/// <summary>
/// Writes current data to a mzid file
/// </summary>
/// <param name="xml">
/// A <see cref="System.String"/> with the output file name
/// </param>
public void Save(string xml)
{
Data.creationDate = DateTime.UtcNow;
// CommonOntology
Data.cvList = ListOntology.ToArray();
// AnalysisSoftwareList
Data.AnalysisSoftwareList = ListSW.ToArray();
// Provider
Data.Provider = Provider;
// AuditCollection
Data.AuditCollection = new FuGECollectionAuditCollectionType();
Data.AuditCollection.Person = ListPeople.ToArray();
Data.AuditCollection.Organization = ListOrganizations.ToArray();
// SequenceCollection
SequenceCollectionType seq = new SequenceCollectionType();
seq.DBSequence = ListProteins.ToArray();
seq.Peptide = ListPeptides.ToArray();
Data.SequenceCollection = seq;
// Serialization
XmlSerializer serializer = new XmlSerializer(typeof(PSIPIMainmzIdentMLType));
TextWriter writer = new StreamWriter(xml);
serializer.Serialize(writer, Data);
writer.Close();
System.GC.Collect();
}
/// <summary>
/// Writes current data to a mzid file
/// </summary>
/// <param name="xml">
/// A <see cref="System.String"/> with the output file name
/// </param>
public void Save(string xml)
{
Data.creationDate = DateTime.UtcNow;
// AnalysisSoftwareList
Data.AnalysisSoftwareList = ListSW.ToArray();
// AuditCollection
List <AbstractContactType> audit = new List <AbstractContactType>();
audit.AddRange(ListOrganizations);
audit.AddRange(ListPeople);
Data.AuditCollection = audit.ToArray();
// SequenceCollection
SequenceCollectionType seq = new SequenceCollectionType();
seq.DBSequence = ListProteins.ToArray();
seq.Peptide = ListPeptides.ToArray();
seq.PeptideEvidence = ListEvidences.ToArray();
Data.SequenceCollection = seq;
// Serialization
XmlSerializer serializer = new XmlSerializer(typeof(MzIdentMLType));
TextWriter writer = new StreamWriter(xml);
serializer.Serialize(writer, Data);
writer.Close();
//Data.SaveToFile( xml );
System.GC.Collect();
}
/// <summary>
/// Helper method for including an additional analysis software to the list
/// </summary>
public void AddAnalysisSoftware(
string id, string name, string version, string uri, string cv, string accession, string customizations)
{
AnalysisSoftwareType sw = new AnalysisSoftwareType();
sw.id = id;
sw.name = name;
sw.version = version;
sw.uri = uri;
if (cv != null && accession != null)
{
CVParamType p = new CVParamType();
p.cvRef = cv;
p.accession = accession;
p.name = name;
sw.SoftwareName.Item = p;
}
if (customizations != null)
{
sw.Customizations = customizations;
}
ListSW.Add(sw);
}
