/// <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)); } }