/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="sil"></param>
/// <param name="idata"></param>
public SpectrumIdentificationListObj(SpectrumIdentificationListType sil, IdentDataObj idata)
: base(sil, idata)
{
Id = sil.id;
Name = sil.name;
_numSequencesSearched = sil.numSequencesSearched;
NumSequencesSearchedSpecified = sil.numSequencesSearchedSpecified;
_fragmentationTables = null;
_spectrumIdentificationResults = null;
if ((sil.FragmentationTable != null) && (sil.FragmentationTable.Count > 0))
{
FragmentationTables = new IdentDataList <MeasureObj>();
foreach (var f in sil.FragmentationTable)
{
FragmentationTables.Add(new MeasureObj(f, IdentData));
}
}
if ((sil.SpectrumIdentificationResult != null) && (sil.SpectrumIdentificationResult.Count > 0))
{
SpectrumIdentificationResults = new IdentDataList <SpectrumIdentificationResultObj>();
foreach (var sir in sil.SpectrumIdentificationResult)
{
SpectrumIdentificationResults.Add(new SpectrumIdentificationResultObj(sir, IdentData));
}
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="sd"></param>
/// <param name="idata"></param>
public SearchDatabaseInfo(SearchDatabaseType sd, IdentDataObj idata)
: base(sd, idata)
{
Id = sd.id;
Name = sd.name;
Version = sd.version;
_releaseDate = sd.releaseDate;
ReleaseDateSpecified = sd.releaseDateSpecified;
_numDatabaseSequences = sd.numDatabaseSequences;
NumDatabaseSequencesSpecified = sd.numDatabaseSequencesSpecified;
_numResidues = sd.numResidues;
NumResiduesSpecified = sd.numResiduesSpecified;
ExternalFormatDocumentation = sd.ExternalFormatDocumentation;
Location = sd.location;
_databaseName = null;
_fileFormat = null;
if (sd.DatabaseName != null)
{
_databaseName = new ParamObj(sd.DatabaseName, IdentData);
}
if (sd.FileFormat != null)
{
_fileFormat = new FileFormatInfo(sd.FileFormat, IdentData);
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="si"></param>
/// <param name="idata"></param>
public SpectrumIdentificationObj(SpectrumIdentificationType si, IdentDataObj idata)
: base(si, idata)
{
SpectrumIdentificationProtocolRef = si.spectrumIdentificationProtocol_ref;
SpectrumIdentificationListRef = si.spectrumIdentificationList_ref;
_inputSpectra = null;
_searchDatabases = null;
if ((si.InputSpectra != null) && (si.InputSpectra.Count > 0))
{
InputSpectra = new IdentDataList <InputSpectraRefObj>();
foreach (var ispec in si.InputSpectra)
{
InputSpectra.Add(new InputSpectraRefObj(ispec, IdentData));
}
}
if ((si.SearchDatabaseRef != null) && (si.SearchDatabaseRef.Count > 0))
{
SearchDatabases = new IdentDataList <SearchDatabaseRefObj>();
foreach (var sd in si.SearchDatabaseRef)
{
SearchDatabases.Add(new SearchDatabaseRefObj(sd, IdentData));
}
}
}
/// <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>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="sii"></param>
/// <param name="idata"></param>
public SpectrumIdentificationItemObj(SpectrumIdentificationItemType sii, IdentDataObj idata)
: base(sii, idata)
{
Id = sii.id;
Name = sii.name;
ChargeState = sii.chargeState;
ExperimentalMassToCharge = sii.experimentalMassToCharge;
_calculatedMassToCharge = sii.calculatedMassToCharge;
CalculatedMassToChargeSpecified = sii.calculatedMassToChargeSpecified;
_calculatedPI = sii.calculatedPI;
CalculatedPISpecified = sii.calculatedPISpecified;
PeptideRef = sii.peptide_ref;
Rank = sii.rank;
PassThreshold = sii.passThreshold;
MassTableRef = sii.massTable_ref;
SampleRef = sii.sample_ref;
PeptideEvidences = new IdentDataList <PeptideEvidenceRefObj>(1);
Fragmentations = new IdentDataList <IonTypeObj>(1);
if (sii.PeptideEvidenceRef?.Count > 0)
{
PeptideEvidences.AddRange(sii.PeptideEvidenceRef, pe => new PeptideEvidenceRefObj(pe, IdentData));
}
if (sii.Fragmentation?.Count > 0)
{
Fragmentations.AddRange(sii.Fragmentation, f => new IonTypeObj(f, IdentData));
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="s"></param>
/// <param name="idata"></param>
