private void RebuildSearchDatabaseList()
{
_searchDbIdCounter = 0;
_searchDatabases.Clear();
foreach (var dbSeq in IdentData.SequenceCollection.DBSequences)
{
if (_searchDatabases.Any(item => item.Equals(dbSeq.SearchDatabase)))
{
continue;
}
dbSeq.SearchDatabase.Id = "SearchDB_" + _searchDbIdCounter;
_searchDbIdCounter++;
_searchDatabases.Add(dbSeq.SearchDatabase);
}
foreach (var specId in IdentData.AnalysisCollection.SpectrumIdentifications)
{
foreach (var dbSeq in specId.SearchDatabases)
{
if (_searchDatabases.Any(item => item.Equals(dbSeq.SearchDatabase)))
{
continue;
}
dbSeq.SearchDatabase.Id = "SearchDB_" + _searchDbIdCounter;
_searchDbIdCounter++;
_searchDatabases.Add(dbSeq.SearchDatabase);
}
}
}
private void RebuildSpectraDataList()
{
_specDataIdCounter = 0;
_spectraDataList.Clear();
foreach (var sil in IdentData.DataCollection.AnalysisData.SpectrumIdentificationList)
{
foreach (var spectraData in sil.SpectrumIdentificationResults)
{
if (_spectraDataList.Any(item => item.Equals(spectraData.SpectraData)))
{
continue;
}
spectraData.SpectraData.Id = "SID_" + _specDataIdCounter;
_specDataIdCounter++;
_spectraDataList.Add(spectraData.SpectraData);
}
}
foreach (var specId in IdentData.AnalysisCollection.SpectrumIdentifications)
{
foreach (var spectraData in specId.InputSpectra)
{
if (_spectraDataList.Any(item => item.Equals(spectraData.SpectraData)))
{
continue;
}
spectraData.SpectraData.Id = "SID_" + _specDataIdCounter;
_specDataIdCounter++;
_spectraDataList.Add(spectraData.SpectraData);
}
}
}
private void RebuildPeptideList()
{
_pepIdCounter = 0;
_peptides.Clear();
foreach (var sil in IdentData.DataCollection.AnalysisData.SpectrumIdentificationList)
{
foreach (var sir in sil.SpectrumIdentificationResults)
{
foreach (var sii in sir.SpectrumIdentificationItems)
{
if (_peptides.Any(item => item.Equals(sii.Peptide)))
{
continue;
}
sii.Peptide.Id = "Pep_" + _pepIdCounter;
_pepIdCounter++;
_peptides.Add(sii.Peptide);
}
}
}
foreach (var pepEv in _peptideEvidences)
{
if (_peptides.Any(item => item.Equals(pepEv.Peptide)))
{
continue;
}
pepEv.Peptide.Id = "Pep_" + _pepIdCounter;
_pepIdCounter++;
_peptides.Add(pepEv.Peptide);
}
}
/// <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="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 = 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="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="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="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="sip"></param>
/// <param name="idata"></param>
public SpectrumIdentificationProtocolObj(SpectrumIdentificationProtocolType sip, IdentDataObj idata)
: base(idata)
{
Id = sip.id;
Name = sip.name;
AnalysisSoftwareRef = sip.analysisSoftware_ref;
_searchType = null;
_additionalSearchParams = null;
_modificationParams = null;
_enzymes = null;
_massTables = null;
_fragmentTolerances = null;
_parentTolerances = null;
_threshold = null;
_databaseFilters = null;
_databaseTranslation = null;
if (sip.SearchType != null)
_searchType = new ParamObj(sip.SearchType, IdentData);
if (sip.AdditionalSearchParams != null)
_additionalSearchParams = new ParamListObj(sip.AdditionalSearchParams, IdentData);
if ((sip.ModificationParams != null) && (sip.ModificationParams.Count > 0))
{
ModificationParams = new IdentDataList<SearchModificationObj>();
foreach (var mp in sip.ModificationParams)
