public override void ReadXml(XmlReader reader) { // Read tag attributes base.ReadXml(reader); ColinearWarning = reader.GetBoolAttribute(ATTR.colinear_warning); // Earlier versions always used decoys only UsesDecoys = reader.GetBoolAttribute(ATTR.uses_decoys, true); UsesSecondBest = reader.GetBoolAttribute(ATTR.uses_false_targets); double bias = reader.GetDoubleAttribute(ATTR.bias); // Consume tag reader.Read(); // Read calculators var calculators = new List <FeatureCalculator>(); reader.ReadElements(calculators); var peakFeatureCalculators = new List <IPeakFeatureCalculator>(calculators.Count); var weights = new double[calculators.Count]; for (int i = 0; i < calculators.Count; i++) { weights[i] = calculators[i].Weight; peakFeatureCalculators.Add(PeakFeatureCalculator.GetCalculator(calculators[i].Type)); } SetPeakFeatureCalculators(peakFeatureCalculators); Parameters = new LinearModelParams(weights, bias); reader.ReadEndElement(); DoValidate(); }
public override void ReadXml(XmlReader reader) { // Read tag attributes base.ReadXml(reader); // Earlier versions always used decoys only UsesDecoys = reader.GetBoolAttribute(ATTR.uses_decoys, true); UsesSecondBest = reader.GetBoolAttribute(ATTR.uses_false_targets, false); double bias = reader.GetDoubleAttribute(ATTR.bias); bool isEmpty = reader.IsEmptyElement; // Consume tag reader.Read(); if (!isEmpty) { // Read calculators var calculators = new List <FeatureCalculator>(); reader.ReadElements(calculators); var weights = new double[calculators.Count]; for (int i = 0; i < calculators.Count; i++) { if (calculators[i].Type != PeakFeatureCalculators[i].GetType()) { throw new InvalidDataException(Resources.LegacyScoringModel_ReadXml_Invalid_legacy_model_); } weights[i] = calculators[i].Weight; } Parameters = new LinearModelParams(weights, bias); reader.ReadEndElement(); } DoValidate(); }
public void ReadXml(XmlReader reader) { string uri = reader.GetAttribute(Attr.panorama_publish_uri); if (!string.IsNullOrEmpty(uri)) { PanoramaPublishUri = new Uri(uri); } string docGuid = reader.GetAttribute(Attr.document_guid); if (!string.IsNullOrEmpty(docGuid)) { DocumentGuid = docGuid; } AuditLogging = reader.GetBoolAttribute(Attr.audit_logging); var allElements = new List <IXmlSerializable>(); // Consume tag if (reader.IsEmptyElement) { reader.Read(); } else { reader.ReadStartElement(); reader.ReadElements(allElements, GetElementHelpers()); reader.ReadEndElement(); } _annotationDefs = MakeReadOnly(allElements.OfType <AnnotationDef>()); _groupComparisonDefs = MakeReadOnly(allElements.OfType <GroupComparisonDef>()); ViewSpecList = allElements.OfType <ViewSpecList>().FirstOrDefault() ?? ViewSpecList.EMPTY; Lists = ImmutableList.ValueOf(allElements.OfType <ListData>()); MetadataRuleSets = ImmutableList.ValueOf(allElements.OfType <MetadataRuleSet>()); }
internal static void ReadTo(this XmlReader reader, IDictionary <string, object> dynamicObject, BindableDynamicObject.XmlSettings xmlSettings) { if (xmlSettings.IsImplicit()) { reader.ReadAttributes(dynamicObject); reader.ReadElements(dynamicObject, xmlSettings); } else if (xmlSettings.SerializePropertyAsAttribute) { reader.ReadAttributes(dynamicObject); reader.Skip(); } else { reader.ReadElements(dynamicObject, xmlSettings); } }
public void ReadXml(XmlReader reader) { bool isEmpty = reader.IsEmptyElement; // Read past the property element reader.Read(); // For empty lists in Settings.Default if (isEmpty) { return; } if (reader.IsStartElement(EL.revision)) { RevisionIndex = reader.GetIntAttribute(ATTR.index); reader.Read(); // Consume tag } var helpers = GetXmlElementHelpers(); var helper = reader.FindHelper(helpers); // Read list items List <TValue> list = new List <TValue>(); if (helper != null) { reader.ReadElements(list, helpers); } else { // Support for v0.1 format if (reader.IsEmptyElement) { reader.Read(); } else { // Try to get through the elements with whatever // names they were given, based on class names. helper = new XmlElementHelper <TValue>(); reader.ReadStartElement(); // <ArrayOfType while (reader.IsStartElement()) { list.Add(helper.Deserialize(reader)); // <Type } reader.ReadEndElement(); } } Clear(); AddRange(list); // Perform final list specific updates ValidateLoad(); }
