letters());
            Assert.AreEqual("tataagtg", matched.SubMatches[1].Letters());
            Assert.AreEqual("ttcaa", matched.SubMatches[2].Letters());

            //And finally the main matched
            Assert.AreEqual("aattttataagtgttcaa", matched.Letters());
        }
		public void TestReadSampleGenbankFileAsFilePath () {
			using ( reader = new BioPatMBF_Reader() ) {
				// TODO: this is not a unit test. We need some way of automatically determining if it worked.
				System.Diagnostics.Debug.WriteLine( reader.Read(
					Global.GetResourceReader( _sampleGenBankFile2 )
				) );
			}
		}
		public void TestRegionalPattern_Gap () {
			BiopatMLFilePath = "BioPaperTestData/RegionalPattern/RegionalGap.xml";

			BioPatMBF_Reader gbReader = new BioPatMBF_Reader();
			BioList = gbReader.Read( Global.GetResourceReader( _singleProteinSeqGenBankFilename ) );
			MyPatterns = DefinitionIO.Read( Global.GetResourceReader( BiopatMLFilePath ) );

			FeatureList Matches = BioList[0].Search( SearchPosition, BioList[0].Length, MyPatterns.Pattern );

			//Total matches according to old jacobi is 309
			Assert.AreEqual( 410, Matches.Count );
			//Checks the first match 
			Assert.AreEqual( "MT", Matches[0].MainSequence.Letters( Matches[0].Start, Matches[0].End ) );
			//Checks if the last Match is in correect start and end pos
			Assert.AreEqual( "CE", Matches[409].MainSequence.Letters( Matches[409].Start, Matches[409].End ) );
		}
        public SequenceContract ParseGenbankFile(string gbContent)
        {
            StringReader sr = new StringReader(gbContent);
            SequenceContract sequence = new SequenceContract();
            SequenceList bioSeqList = null; //BioPatML's data structure

            using (ReaderBase reader = new BioPatMBF_Reader())
            {
                bioSeqList = reader.Read(sr);
            }

            //for now we only always use the first sequence SequenceName
            sequence.Name = bioSeqList[0].Annotations("SequenceName").AnnotationValue as string;
            //sequence.Name = bioSeqList[0].Name;
            sequence.AlphabetName = bioSeqList[0].Alphabet.Name;
            sequence.Characters = bioSeqList[0].Letters();

            return sequence;
        }
		public void TestRegionalPattern_Composition () {
			BiopatMLFilePath = "BioPaperTestData/RegionalPattern/RegionalComposition.xml";

			using ( BioPatMBF_Reader gbReader = new BioPatMBF_Reader() ) {
				BioList = gbReader.Read( Global.GetResourceReader( _singleProteinSeqGenBankFilename ) );
			}

			MyPatterns = DefinitionIO.Read( Global.GetResourceReader( BiopatMLFilePath ) );

			FeatureList Matches = BioList[0].Search( SearchPosition, BioList[0].Length, MyPatterns.Pattern );

			//Total matches according to old jacobi is 309
			Assert.AreEqual( 49, Matches.Count );
			//Checks the first match 
			Assert.AreEqual( "GATLFKTRCLQCHTV", Matches[0].MainSequence.Letters( Matches[0].Start, Matches[0].End ) );
			//Check see if the pattern used to match has the correct name for its matches
			Assert.AreEqual( "transmembrane domain", Matches.Name );
			Assert.AreEqual( 12, Matches[0].Start );
			Assert.AreEqual( 26, Matches[0].End );
			//Checks if the last Match is in correect start and end pos
			Assert.AreEqual( "KDRNDLITYLKKACE", Matches[48].MainSequence.Letters( Matches[48].Start, Matches[48].End ) );
		}
		/** Tests the match method of a series of patterns with two gaps */
		public void TestMatchSigma70InChlamydia () {
			SequenceList sequences = null;

			using ( BioPatMBF_Reader reader = new BioPatMBF_Reader() ) {
				sequences = reader.Read(
					Global.GetResourceReader( "data/GenBank/NC_000117-Chlamydia trachomatis D-UW-3CX.gbk" )
				);
			}