ModificationParams.Add(new SearchModificationObj(mp, IdentData));
}
if (sip.Enzymes != null)
_enzymes = new EnzymeListObj(sip.Enzymes, IdentData);
if ((sip.MassTable != null) && (sip.MassTable.Count > 0))
{
MassTables = new IdentDataList<MassTableObj>();
foreach (var mt in sip.MassTable)
MassTables.Add(new MassTableObj(mt, IdentData));
}
if ((sip.FragmentTolerance != null) && (sip.FragmentTolerance.Count > 0))
{
FragmentTolerances = new IdentDataList<CVParamObj>();
foreach (var ft in sip.FragmentTolerance)
FragmentTolerances.Add(new CVParamObj(ft, IdentData));
}
if (sip.ParentTolerance != null)
{
ParentTolerances = new IdentDataList<CVParamObj>();
foreach (var pt in sip.ParentTolerance)
ParentTolerances.Add(new CVParamObj(pt, IdentData));
}
if (sip.Threshold != null)
_threshold = new ParamListObj(sip.Threshold, IdentData);
if ((sip.DatabaseFilters != null) && (sip.DatabaseFilters.Count > 0))
{
DatabaseFilters = new IdentDataList<FilterInfo>();
foreach (var df in sip.DatabaseFilters)
DatabaseFilters.Add(new FilterInfo(df, IdentData));
}
if (sip.DatabaseTranslation != null)
_databaseTranslation = new DatabaseTranslationObj(sip.DatabaseTranslation, IdentData);
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="pl"></param>
/// <param name="idata"></param>
public ParamListObj(ParamListType pl, IdentDataObj idata)
: base(idata)
{
_items = null;
if (pl != null && pl.Items.Count > 0)
{
Items = new IdentDataList <ParamBaseObj>();
foreach (var p in pl.Items)
{
if (p is CVParamType)
{
Items.Add(new CVParamObj(p as CVParamType, IdentData));
}
else if (p is UserParamType)
{
Items.Add(new UserParamObj(p as UserParamType, IdentData));
}
}
}
}
/// <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 = null;
if (pg.userParam != null && pg.userParam.Count > 0)
{
UserParams = new IdentDataList <UserParamObj>();
foreach (var up in pg.userParam)
{
UserParams.Add(new UserParamObj(up, IdentData));
}
}
}
/// <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 = null;
if (cvpg.cvParam != null && cvpg.cvParam.Count > 0)
{
CVParams = new IdentDataList <CVParamObj>();
foreach (var cvp in cvpg.cvParam)
{
CVParams.Add(new CVParamObj(cvp, IdentData));
}
}
}
/// <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 = null;
if (ph.SpectrumIdentificationItemRef != null && ph.SpectrumIdentificationItemRef.Count > 0)
{
SpectrumIdentificationItems = new IdentDataList <SpectrumIdentificationItemRefObj>();
foreach (var siir in ph.SpectrumIdentificationItemRef)
{
SpectrumIdentificationItems.Add(new SpectrumIdentificationItemRefObj(siir, 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 = null;
if ((pdl.ProteinAmbiguityGroup != null) && (pdl.ProteinAmbiguityGroup.Count > 0))
{
ProteinAmbiguityGroups = new IdentDataList <ProteinAmbiguityGroupObj>();
foreach (var pag in pdl.ProteinAmbiguityGroup)
{
ProteinAmbiguityGroups.Add(new ProteinAmbiguityGroupObj(pag, 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 = null;
if ((el.Enzyme != null) && (el.Enzyme.Count > 0))
{
Enzymes = new IdentDataList <EnzymeObj>();
foreach (var e in el.Enzyme)
{
Enzymes.Add(new EnzymeObj(e, 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 = null;
if ((pd.InputSpectrumIdentifications != null) && (pd.InputSpectrumIdentifications.Count > 0))
{
InputSpectrumIdentifications = new IdentDataList <InputSpectrumIdentificationsObj>();
