/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="sc"></param>
/// <param name="idata"></param>
public SequenceCollectionObj(SequenceCollectionType sc, IdentDataObj idata)
: base(idata)
{
_dBSequences = null;
_peptides = null;
_peptideEvidences = null;
idata.SequenceCollection = this;
if ((sc.DBSequence != null) && (sc.DBSequence.Count > 0))
{
DBSequences = new IdentDataList <DbSequenceObj>();
foreach (var dbs in sc.DBSequence)
{
DBSequences.Add(new DbSequenceObj(dbs, IdentData));
}
}
if ((sc.Peptide != null) && (sc.Peptide.Count > 0))
{
Peptides = new IdentDataList <PeptideObj>();
foreach (var p in sc.Peptide)
{
Peptides.Add(new PeptideObj(p, IdentData));
}
}
if ((sc.PeptideEvidence != null) && (sc.PeptideEvidence.Count > 0))
{
PeptideEvidences = new IdentDataList <PeptideEvidenceObj>();
foreach (var pe in sc.PeptideEvidence)
{
PeptideEvidences.Add(new PeptideEvidenceObj(pe, IdentData));
}
}
}
/// <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>
/// 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>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="sc"></param>
/// <param name="idata"></param>
public SequenceCollectionObj(SequenceCollectionType sc, IdentDataObj idata)
: base(idata)
{
DBSequences = new IdentDataList <DbSequenceObj>(1);
Peptides = new IdentDataList <PeptideObj>(1);
PeptideEvidences = new IdentDataList <PeptideEvidenceObj>(1);
idata.SequenceCollection = this;
if (sc.DBSequence?.Count > 0)
{
DBSequences.AddIdMap();
DBSequences.AddRange(sc.DBSequence, dbs => new DbSequenceObj(dbs, IdentData));
}
if (sc.Peptide?.Count > 0)
{
Peptides.AddIdMap();
Peptides.AddRange(sc.Peptide, p => new PeptideObj(p, IdentData));
}
if (sc.PeptideEvidence?.Count > 0)
{
PeptideEvidences.AddIdMap();
PeptideEvidences.AddRange(sc.PeptideEvidence, pe => new PeptideEvidenceObj(pe, IdentData));
}
}
