public void mzidTest()
{
XmlSerializer _indexedSerializer = new XmlSerializer(typeof(mzIdentML.Generated.MzIdentMLType));
var _mzid = new mzIdentML.Generated.MzIdentMLType();
_mzid.DataCollection = new mzIdentML.Generated.DataCollectionType();
_mzid.DataCollection.AnalysisData = new mzIdentML.Generated.AnalysisDataType();
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList = new mzIdentML.Generated.SpectrumIdentificationListType[1];
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0] = new mzIdentML.Generated.SpectrumIdentificationListType();
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult = new mzIdentML.Generated.SpectrumIdentificationResultType[1];
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0] = new mzIdentML.Generated.SpectrumIdentificationResultType();
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].spectrumID = "spectrum 2";
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem = new mzIdentML.Generated.SpectrumIdentificationItemType[1];
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0] = new mzIdentML.Generated.SpectrumIdentificationItemType();
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0].experimentalMassToCharge = 1134.2609130203 + 0.000001 * 1134.2609130203 + 0.000001;
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0].calculatedMassToCharge = 1134.26091302033;
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0].calculatedMassToChargeSpecified = true;
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0].chargeState = 3;
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0].cvParam = new mzIdentML.Generated.CVParamType[1];
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0].cvParam[0] = new mzIdentML.Generated.CVParamType();
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0].cvParam[0].value = 100.ToString();
_mzid.SequenceCollection = new mzIdentML.Generated.SequenceCollectionType();
_mzid.SequenceCollection.PeptideEvidence = new mzIdentML.Generated.PeptideEvidenceType[1];
_mzid.SequenceCollection.PeptideEvidence[0] = new mzIdentML.Generated.PeptideEvidenceType();
_mzid.SequenceCollection.PeptideEvidence[0].isDecoy = false;
_mzid.SequenceCollection.Peptide = new mzIdentML.Generated.PeptideType[1];
_mzid.SequenceCollection.Peptide[0] = new mzIdentML.Generated.PeptideType();
_mzid.SequenceCollection.Peptide[0].PeptideSequence = "GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR";
_mzid.SequenceCollection.Peptide[0].Modification = new mzIdentML.Generated.ModificationType[1];
_mzid.SequenceCollection.Peptide[0].Modification[0] = new mzIdentML.Generated.ModificationType();
_mzid.SequenceCollection.Peptide[0].Modification[0].locationSpecified = true;
_mzid.SequenceCollection.Peptide[0].Modification[0].location = 17;
_mzid.SequenceCollection.Peptide[0].Modification[0].monoisotopicMassDeltaSpecified = true;
_mzid.SequenceCollection.Peptide[0].Modification[0].monoisotopicMassDelta = 57.02146373;
_mzid.SequenceCollection.Peptide[0].Modification[0].cvParam = new mzIdentML.Generated.CVParamType[1];
_mzid.SequenceCollection.Peptide[0].Modification[0].cvParam[0] = new mzIdentML.Generated.CVParamType();
_mzid.SequenceCollection.Peptide[0].Modification[0].cvParam[0].accession = "UNIMOD:4";
_mzid.SequenceCollection.Peptide[0].Modification[0].cvParam[0].name = "Carbamidomethyl";
_mzid.SequenceCollection.Peptide[0].Modification[0].cvParam[0].cvRef = "UNIMOD";
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));
Assert.AreEqual(3, identifications.chargeState(0));
Assert.AreEqual(1, identifications.Count);
Assert.AreEqual(1134.26091302033 + 0.000001 * 1134.2609130203 + 0.000001, identifications.experimentalMassToCharge(0), 1e-10);
Assert.IsFalse(identifications.isDecoy(0));
Assert.AreEqual("UNIMOD:4", identifications.modificationAcession(0, 0));
Assert.AreEqual("UNIMOD", identifications.modificationDictionary(0, 0));
Assert.AreEqual(17, identifications.modificationLocation(0, 0));
Assert.AreEqual(2, identifications.ms2spectrumIndex(0));
Assert.AreEqual(1, identifications.NumModifications(0));
Assert.AreEqual("GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR", identifications.PeptideSequenceWithoutModifications(0));
}
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));
}
