/// <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="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="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 AnalysisSoftwareObj() { Id = null; Name = null; Customizations = null; Version = null; URI = null; _contactRole = null; _softwareName = null; }
/// <summary> /// Constructor /// </summary> public SearchDatabaseInfo() { Id = null; Name = null; Version = null; _releaseDate = DateTime.Now; ReleaseDateSpecified = false; _numDatabaseSequences = -1; NumDatabaseSequencesSpecified = false; _numResidues = -1; NumResiduesSpecified = false; ExternalFormatDocumentation = null; Location = null; _databaseName = null; _fileFormat = null; }
/// <summary> /// Constructor /// </summary> public SpectrumIdentificationProtocolObj() { Id = null; Name = null; _analysisSoftwareRef = null; _analysisSoftware = null; _searchType = null; _additionalSearchParams = null; ModificationParams = new IdentDataList <SearchModificationObj>(1); _enzymes = null; MassTables = new IdentDataList <MassTableObj>(1); FragmentTolerances = new IdentDataList <CVParamObj>(1); ParentTolerances = new IdentDataList <CVParamObj>(1); _threshold = null; DatabaseFilters = new IdentDataList <FilterInfo>(1); _databaseTranslation = null; }
/// <summary> /// Create an object using the contents of the corresponding MzIdentML object /// </summary> /// <param name="f"></param> /// <param name="idata"></param> public FilterInfo(FilterType f, IdentDataObj idata) : base(idata) { _filterType = null; _include = null; _exclude = null; if (f.FilterType1 != null) { _filterType = new ParamObj(f.FilterType1, IdentData); } if (f.Include != null) { _include = new ParamListObj(f.Include, IdentData); } if (f.Exclude != null) { _exclude = new ParamListObj(f.Exclude, IdentData); } }
/// <summary> /// Create an object using the contents of the corresponding MzIdentML object /// </summary> /// <param name="asi"></param> /// <param name="idata"></param> public AnalysisSoftwareObj(AnalysisSoftwareType asi, IdentDataObj idata) : base(idata) { Id = asi.id; Name = asi.name; Customizations = asi.Customizations; Version = asi.version; URI = asi.uri; _contactRole = null; _softwareName = null; if (asi.ContactRole != null) { _contactRole = new ContactRoleObj(asi.ContactRole, IdentData); } if (asi.SoftwareName != null) { _softwareName = new ParamObj(asi.SoftwareName, IdentData); } }
/// <summary> /// Constructor /// </summary> public FilterInfo() { _filterType = null; _include = null; _exclude = null; }