public void Open()
{
if (File.Exists(FilePath))
{
_connection = MzIdentMLType.LoadFromFile(FilePath);
}
else
{
// Create a new file
_connection = new MzIdentMLType();
}
}
/// <summary>
/// Write the provided data to the file
/// </summary>
/// <param name="identData"></param>
/// <param name="filePath">Path to file to be written, with extension of .mzid[.gz]</param>
/// <param name="bufferSize">File stream buffer size</param>
public static void Write(MzIdentMLType identData, string filePath, int bufferSize = 65536)
{
var xRoot = new XmlRootAttribute()
{
ElementName = "MzIdentML",
Namespace = "http://psidev.info/psi/pi/mzIdentML/1.1",
IsNullable = false,
};
var serializer = new XmlSerializer(typeof(MzIdentMLType), xRoot);
using (var writer = CreateWriter(filePath, bufferSize))
{
serializer.Serialize(writer, identData);
}
}
/// <summary>
/// Write the provided data to the file
/// </summary>
/// <param name="identData"></param>
/// <param name="filePath">Path to file to be written, with extension of .mzid[.gz]</param>
/// <param name="bufferSize">File stream buffer size</param>
public static void Write(MzIdentMLType identData, string filePath, int bufferSize = 65536)
{
XmlSerializer serializer;
if (identData.version.StartsWith("1.2"))
{
var overrides = GetMzIdentMl12Overrides(out var ns, out var xsdUrl);
identData.xsiSchemaLocation = $"{ns} {xsdUrl}";
serializer = new XmlSerializer(typeof(MzIdentMLType), overrides);
}
else
{
serializer = new XmlSerializer(typeof(MzIdentMLType), "http://psidev.info/psi/pi/mzIdentML/1.1");
}
using (var writer = CreateWriter(filePath, bufferSize))
{
serializer.Serialize(writer, identData);
}
}
/// <summary>
/// Create an IdentDataObj directly from an MzIdentMLType object - fully cascades for the entire contents of
/// MzIdentMLType
/// </summary>
/// <param name="mzid"></param>
public IdentDataObj(MzIdentMLType mzid)
{
Id = mzid.id;
Name = mzid.name;
Version = mzid.version;
_creationDate = mzid.creationDate;
CreationDateSpecified = mzid.creationDateSpecified;
CvTranslator = new CVTranslator();
_cvList = null;
_analysisSoftwareList = null;
_provider = null;
_auditCollection = null;
_analysisSampleCollection = null;
_sequenceCollection = null;
_analysisCollection = null;
_analysisProtocolCollection = null;
_dataCollection = null;
_bibliographicReferences = null;
CVList = new IdentDataList <CVInfo>(1);
BibliographicReferences = new IdentDataList <BibliographicReferenceObj>(1);
AuditCollection = new IdentDataList <AbstractContactObj>(1);
AnalysisSampleCollection = new IdentDataList <SampleObj>(1);
AnalysisSoftwareList = new IdentDataList <AnalysisSoftwareObj>(1);
// Referenced by anything using CV/User params
if (mzid.cvList?.Count > 0)
{
CVList.AddRange(mzid.cvList, cv => new CVInfo(cv, this));
CvTranslator = new CVTranslator(_cvList);
}
// Referenced by nothing
if (mzid.BibliographicReference?.Count > 0)
{
BibliographicReferences.AddRange(mzid.BibliographicReference, br => new BibliographicReferenceObj(br, this));
}
// Referenced by anything using organization, person, contactRoleInfo - SampleInfo, ProviderInfo, AnalysisSoftwareInfo
if (mzid.AuditCollection?.Count > 0)
{
AuditCollection.AddRange(mzid.AuditCollection, ac =>
{
if (ac is PersonType p)
{
return(new PersonObj(p, this));
}
if (ac is OrganizationType o)
{
return(new OrganizationObj(o, this));
}
return(null);