public SampleObj(SampleType s, IdentDataObj idata)
: base(s, idata)
{
Id = s.id;
Name = s.name;
_contactRoles = null;
_subSamples = null;
if ((s.ContactRole != null) && (s.ContactRole.Count > 0))
{
ContactRoles = new IdentDataList <ContactRoleObj>();
foreach (var cr in s.ContactRole)
{
ContactRoles.Add(new ContactRoleObj(cr, IdentData));
}
}
if ((s.SubSample != null) && (s.SubSample.Count > 0))
{
SubSamples = new IdentDataList <SubSampleObj>();
foreach (var ss in s.SubSample)
{
SubSamples.Add(new SubSampleObj(ss, IdentData));
}
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="it"></param>
/// <param name="idata"></param>
public IonTypeObj(IonTypeType it, IdentDataObj idata)
: base(idata)
{
Charge = it.charge;
FragmentArrays = new IdentDataList <FragmentArrayObj>(1);
CVParams = new IdentDataList <CVParamObj>(1);
UserParams = new IdentDataList <UserParamObj>(1);
Index = new List <string>();
if (it.FragmentArray?.Count > 0)
{
FragmentArrays.AddRange(it.FragmentArray, f => new FragmentArrayObj(f, IdentData));
}
if (it.cvParam?.Count > 0)
{
CVParams.AddRange(it.cvParam.Select(cvp => new CVParamObj(cvp, idata)));
}
if (it.userParam?.Count > 0)
{
UserParams.AddRange(it.userParam.Select(up => new UserParamObj(up, idata)));
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="i"></param>
/// <param name="idata"></param>
public InputsObj(InputsType i, IdentDataObj idata)
: base(idata)
{
_sourceFiles = null;
_searchDatabases = null;
_spectraDataList = null;
if ((i.SourceFile != null) && (i.SourceFile.Count > 0))
{
SourceFiles = new IdentDataList <SourceFileInfo>();
foreach (var sf in i.SourceFile)
{
SourceFiles.Add(new SourceFileInfo(sf, IdentData));
}
}
if ((i.SearchDatabase != null) && (i.SearchDatabase.Count > 0))
{
SearchDatabases = new IdentDataList <SearchDatabaseInfo>();
foreach (var sd in i.SearchDatabase)
{
SearchDatabases.Add(new SearchDatabaseInfo(sd, IdentData));
}
}
if ((i.SpectraData != null) && (i.SpectraData.Count > 0))
{
SpectraDataList = new IdentDataList <SpectraDataObj>();
foreach (var sd in i.SpectraData)
{
SpectraDataList.Add(new SpectraDataObj(sd, IdentData));
}
}
}
/// <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));
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="mt"></param>
/// <param name="idata"></param>
public MassTableObj(MassTableType mt, IdentDataObj idata)
: base(mt, idata)
{
Id = mt.id;
Name = mt.name;
_residues = null;
_ambiguousResidues = null;
MsLevels = null;
if ((mt.Residue != null) && (mt.Residue.Count > 0))
{
Residues = new IdentDataList <ResidueObj>();
foreach (var r in mt.Residue)
{
Residues.Add(new ResidueObj(r, IdentData));
}
}
if ((mt.AmbiguousResidue != null) && (mt.AmbiguousResidue.Count > 0))
{
AmbiguousResidues = new IdentDataList <AmbiguousResidueObj>();
foreach (var ar in mt.AmbiguousResidue)
{
AmbiguousResidues.Add(new AmbiguousResidueObj(ar, IdentData));
}
}
if (mt.msLevel != null)
{
MsLevels = new List <string>(mt.msLevel);
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="pa"></param>
/// <param name="idata"></param>
protected ProtocolApplicationObj(ProtocolApplicationType pa, IdentDataObj idata)
: base(idata)
{
Id = pa.id;
Name = pa.name;
_activityDate = pa.activityDate;
ActivityDateSpecified = pa.activityDateSpecified;
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="cv"></param>
/// <param name="idata"></param>
public CVInfo(cvType cv, IdentDataObj idata)
: base(idata)
{
FullName = cv.fullName;
Version = cv.version;
URI = cv.uri;
Id = cv.id;
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="cvpg"></param>
/// <param name="idata"></param>
public CVParamGroupObj(ICVParamGroup cvpg, IdentDataObj idata)
: base(idata)
{
CVParams = new IdentDataList <CVParamObj>(1);
if (cvpg.cvParam?.Count > 0)
{
CVParams.AddRange(cvpg.cvParam, cvp => new CVParamObj(cvp, IdentData));
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="p"></param>