			Sequence seq = sequences[0];
			SeriesAll series = new SeriesAll();

			series.Add( new Motif( "", AlphabetType.DNA, "attata", 1.0 ) );
			series.Add( new Gap( "", 1, 200, 1 ) );
			series.Add( new Motif( "", AlphabetType.DNA, "tgtcaa", 1.0 ) );

			FeatureList matches = seq.Search( 2, seq.Length, series );
			Assert.AreEqual( 11, matches.Count );

			//Assert.AreEqual( "taaaagcc", matches[0].Letters() );
			//Assert.AreEqual( 1.0, ( (Match) matches[0] ).Similarity, 1e-1 );
			//Assert.AreEqual( "taaaagccc", matches[1].Letters() );
			//Assert.AreEqual( 1.0, ( (Match) matches[1] ).Similarity, 1e-1 );
			//Assert.AreEqual( "taaaagccc", matches[2].Letters() );
			//Assert.AreEqual( 0.9, ( (Match) matches[2] ).Similarity, 1e-1 );
		}
		public void TestMotifPattern_PWM () {
			BiopatMLFilePath = "BioPaperTestData/MotifPattern/PWM.xml";

			using ( BioPatMBF_Reader gbReader = new BioPatMBF_Reader() ) {
				BioList = gbReader.Read( Global.GetResourceReader( _sampleGenBankFile2 ) );
			}

			MyPatterns = DefinitionIO.Read( Global.GetResourceReader( BiopatMLFilePath ) );
			FeatureList Matches = BioList[0].Search( SearchPosition, BioList[0].Length, MyPatterns.Pattern );

			Assert.AreEqual( 14, Matches.Count );
			Assert.AreEqual( "Pribnow-box", Matches.Name );

			Match matched = (Match) Matches[0];
			Assert.AreEqual( 17, matched.Start );
			Assert.AreEqual( 22, matched.End );
			Assert.AreEqual( 0.67, matched.Similarity, 1e-2 );
			Assert.AreEqual( "tctcct", matched.Letters() );

			matched = (Match) Matches[1];

			Assert.AreEqual( 25, matched.Start );
			Assert.AreEqual( 30, matched.End );
			Assert.AreEqual( 0.61, matched.Similarity, 1e-2 );
			Assert.AreEqual( "ttggct", matched.Letters() );

			matched = (Match) Matches[13];
			Assert.AreEqual( 268, matched.Start );
			Assert.AreEqual( 273, matched.End );
			Assert.AreEqual( 0.67, matched.Similarity, 1e-2 );
			Assert.AreEqual( "tgtgct", matched.Letters() );
		}
		public void TestMotifPattern_Block () {
			BiopatMLFilePath = "BioPaperTestData/MotifPattern/Block.xml";

			BioPatMBF_Reader gbReader = new BioPatMBF_Reader();
			BioList = gbReader.Read( Global.GetResourceReader( _sampleGenBankFile2 ) );

			MyPatterns = DefinitionIO.Read( Global.GetResourceReader( BiopatMLFilePath ) );
			FeatureList Matches = BioList[0].Search( SearchPosition, BioList[0].Length, MyPatterns.Pattern );

			Assert.AreEqual( 3, Matches.Count );
			Assert.AreEqual( "Pribnow-box", Matches.Name );

			Match matched = (Match) Matches[0];
			Assert.AreEqual( 0.83, matched.Similarity, 1e-2 );
			Assert.AreEqual( "tataac", matched.Letters() );

			matched = (Match) Matches[1];
			Assert.AreEqual( 0.76, matched.Similarity, 1e-2 );
			Assert.AreEqual( "taacat", matched.Letters() );

			matched = (Match) Matches[2];
			Assert.AreEqual( 0.72, matched.Similarity, 1e-2 );
			Assert.AreEqual( "cataaa", matched.Letters() );
		}