foreach (var isi in pd.InputSpectrumIdentifications)
{
InputSpectrumIdentifications.Add(new InputSpectrumIdentificationsObj(isi, IdentData));
}
}
}
internal void RebuildSIPList()
{
_idCounter = 0;
_spectrumIdentificationProtocols.Clear();
foreach (var specId in IdentData.AnalysisCollection.SpectrumIdentifications)
{
if (_spectrumIdentificationProtocols.Any(item => item.Equals(specId.SpectrumIdentificationProtocol)))
{
continue;
}
specId.SpectrumIdentificationProtocol.Id = "SpecIdentProtocol_" + _idCounter;
_idCounter++;
_spectrumIdentificationProtocols.Add(specId.SpectrumIdentificationProtocol);
}
}
private void RebuildDbSequenceList()
{
_dBSeqIdCounter = 0;
_dBSequences.Clear();
foreach (var pepEv in _peptideEvidences)
{
if (_dBSequences.Any(item => item.Equals(pepEv.DBSequence)))
{
continue;
}
pepEv.DBSequence.Id = "DBSeq_" + _dBSeqIdCounter;
_dBSeqIdCounter++;
_dBSequences.Add(pepEv.DBSequence);
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="pag"></param>
/// <param name="idata"></param>
public ProteinAmbiguityGroupObj(ProteinAmbiguityGroupType pag, IdentDataObj idata)
: base(pag, idata)
{
Id = pag.id;
Name = pag.name;
_proteinDetectionHypotheses = null;
if ((pag.ProteinDetectionHypothesis != null) && (pag.ProteinDetectionHypothesis.Count > 0))
{
ProteinDetectionHypotheses = new IdentDataList <ProteinDetectionHypothesisObj>();
foreach (var pdh in pag.ProteinDetectionHypothesis)
{
ProteinDetectionHypotheses.Add(new ProteinDetectionHypothesisObj(pdh, 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 = null;
_cvParam = null;
Index = null;
if (it.FragmentArray != null && it.FragmentArray.Count > 0)
{
FragmentArrays = new IdentDataList <FragmentArrayObj>();
foreach (var f in it.FragmentArray)
{
FragmentArrays.Add(new FragmentArrayObj(f, IdentData));
}
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="sm"></param>
/// <param name="idata"></param>
public SearchModificationObj(SearchModificationType sm, IdentDataObj idata)
: base(sm, idata)
{
FixedMod = sm.fixedMod;
MassDelta = sm.massDelta;
Residues = sm.residues;
_specificityRules = null;
if ((sm.SpecificityRules != null) && (sm.SpecificityRules.Count > 0))
{
SpecificityRules = new IdentDataList <SpecificityRulesListObj>();
foreach (var sr in sm.SpecificityRules)
{
SpecificityRules.Add(new SpecificityRulesListObj(sr, IdentData));
}
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="p"></param>
/// <param name="idata"></param>
public PersonObj(PersonType p, IdentDataObj idata)
: base(p, idata)
{
LastName = p.lastName;
FirstName = p.firstName;
MidInitials = p.midInitials;
_affiliations = null;
if ((p.Affiliation != null) && (p.Affiliation.Count > 0))
{
Affiliations = new IdentDataList <AffiliationObj>();
foreach (var a in p.Affiliation)
{
Affiliations.Add(new AffiliationObj(a, IdentData));
}
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="sir"></param>
/// <param name="idata"></param>
public SpectrumIdentificationResultObj(SpectrumIdentificationResultType sir, IdentDataObj idata)
: base(sir, idata)
{
Id = sir.id;
Name = sir.name;
SpectrumID = sir.spectrumID;
SpectraDataRef = sir.spectraData_ref;
_spectrumIdentificationItems = null;
if ((sir.SpectrumIdentificationItem != null) && (sir.SpectrumIdentificationItem.Count > 0))
{
SpectrumIdentificationItems = new IdentDataList <SpectrumIdentificationItemObj>();
foreach (var sii in sir.SpectrumIdentificationItem)