});
}
// Referenced by anything using SampleInfo: SubSample, SpectrumIdentificationItem
if (mzid.AnalysisSampleCollection?.Count > 0)
{
AnalysisSampleCollection.AddRange(mzid.AnalysisSampleCollection, asc => new SampleObj(asc, this));
}
// Referenced by ProviderInfo, ProteinDetectionProtocol, SpectrumIdentificationProtocol, references AbstractContactInfo through ContactRoleInfo
if (mzid.AnalysisSoftwareList?.Count > 0)
{
AnalysisSoftwareList.AddRange(mzid.AnalysisSoftwareList, asl => new AnalysisSoftwareObj(asl, this));
}
// Referenced by nothing, references AnalysisSoftwareInfo
if (mzid.Provider != null)
{
_provider = new ProviderObj(mzid.Provider, this);
}
// Referenced by SpectrumIdentification, ProteinDetection, SpectrumIdentificationItem, PeptideEvidence, references AnalysisSoftwareInfo
if (mzid.AnalysisProtocolCollection != null)
{
_analysisProtocolCollection = new AnalysisProtocolCollectionObj(mzid.AnalysisProtocolCollection, this);
}
// InputsInfo referenced by DBSequence, SpectrumIdentification.SearchDatabaseRefInfo, SpectrumIdentificationResult, SpectrumIdentification.InputSpectraRef
if (mzid.DataCollection != null)
{
//this._dataCollection = new DataCollection(mzid.DataCollection, this);
_dataCollection = new DataCollectionObj {
Inputs = new InputsObj(mzid.DataCollection.Inputs, this)
};
}
// Referenced by SpectrumIdentificationItem, ProteinDetectionHypothesis, PeptideHypothesis
// References InputsInfo.DBSequence, AnalysisProtocolCollection.SoftwareIdentificationProtocol.DatabaseTranslation.TranslationTable
if (mzid.SequenceCollection != null)
{
_sequenceCollection = new SequenceCollectionObj(mzid.SequenceCollection, this);
}
// AnalysisData referenced by SpectrumIdentification, InputSpectrumIdentifications, ProteinDetection, references Peptides, PeptideEvidence, SampleInfo, MassTable,
if (mzid.DataCollection != null && _dataCollection != null)
{
_dataCollection.AnalysisData = new AnalysisDataObj(mzid.DataCollection.AnalysisData, this);
}
// References SpectrumIdentificationProtocol, SpectrumIdentificationList, SpectraData, SearchDatabaseInfo, ProteinDetectionList, ProteinDetectionProtocol
if (mzid.AnalysisCollection != null)
{
_analysisCollection = new AnalysisCollectionObj(mzid.AnalysisCollection, this);
}
// Reduce memory footprint by removing IdentDataList IdMaps that are created during the translation process
SequenceCollection?.DBSequences?.RemoveIdMap();
SequenceCollection?.PeptideEvidences?.RemoveIdMap();
SequenceCollection?.Peptides?.RemoveIdMap();
}
/// <summary>
/// Create an IdentDataObj directly from an MzIdentMLType object - fully cascades for the entire contents of
/// MzIdentMLType
/// </summary>
/// <param name="mzid"></param>
public IdentDataObj(MzIdentMLType mzid)
{
Id = mzid.id;
Name = mzid.name;
Version = mzid.version;
_creationDate = mzid.creationDate;
CreationDateSpecified = mzid.creationDateSpecified;
CvTranslator = new CVTranslator();
_cvList = null;
_analysisSoftwareList = null;
_provider = null;
_auditCollection = null;
_analysisSampleCollection = null;
_sequenceCollection = null;
_analysisCollection = null;
_analysisProtocolCollection = null;
_dataCollection = null;
_bibliographicReferences = null;
// Referenced by anything using CV/User params
if (mzid.cvList != null && mzid.cvList.Count > 0)
{
CVList = new IdentDataList <CVInfo>();
