/// <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="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>
/// Object equality
/// </summary>
/// <param name="other"></param>
/// <returns></returns>
public bool Equals(IdentDataList <T> other)
{
if (this.Count == 0 && (other == null || other.Count == 0))
{
return(true);
}
if (other == null || other.Count == 0)
{
return(false);
}
if (this.Count != other.Count)
{
return(false);
}
foreach (var item in this)
{
var found = false;
foreach (var item2 in other)
{
if (item.Equals(item2))
{
found = true;
break;
}
}
if (!found)
{
return(false);
}
}
return(true);
}
/// <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="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="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>
/// Constructor
/// </summary>
public EnzymeListObj()
{
_independent = false;
IndependentSpecified = false;
Enzymes = new IdentDataList <EnzymeObj>(1);
}
/// <summary>
/// Constructor
/// </summary>
public ProteinDetectionListObj()
{
Id = null;
Name = null;
ProteinAmbiguityGroups = new IdentDataList <ProteinAmbiguityGroupObj>(1);
}
/// <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="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>
/// Constructor
/// </summary>
public PeptideHypothesisObj()
{
_peptideEvidenceRef = null;
_peptideEvidence = null;
SpectrumIdentificationItems = new IdentDataList <SpectrumIdentificationItemRefObj>();
}
/// <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;
_enzymes = null;
_threshold = null;
_databaseTranslation = null;
ModificationParams = new IdentDataList <SearchModificationObj>(1);
MassTables = new IdentDataList <MassTableObj>(1);
FragmentTolerances = new IdentDataList <CVParamObj>(1);
ParentTolerances = new IdentDataList <CVParamObj>(1);
DatabaseFilters = new IdentDataList <FilterInfo>(1);
if (sip.SearchType != null)
{
_searchType = new ParamObj(sip.SearchType, IdentData);
}
if (sip.AdditionalSearchParams != null)
{
_additionalSearchParams = new ParamListObj(sip.AdditionalSearchParams, IdentData);
}
if (sip.ModificationParams?.Count > 0)
{
ModificationParams.AddRange(sip.ModificationParams, mp => new SearchModificationObj(mp, IdentData));
}
if (sip.Enzymes != null)
{
_enzymes = new EnzymeListObj(sip.Enzymes, IdentData);
}
if (sip.MassTable?.Count > 0)
{
MassTables.AddRange(sip.MassTable, mt => new MassTableObj(mt, IdentData));
}
if (sip.FragmentTolerance?.Count > 0)
{
FragmentTolerances.AddRange(sip.FragmentTolerance, ft => new CVParamObj(ft, IdentData));
}
if (sip.ParentTolerance?.Count > 0)
{
ParentTolerances.AddRange(sip.ParentTolerance, pt => new CVParamObj(pt, IdentData));
}
if (sip.Threshold != null)
{
_threshold = new ParamListObj(sip.Threshold, IdentData);
}
if (sip.DatabaseFilters?.Count > 0)
{
DatabaseFilters.AddRange(sip.DatabaseFilters, df => 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="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>
/// Constructor
/// </summary>
public ProteinAmbiguityGroupObj()
{
Id = null;
Name = null;
ProteinDetectionHypotheses = new IdentDataList <ProteinDetectionHypothesisObj>();
}
/// <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="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>
/// Constructor
/// </summary>
public IonTypeObj()
{
Charge = 0;
FragmentArrays = new IdentDataList <FragmentArrayObj>();
_cvParam = null;
Index = new List <string>();
}
/// <summary>
/// Constructor
/// </summary>
public PersonObj()
{
LastName = null;
FirstName = null;
MidInitials = null;
Affiliations = new IdentDataList <AffiliationObj>();
}
/// <summary>
/// Constructor
/// </summary>
public SearchModificationObj()
{
FixedMod = false;
MassDelta = 0;
Residues = null;
SpecificityRules = new IdentDataList<SpecificityRulesListObj>(1);
}
/// <summary>
/// Constructor
/// </summary>
public SampleObj()
{
Id = null;
Name = null;
ContactRoles = new IdentDataList <ContactRoleObj>();
SubSamples = new IdentDataList <SubSampleObj>();
}
/// <summary>
/// Constructor
/// </summary>
public MassTableObj()
{
Id = null;
Name = null;
Residues = new IdentDataList <ResidueObj>();
AmbiguousResidues = new IdentDataList <AmbiguousResidueObj>();
MsLevels = new List <string>();
}
/// <summary>
/// Constructor
/// </summary>
public IonTypeObj()
{
Charge = 0;
FragmentArrays = new IdentDataList <FragmentArrayObj>(1);
CVParams = new IdentDataList <CVParamObj>(1);
UserParams = new IdentDataList <UserParamObj>(1);
Index = new List <string>();
}
/// <summary>
/// Constructor
/// </summary>
public ProteinDetectionObj()
{
_proteinDetectionListRef = null;
_proteinDetectionProtocolRef = null;
_proteinDetectionList = null;
_proteinDetectionProtocol = null;
InputSpectrumIdentifications = new IdentDataList <InputSpectrumIdentificationsObj>(1);
}
/// <summary>
/// Constructor
/// </summary>
public PeptideObj()
{
Id = null;
Name = null;
PeptideSequence = null;
Modifications = new IdentDataList <ModificationObj>(1);
SubstitutionModifications = new IdentDataList <SubstitutionModificationObj>(1);
}
/// <summary>
/// Constructor
/// </summary>
public SpectrumIdentificationObj()
{
_spectrumIdentificationProtocolRef = null;
_spectrumIdentificationListRef = null;
_spectrumIdentificationProtocol = null;
_spectrumIdentificationList = null;
InputSpectra = new IdentDataList <InputSpectraRefObj>();
SearchDatabases = new IdentDataList <SearchDatabaseRefObj>();
}
/// <summary>
/// Constructor
/// </summary>
public SpectrumIdentificationResultObj()
{
Id = null;
Name = null;
SpectrumID = null;
_spectraDataRef = null;
_spectraData = null;
SpectrumIdentificationItems = new IdentDataList <SpectrumIdentificationItemObj>();
}
/// <summary>
/// Constructor
/// </summary>
public SpectrumIdentificationListObj()
{
Id = null;
Name = null;
_numSequencesSearched = -1;
NumSequencesSearchedSpecified = false;
FragmentationTables = new IdentDataList <MeasureObj>(1);
SpectrumIdentificationResults = new IdentDataList <SpectrumIdentificationResultObj>(1);
}
/// <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="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));
}
}