{
SpectrumIdentificationItems.Add(new SpectrumIdentificationItemObj(sii, IdentData));
}
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="dt"></param>
/// <param name="idata"></param>
public DatabaseTranslationObj(DatabaseTranslationType dt, IdentDataObj idata)
: base(idata)
{
_translationTables = null;
Frames = null;
if ((dt.TranslationTable != null) && (dt.TranslationTable.Count > 0))
{
TranslationTables = new IdentDataList <TranslationTableObj>();
foreach (var t in dt.TranslationTable)
{
TranslationTables.Add(new TranslationTableObj(t, IdentData));
}
}
if (dt.frames != null)
{
Frames = new List <int>(dt.frames);
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="ad"></param>
/// <param name="idata"></param>
public AnalysisDataObj(AnalysisDataType ad, IdentDataObj idata)
: base(idata)
{
_spectrumIdentificationList = null;
_proteinDetectionList = null;
if (ad.SpectrumIdentificationList != null && ad.SpectrumIdentificationList.Count > 0)
{
SpectrumIdentificationList = new IdentDataList <SpectrumIdentificationListObj>();
foreach (var sil in ad.SpectrumIdentificationList)
{
SpectrumIdentificationList.Add(new SpectrumIdentificationListObj(sil, IdentData));
}
}
if (ad.ProteinDetectionList != null)
{
_proteinDetectionList = new ProteinDetectionListObj(ad.ProteinDetectionList, IdentData);
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="ac"></param>
/// <param name="idata"></param>
public AnalysisCollectionObj(AnalysisCollectionType ac, IdentDataObj idata)
: base(idata)
{
_spectrumIdentifications = null;
_proteinDetection = null;
idata.AnalysisCollection = this;
if (ac.SpectrumIdentification != null && ac.SpectrumIdentification.Count > 0)
{
SpectrumIdentifications = new IdentDataList <SpectrumIdentificationObj>();
foreach (var si in ac.SpectrumIdentification)
{
SpectrumIdentifications.Add(new SpectrumIdentificationObj(si, IdentData));
}
}
if (ac.ProteinDetection != null)
{
ProteinDetection = new ProteinDetectionObj(ac.ProteinDetection, IdentData);
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="apc"></param>
/// <param name="idata"></param>
public AnalysisProtocolCollectionObj(AnalysisProtocolCollectionType apc, IdentDataObj idata)
: base(idata)
{
_spectrumIdentificationProtocols = null;
_proteinDetectionProtocol = null;
idata.AnalysisProtocolCollection = this;
if (apc.SpectrumIdentificationProtocol != null && apc.SpectrumIdentificationProtocol.Count > 0)
{
SpectrumIdentificationProtocols = new IdentDataList <SpectrumIdentificationProtocolObj>();
foreach (var sip in apc.SpectrumIdentificationProtocol)
{
SpectrumIdentificationProtocols.Add(new SpectrumIdentificationProtocolObj(sip, IdentData));
}
}
if (apc.ProteinDetectionProtocol != null)
{
_proteinDetectionProtocol = new ProteinDetectionProtocolObj(apc.ProteinDetectionProtocol, 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 = null;
_fragmentations = null;
if ((sii.PeptideEvidenceRef != null) && (sii.PeptideEvidenceRef.Count > 0))
{
PeptideEvidences = new IdentDataList <PeptideEvidenceRefObj>();
foreach (var pe in sii.PeptideEvidenceRef)
{
PeptideEvidences.Add(new PeptideEvidenceRefObj(pe, IdentData));
}
}
if ((sii.Fragmentation != null) && (sii.Fragmentation.Count > 0))
{
Fragmentations = new IdentDataList <IonTypeObj>();
foreach (var f in sii.Fragmentation)
{
Fragmentations.Add(new IonTypeObj(f, IdentData));
}
}
}