public void ReadXml(XmlReader reader) { if (RetentionTimeSources != null || FileAlignments != null) { throw new InvalidOperationException(); } var sources = new List <RetentionTimeSource>(); var fileAlignments = new List <FileRetentionTimeAlignments>(); if (reader.IsEmptyElement) { reader.Read(); } else { reader.Read(); reader.ReadElements(sources); reader.ReadElements(fileAlignments); reader.ReadEndElement(); } RetentionTimeSources = ResultNameMap.FromNamedElements(sources); FileAlignments = ResultNameMap.FromNamedElements(fileAlignments); }
public static void ReadElementList <TItem>(this XmlReader reader, Enum name, List <TItem> list, params IXmlElementHelper <TItem>[] helpers) { if (reader.IsStartElement(name)) { if (reader.IsEmptyElement) { reader.ReadStartElement(name); } else { reader.ReadStartElement(name); reader.ReadElements(list, helpers); reader.ReadEndElement(); } } }
public override void ReadXml(XmlReader reader) { // Read tag attributes base.ReadXml(reader); // Consume tag reader.ReadStartElement(); var list = new List <IsotopeEnrichmentItem>(); reader.ReadElements(list); _isotopeEnrichments = MakeReadOnly(list); reader.ReadEndElement(); 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_filter_margin); UseMargin = PrecursorFilter.HasValue; } 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(); }
public override void ReadXml(XmlReader reader) { if (null != RetentionTimeAlignments) { throw new InvalidOperationException(); } base.ReadXml(reader); var retentionTimeAlignments = new List <RetentionTimeAlignment>(); if (reader.IsEmptyElement) { reader.Read(); } else { // Read past the property element reader.Read(); reader.ReadElements(retentionTimeAlignments); reader.ReadEndElement(); } RetentionTimeAlignments = ResultNameMap.FromNamedElements(retentionTimeAlignments); }
public override void ReadXml(XmlReader reader) { // Read tag attributes base.ReadXml(reader); // Earlier versions always used decoys only UsesDecoys = reader.GetBoolAttribute(ATTR.uses_decoys, true); UsesSecondBest = reader.GetBoolAttribute(ATTR.uses_false_targets, false); double bias = reader.GetDoubleAttribute(ATTR.bias); bool isEmpty = reader.IsEmptyElement; // Consume tag reader.Read(); if (!isEmpty) { // Read calculators var calculators = new List<FeatureCalculator>(); reader.ReadElements(calculators); var weights = new double[calculators.Count]; for (int i = 0; i < calculators.Count; i++) { if (calculators[i].Type != PeakFeatureCalculators[i].GetType()) throw new InvalidDataException(Resources.LegacyScoringModel_ReadXml_Invalid_legacy_model_); weights[i] = calculators[i].Weight; } Parameters = new LinearModelParams(weights, bias); reader.ReadEndElement(); } DoValidate(); }
public static void ReadElements <TItem>(this XmlReader reader, List <TItem> list) { reader.ReadElements(list, new XmlElementHelper <TItem>()); }
public override void ReadXml(XmlReader reader) { // Read tag attributes base.ReadXml(reader); // Consume tag reader.ReadStartElement(); var list = new List<IsotopeEnrichmentItem>(); reader.ReadElements(list); _isotopeEnrichments = MakeReadOnly(list); reader.ReadEndElement(); DoValidate(); }
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); ColinearWarning = reader.GetBoolAttribute(ATTR.colinear_warning); // Earlier versions always used decoys only UsesDecoys = reader.GetBoolAttribute(ATTR.uses_decoys, true); UsesSecondBest = reader.GetBoolAttribute(ATTR.uses_false_targets); double bias = reader.GetDoubleAttribute(ATTR.bias); // Consume tag reader.Read(); // Read calculators var calculators = new List<FeatureCalculator>(); reader.ReadElements(calculators); var peakFeatureCalculators = new List<IPeakFeatureCalculator>(calculators.Count); var weights = new double[calculators.Count]; for (int i = 0; i < calculators.Count; i++) { weights[i] = calculators[i].Weight; peakFeatureCalculators.Add(PeakFeatureCalculator.GetCalculator(calculators[i].Type)); } SetPeakFeatureCalculators(peakFeatureCalculators); Parameters = new LinearModelParams(weights, bias); reader.ReadEndElement(); 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(); }