/// <param name="idata"></param>
public PeptideObj(PeptideType p, IdentDataObj idata)
: base(p, idata)
{
Id = p.id;
Name = p.name;
PeptideSequence = p.PeptideSequence;
_modifications = null;
_substitutionModifications = null;
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="pg"></param>
/// <param name="idata"></param>
public ParamGroupObj(IParamGroup pg, IdentDataObj idata)
: base(pg, idata)
{
UserParams = new IdentDataList <UserParamObj>(1);
if (pg.userParam?.Count > 0)
{
UserParams.AddRange(pg.userParam, up => new UserParamObj(up, IdentData));
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="sidf"></param>
/// <param name="idata"></param>
public SpectrumIDFormatObj(SpectrumIDFormatType sidf, IdentDataObj idata)
: base(idata)
{
_cvParam = null;
if (sidf.cvParam != null)
{
_cvParam = new CVParamObj(sidf.cvParam, IdentData);
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="ff"></param>
/// <param name="idata"></param>
public FileFormatInfo(FileFormatType ff, IdentDataObj idata)
: base(idata)
{
_cvParam = null;
if (ff.cvParam != null)
{
_cvParam = new CVParamObj(ff.cvParam, IdentData);
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="r"></param>
/// <param name="idata"></param>
public RoleObj(RoleType r, IdentDataObj idata)
: base(idata)
{
_cvParam = null;
if (r.cvParam != null)
{
_cvParam = new CVParamObj(r.cvParam, IdentData);
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="o"></param>
/// <param name="idata"></param>
public OrganizationObj(OrganizationType o, IdentDataObj idata)
: base(o, idata)
{
_parent = null;
if (o.Parent != null)
{
_parent = new ParentOrganizationObj(o.Parent, IdentData);
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="fa"></param>
/// <param name="idata"></param>
public FragmentArrayObj(FragmentArrayType fa, IdentDataObj idata)
: base(idata)
{
MeasureRef = fa.measure_ref;
Values = null;
if (fa.values != null)
{
Values = new List <float>(fa.values);
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="dbs"></param>
/// <param name="idata"></param>
public DbSequenceObj(DBSequenceType dbs, IdentDataObj idata)
: base(dbs, idata)
{
Id = dbs.id;
Name = dbs.name;
Seq = dbs.Seq;
_length = dbs.length;
LengthSpecified = dbs.lengthSpecified;
SearchDatabaseRef = dbs.searchDatabase_ref;
Accession = dbs.accession;
}
/*public ParamBase(AbstractParamType ap, IdentData idata)
* : base(idata)
* {
* this._unitsSet = false;
* this.UnitCvRef = ap.unitCvRef;
* //this._unitAccession = ap.unitAccession;
* this.UnitAccession = ap.unitAccession;
* //this._unitName = ap.unitName;
*
* //this._unitCvid = CV.CV.CVID.CVID_Unknown;
* }*/
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="idata"></param>
protected ParamBaseObj(IdentDataObj idata)
: base(idata)
{
_unitsSet = false;
//this.UnitCvRef = ap.unitCvRef;
//this._unitAccession = ap.unitAccession;
//this.UnitAccession = ap.unitAccession;
//this._unitName = ap.unitName;
//this._unitCvid = CV.CV.CVID.CVID_Unknown;
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="up"></param>
/// <param name="idata"></param>
public UserParamObj(UserParamType up, IdentDataObj idata)
: base(idata)
{
_name = up.name;
_value = up.value;
Type = up.type;
UnitCvRef = up.unitCvRef;
//this._unitAccession = up.unitAccession;
UnitAccession = up.unitAccession;
//this._unitName = up.unitName;
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="sm"></param>
/// <param name="idata"></param>
public SubstitutionModificationObj(SubstitutionModificationType sm, IdentDataObj idata)
: base(idata)
{
OriginalResidue = sm.originalResidue;
ReplacementResidue = sm.replacementResidue;
_location = sm.location;
LocationSpecified = sm.locationSpecified;
_avgMassDelta = sm.avgMassDelta;
AvgMassDeltaSpecified = sm.avgMassDeltaSpecified;
_monoisotopicMassDelta = sm.monoisotopicMassDelta;
MonoisotopicMassDeltaSpecified = sm.monoisotopicMassDeltaSpecified;
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="cr"></param>
