コード例 #1
0
ファイル: TestMzML.cs プロジェクト: NRTDP/mzLib
        public void Mzid110Test()
        {
            XmlSerializer _indexedSerializer = new XmlSerializer(typeof(mzIdentML110.Generated.MzIdentMLType));
            var           _mzid = new mzIdentML110.Generated.MzIdentMLType()
            {
                DataCollection = new mzIdentML110.Generated.DataCollectionType()
            };

            _mzid.DataCollection.AnalysisData = new mzIdentML110.Generated.AnalysisDataType()
            {
                SpectrumIdentificationList = new mzIdentML110.Generated.SpectrumIdentificationListType[1]
            };
            _mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0] = new mzIdentML110.Generated.SpectrumIdentificationListType()
            {
                SpectrumIdentificationResult = new mzIdentML110.Generated.SpectrumIdentificationResultType[1]
            };
            _mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0] = new mzIdentML110.Generated.SpectrumIdentificationResultType()
            {
                spectrumID = "spectrum 2",
                SpectrumIdentificationItem = new mzIdentML110.Generated.SpectrumIdentificationItemType[50]
            };
            _mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0] = new mzIdentML110.Generated.SpectrumIdentificationItemType()
            {
                experimentalMassToCharge        = 1134.2609130203 + 0.000001 * 1134.2609130203 + 0.000001,
                calculatedMassToCharge          = 1134.26091302033,
                calculatedMassToChargeSpecified = true,
                chargeState = 3,
                cvParam     = new mzIdentML110.Generated.CVParamType[1]
                {
                    new mzIdentML110.Generated.CVParamType()
                    {
                        accession = "MS:1002354",
                        value     = "0.05"
                    }
                }
            };
            _mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[1] = new mzIdentML110.Generated.SpectrumIdentificationItemType();
            _mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0].Fragmentation    = new mzIdentML110.Generated.IonTypeType[1];
            _mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0].Fragmentation[0] = new mzIdentML110.Generated.IonTypeType()
            {
                FragmentArray = new mzIdentML110.Generated.FragmentArrayType[1]
            };
            _mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0].Fragmentation[0].FragmentArray[0] = new mzIdentML110.Generated.FragmentArrayType()
            {
                values = new float[3] {
                    200, 300, 400
                }
            };
            _mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0].PeptideEvidenceRef    = new mzIdentML110.Generated.PeptideEvidenceRefType[1];
            _mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0].PeptideEvidenceRef[0] = new mzIdentML110.Generated.PeptideEvidenceRefType()
            {
                peptideEvidence_ref = "PE_1"
            };
            _mzid.DataCollection.Inputs = new mzIdentML110.Generated.InputsType()
            {
                SpectraData = new mzIdentML110.Generated.SpectraDataType[1]
            };
            _mzid.DataCollection.Inputs.SpectraData[0] = new mzIdentML110.Generated.SpectraDataType()
            {
                FileFormat = new mzIdentML110.Generated.FileFormatType()
            };
            _mzid.DataCollection.Inputs.SpectraData[0].FileFormat.cvParam = new mzIdentML110.Generated.CVParamType()
            {
                name = "mzML format"
            };
            _mzid.SequenceCollection = new mzIdentML110.Generated.SequenceCollectionType()
            {
                PeptideEvidence = new mzIdentML110.Generated.PeptideEvidenceType[1]
            };
            _mzid.SequenceCollection.PeptideEvidence[0] = new mzIdentML110.Generated.PeptideEvidenceType()
            {
                endSpecified   = true,
                startSpecified = true,
                isDecoy        = false,
                start          = 2,
                end            = 34,
                dBSequence_ref = "DB_1",
                peptide_ref    = "P_1",
                id             = "PE_1",
            };
            _mzid.SequenceCollection.Peptide    = new mzIdentML110.Generated.PeptideType[1];
            _mzid.SequenceCollection.Peptide[0] = new mzIdentML110.Generated.PeptideType()
            {
                id = "P_1",
                PeptideSequence = "GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR",
                Modification    = new mzIdentML110.Generated.ModificationType[1]
            };
            _mzid.SequenceCollection.DBSequence    = new mzIdentML110.Generated.DBSequenceType[1];
            _mzid.SequenceCollection.DBSequence[0] = new mzIdentML110.Generated.DBSequenceType()
            {
                id        = "DB_1",
                name      = "Protein name",
                accession = "ACCESSION",
            };
            _mzid.SequenceCollection.Peptide[0].Modification[0] = new mzIdentML110.Generated.ModificationType()
            {
                locationSpecified = true,
                location          = 17,
                monoisotopicMassDeltaSpecified = true,
                monoisotopicMassDelta          = 57.02146373,
                cvParam = new mzIdentML110.Generated.CVParamType[1]
            };
            _mzid.SequenceCollection.Peptide[0].Modification[0].cvParam[0] = new mzIdentML110.Generated.CVParamType()
            {
                accession = "UNIMOD:4",
                name      = "Carbamidomethyl",
                cvRef     = "UNIMOD"
            };
            _mzid.AnalysisProtocolCollection = new mzIdentML110.Generated.AnalysisProtocolCollectionType()
            {
                SpectrumIdentificationProtocol = new mzIdentML110.Generated.SpectrumIdentificationProtocolType[1]
            };
            _mzid.AnalysisProtocolCollection.SpectrumIdentificationProtocol[0] = new mzIdentML110.Generated.SpectrumIdentificationProtocolType()
            {
                ParentTolerance = new mzIdentML110.Generated.CVParamType[1]
            };
            _mzid.AnalysisProtocolCollection.SpectrumIdentificationProtocol[0].ParentTolerance[0] = new mzIdentML110.Generated.CVParamType()
            {
                unitName = "dalton",
                value    = "0.1"
            };
            _mzid.AnalysisProtocolCollection.SpectrumIdentificationProtocol[0].FragmentTolerance    = new mzIdentML110.Generated.CVParamType[1];
            _mzid.AnalysisProtocolCollection.SpectrumIdentificationProtocol[0].FragmentTolerance[0] = new mzIdentML110.Generated.CVParamType()
            {
                unitName = "dalton",
                value    = "0.01"
            };
            TextWriter writer = new StreamWriter("myIdentifications.mzid");

