public override void ReadXml(XmlReader reader) { // Read tag attributes base.ReadXml(reader); string aas = reader.GetAttribute(ATTR.aminoacid); if (!string.IsNullOrEmpty(aas)) { AAs = aas; // Support v0.1 format. if (AAs[0] == '\0') // Not L10N AAs = null; } Terminus = reader.GetAttribute(ATTR.terminus, ToModTerminus); IsVariable = IsExplicit = reader.GetBoolAttribute(ATTR.variable); Formula = reader.GetAttribute(ATTR.formula); if (reader.GetBoolAttribute(ATTR.label_13C)) LabelAtoms |= LabelAtoms.C13; if (reader.GetBoolAttribute(ATTR.label_15N)) LabelAtoms |= LabelAtoms.N15; if (reader.GetBoolAttribute(ATTR.label_18O)) LabelAtoms |= LabelAtoms.O18; if (reader.GetBoolAttribute(ATTR.label_2H)) LabelAtoms |= LabelAtoms.H2; RelativeRT = reader.GetEnumAttribute(ATTR.relative_rt, RelativeRT.Matching); // Allow specific masses always, but they will generate an error, // in Validate() if there is already a formula. MonoisotopicMass = reader.GetNullableDoubleAttribute(ATTR.massdiff_monoisotopic); AverageMass = reader.GetNullableDoubleAttribute(ATTR.massdiff_average); if (!IsVariable) IsExplicit = reader.GetBoolAttribute(ATTR.explicit_decl); UnimodId = reader.GetNullableIntAttribute(ATTR.unimod_id); // Backward compatibility with early code that assigned -1 to some custom modifications if (UnimodId.HasValue && UnimodId.Value == -1) UnimodId = null; ShortName = reader.GetAttribute(ATTR.short_name); // Consume tag reader.Read(); var listLosses = new List<FragmentLoss>(); reader.ReadElements(listLosses); if (listLosses.Count > 0) { Losses = listLosses.ToArray(); reader.ReadEndElement(); } Validate(); }
public override void ReadXml(XmlReader reader) { // Read tag attributes base.ReadXml(reader); Fragment = reader.GetAttribute(ATTR.cut); if (IsFragment) { Restrict = reader.GetAttribute(ATTR.no_cut); Terminus = reader.GetAttribute(ATTR.sense, ToSeqTerminus); MinFragmentLength = reader.GetNullableIntAttribute(ATTR.min_length) ?? DEFAULT_MIN_FRAGMENT_LENGTH; } else { var charges = TextUtil.ParseInts(reader.GetAttribute(ATTR.charges)); // Old version? if (charges.Count() > 1) throw new InvalidDataException(Resources.MeasuredIon_ReadXml_Multiple_charge_states_for_custom_ions_are_no_longer_supported_); SettingsCustomIon = SettingsCustomIon.Deserialize(reader); if (charges.Any()) // Old style - fix it up a little for our revised ideas about custom ion ionization { Charge = charges[0]; if (string.IsNullOrEmpty(SettingsCustomIon.Formula)) // Adjust the user-supplied masses { SettingsCustomIon = new SettingsCustomIon(SettingsCustomIon.Formula, Math.Round(SettingsCustomIon.MonoisotopicMass + BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.H), SequenceMassCalc.MassPrecision), // Assume user provided neutral mass. Round new value easiest XML roundtripping. Math.Round(SettingsCustomIon.AverageMass + BioMassCalc.AVERAGE.GetMass(BioMassCalc.H), SequenceMassCalc.MassPrecision), // Assume user provided neutral mass. Round new value easiest XML roundtripping. SettingsCustomIon.Name); } } else { Charge = reader.GetIntAttribute(ATTR.charge); } IsOptional = reader.GetBoolAttribute(ATTR.optional); } // Consume tag reader.Read(); Validate(); }
public void ReadXml(XmlReader reader) { Pick = reader.GetEnumAttribute(ATTR.pick, PeptidePick.library); PeptideCount = reader.GetNullableIntAttribute(ATTR.peptide_count); HasDocumentLibrary = reader.GetBoolAttribute(ATTR.document_library); _rankIdName = reader.GetAttribute(ATTR.rank_type); var list = new List<XmlNamedElement>(); // Consume tag if (reader.IsEmptyElement) reader.Read(); else { reader.ReadStartElement(); // Read child elements IXmlElementHelper<Library> helperLib; IXmlElementHelper<LibrarySpec> helperSpec = null; while ((helperLib = reader.FindHelper(LIBRARY_HELPERS)) != null || (helperSpec = reader.FindHelper(LIBRARY_SPEC_HELPERS)) != null) { if (helperLib != null) list.Add(helperLib.Deserialize(reader)); else list.Add(helperSpec.Deserialize(reader)); } reader.ReadEndElement(); } var libraries = new Library[list.Count]; var librarySpecs = new LibrarySpec[list.Count]; for (int i = 0; i < list.Count; i++) { var library = list[i] as Library; if (library != null) libraries[i] = library; else librarySpecs[i] = (LibrarySpec) list[i]; } Libraries = libraries; LibrarySpecs = librarySpecs; DoValidate(); }
public override void ReadXml(XmlReader reader) { // Read tag attributes. SpecialHandling = reader.GetAttribute(ATTR.special_handling) ?? SpecialHandlingType.NONE; // Backward compatibility with v1.3: force all ions name to all ions (may be MSe) if (!SpecialHandlingType.IsAllIons(SpecialHandling)) base.ReadXml(reader); else { ReadXmlName(SpecialHandlingType.ALL_IONS); SpecialHandling = SpecialHandlingType.ALL_IONS; } PrecursorFilter = reader.GetNullableDoubleAttribute(ATTR.precursor_filter); if (!PrecursorFilter.HasValue) { PrecursorFilter = reader.GetNullableDoubleAttribute(ATTR.precursor_left_filter); PrecursorRightFilter = reader.GetNullableDoubleAttribute(ATTR.precursor_right_filter); } WindowsPerScan = reader.GetNullableIntAttribute(ATTR.windows_per_scan); if (reader.IsEmptyElement) reader.Read(); else { // Consume tag reader.ReadStartElement(); var list = new List<IsolationWindow>(); reader.ReadElements(list); PrespecifiedIsolationWindows = list; reader.ReadEndElement(); } DoValidate(); }