/// <param name="idata"></param>
public ContactRoleObj(ContactRoleType cr, IdentDataObj idata)
: base(idata)
{
ContactRef = cr.contact_ref;
_role = null;
if (cr.Role != null)
{
_role = new RoleObj(cr.Role, IdentData);
}
}
public void MzIdentMLReadTest(string path, int expectedSpecLists, int expectedSpecResults, int expectedSpecItems, int expectedPeptides, int expectedSeqs)
{
var sourceFile = new FileInfo(Path.Combine(TestPath.ExtTestDataDirectory, path));
if (!sourceFile.Exists)
{
Console.WriteLine("File not found: " + sourceFile.FullName);
return;
}
var identData = new IdentDataObj(MzIdentMlReaderWriter.Read(sourceFile.FullName));
var specResults = 0;
var specItems = 0;
foreach (var specList in identData.DataCollection.AnalysisData.SpectrumIdentificationList)
{
if (specList.SpectrumIdentificationResults == null)
{
continue;
}
specResults += specList.SpectrumIdentificationResults.Count;
foreach (var specResult in specList.SpectrumIdentificationResults)
{
specItems += specResult.SpectrumIdentificationItems.Count;
}
}
var observedPeptides = 0;
if (identData.SequenceCollection.Peptides != null)
{
observedPeptides = identData.SequenceCollection.Peptides.Count;
}
var observeProteins = 0;
if (identData.SequenceCollection.DBSequences != null)
{
observeProteins = identData.SequenceCollection.DBSequences.Count;
}
Console.WriteLine();
Console.WriteLine("Spectrum Identification Results: {0,6:N0}", specResults);
Console.WriteLine("Native IDs: {0,6:N0}", specItems);
Console.WriteLine("Unique Peptides: {0,6:N0}", observedPeptides);
Console.WriteLine("Unique Protein Sequences: {0,6:N0}", observeProteins);
Assert.AreEqual(expectedSpecResults, specResults, "Spectrum Identification Results");
Assert.AreEqual(expectedSpecItems, specItems, "Native IDs");
Assert.AreEqual(expectedPeptides, observedPeptides, "Unique Peptides");
Assert.AreEqual(expectedSeqs, observeProteins, "Unique Protein Sequences");
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="ph"></param>
/// <param name="idata"></param>
public PeptideHypothesisObj(PeptideHypothesisType ph, IdentDataObj idata)
: base(idata)
{
PeptideEvidenceRef = ph.peptideEvidence_ref;
SpectrumIdentificationItems = new IdentDataList <SpectrumIdentificationItemRefObj>(1);
if (ph.SpectrumIdentificationItemRef?.Count > 0)
{
SpectrumIdentificationItems.AddRange(ph.SpectrumIdentificationItemRef, spectrumIdItemRef => new SpectrumIdentificationItemRefObj(spectrumIdItemRef, IdentData));
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="pdl"></param>
/// <param name="idata"></param>
public ProteinDetectionListObj(ProteinDetectionListType pdl, IdentDataObj idata)
: base(pdl, idata)
{
Id = pdl.id;
Name = pdl.name;
ProteinAmbiguityGroups = new IdentDataList <ProteinAmbiguityGroupObj>(1);
if (pdl.ProteinAmbiguityGroup?.Count > 0)
{
ProteinAmbiguityGroups.AddRange(pdl.ProteinAmbiguityGroup, pag => new ProteinAmbiguityGroupObj(pag, IdentData));
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="pd"></param>
/// <param name="idata"></param>
public ProteinDetectionObj(ProteinDetectionType pd, IdentDataObj idata)
: base(pd, idata)
{
ProteinDetectionListRef = pd.proteinDetectionList_ref;
ProteinDetectionProtocolRef = pd.proteinDetectionProtocol_ref;
InputSpectrumIdentifications = new IdentDataList <InputSpectrumIdentificationsObj>(1);
if (pd.InputSpectrumIdentifications?.Count > 0)
{
InputSpectrumIdentifications.AddRange(pd.InputSpectrumIdentifications, isi => new InputSpectrumIdentificationsObj(isi, IdentData));
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="el"></param>
/// <param name="idata"></param>
public EnzymeListObj(EnzymesType el, IdentDataObj idata)
: base(idata)
{
_independent = el.independent;
IndependentSpecified = el.independentSpecified;
Enzymes = new IdentDataList <EnzymeObj>(1);
if (el.Enzyme?.Count > 0)
{
Enzymes.AddRange(el.Enzyme, e => new EnzymeObj(e, IdentData));
}
}