            _indexedSerializer.Serialize(writer, _mzid);
            writer.Close();

            var identifications = new MzidIdentifications("myIdentifications.mzid");

            Assert.AreEqual(1134.26091302033, identifications.CalculatedMassToCharge(0, 0));
            Assert.AreEqual(3, identifications.ChargeState(0, 0));
            Assert.AreEqual(1, identifications.Count);
            Assert.AreEqual(1134.26091302033 + 0.000001 * 1134.2609130203 + 0.000001, identifications.ExperimentalMassToCharge(0, 0), 1e-10);
            Assert.IsFalse(identifications.IsDecoy(0, 0));
            Assert.AreEqual("UNIMOD:4", identifications.ModificationAcession(0, 0, 0));
            Assert.AreEqual("UNIMOD", identifications.ModificationDictionary(0, 0, 0));
            Assert.AreEqual(17, identifications.ModificationLocation(0, 0, 0));
            Assert.AreEqual("spectrum 2", identifications.Ms2SpectrumID(0));
            Assert.AreEqual(1, identifications.NumModifications(0, 0));
            Assert.AreEqual("GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR", identifications.PeptideSequenceWithoutModifications(0, 0));
            Assert.AreEqual(0.1, identifications.ParentTolerance.Value);
            Assert.AreEqual(0.01, identifications.FragmentTolerance.Value);
            Assert.AreEqual(.05, identifications.QValue(0, 0));
            Assert.AreEqual("Protein name", identifications.ProteinFullName(0, 0));
            Assert.AreEqual("ACCESSION", identifications.ProteinAccession(0, 0));
            Assert.AreEqual(new float[3] {
                200, 300, 400
            }, identifications.MatchedIons(0, 0, 0));
            Assert.AreEqual(3, identifications.MatchedIonCounts(0, 0, 0));
            Assert.AreEqual("2", identifications.StartResidueInProtein(0, 0));
            Assert.AreEqual("34", identifications.EndResidueInProtein(0, 0));
            Assert.AreEqual(2, identifications.NumPSMsFromScan(0));
        }