foreach (var cv in mzid.cvList)
{
CVList.Add(new CVInfo(cv, this));
}
CvTranslator = new CVTranslator(_cvList);
}
// Referenced by nothing
if (mzid.BibliographicReference != null && mzid.BibliographicReference.Count > 0)
{
BibliographicReferences = new IdentDataList <BibliographicReferenceObj>();
foreach (var br in mzid.BibliographicReference)
{
BibliographicReferences.Add(new BibliographicReferenceObj(br, this));
}
}
// Referenced by anything using organization, person, contactRoleInfo - SampleInfo, ProviderInfo, AnalysisSoftwareInfo
if (mzid.AuditCollection != null && mzid.AuditCollection.Count > 0)
{
AuditCollection = new IdentDataList <AbstractContactObj>();
foreach (var ac in mzid.AuditCollection)
{
if (ac is PersonType)
{
AuditCollection.Add(new PersonObj(ac as PersonType, this));
}
else if (ac is OrganizationType)
{
AuditCollection.Add(new OrganizationObj(ac as OrganizationType, this));
}
}
}
// Referenced by anything using SampleInfo: SubSample, SpectrumIdentificationItem
if (mzid.AnalysisSampleCollection != null && mzid.AnalysisSampleCollection.Count > 0)
{
AnalysisSampleCollection = new IdentDataList <SampleObj>();
foreach (var asc in mzid.AnalysisSampleCollection)
{
AnalysisSampleCollection.Add(new SampleObj(asc, this));
}
}
// Referenced by ProviderInfo, ProteinDetectionProtocol, SpectrumIdentificationProtocol, references AbstractContactInfo through ContactRoleInfo
if (mzid.AnalysisSoftwareList != null && mzid.AnalysisSoftwareList.Count > 0)
{
AnalysisSoftwareList = new IdentDataList <AnalysisSoftwareObj>();
foreach (var asl in mzid.AnalysisSoftwareList)
{
AnalysisSoftwareList.Add(new AnalysisSoftwareObj(asl, this));
}
}
// Referenced by nothing, references AnalysisSoftwareInfo
if (mzid.Provider != null)
{
_provider = new ProviderObj(mzid.Provider, this);
}
// Referenced by SpectrumIdentification, ProteinDetection, SpectrumIdentificationItem, PeptideEvidence, references AnalysisSoftwareInfo
if (mzid.AnalysisProtocolCollection != null)
{
_analysisProtocolCollection = new AnalysisProtocolCollectionObj(mzid.AnalysisProtocolCollection, this);
}
// InputsInfo referenced by DBSequence, SpectrumIdentification.SearchDatabaseRefInfo, SpectrumIdentificationResult, SpectrumIdentification.InputSpectraRef
if (mzid.DataCollection != null)
{
//this._dataCollection = new DataCollection(mzid.DataCollection, this);
_dataCollection = new DataCollectionObj {
Inputs = new InputsObj(mzid.DataCollection.Inputs, this)
};
}
// Referenced by SpectrumIdentificationItem, ProteinDetectionHypothesis, PeptideHypothesis
// References InputsInfo.DBSequence, AnalysisProtocolCollection.SoftwareIdentificationProtocol.DatabaseTranslation.TranslationTable
if (mzid.SequenceCollection != null)
{
_sequenceCollection = new SequenceCollectionObj(mzid.SequenceCollection, this);
}
// AnalysisData referenced by SpectrumIdentification, InputSpectrumIdentifications, ProteinDetection, references Peptides, PeptideEvidence, SampleInfo, MassTable,
if (mzid.DataCollection != null)
{
_dataCollection.AnalysisData = new AnalysisDataObj(mzid.DataCollection.AnalysisData, this);
}
// References SpectrumIdentificationProtocol, SpectrumIdentificationList, SpectraData, SeqrchDatabaseInfo, ProteinDetectionList, ProteinDetectionProtocol
if (mzid.AnalysisCollection != null)
{
_analysisCollection = new AnalysisCollectionObj(mzid.AnalysisCollection, this);
}
}
