public override void WriteXml(XmlWriter writer)
        {
            // Write tag attributes
            base.WriteXml(writer);

            writer.WriteElements(_isotopeEnrichments);
        }
        public override void WriteXml(XmlWriter writer)
        {
            // Write tag attributes
            base.WriteXml(writer);

            if (IsTrained)
            {
                writer.WriteAttribute(ATTR.uses_decoys, UsesDecoys, true);
                writer.WriteAttribute(ATTR.uses_false_targets, UsesSecondBest);
                writer.WriteAttribute(ATTR.bias, Parameters.Bias);

                // Write calculators
                var calculators = new List<FeatureCalculator>(PeakFeatureCalculators.Count);
                for (int i = 0; i < PeakFeatureCalculators.Count; i++)
                    calculators.Add(new FeatureCalculator(PeakFeatureCalculators[i].GetType(), Parameters.Weights[i]));
                writer.WriteElements(calculators);
            }
        }
Exemple #3
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        public override void WriteXml(XmlWriter writer)
        {
            // Write tag attributes
            base.WriteXml(writer);
            writer.WriteAttributeIfString(ATTR.aminoacid, AAs);
            writer.WriteAttributeNullable(ATTR.terminus, Terminus);
            writer.WriteAttribute(ATTR.variable, IsVariable);
            writer.WriteAttributeIfString(ATTR.formula, Formula);
            writer.WriteAttribute(ATTR.label_13C, Label13C);
            writer.WriteAttribute(ATTR.label_15N, Label15N);
            writer.WriteAttribute(ATTR.label_18O, Label18O);
            writer.WriteAttribute(ATTR.label_2H, Label2H);
            writer.WriteAttribute(ATTR.relative_rt, RelativeRT, RelativeRT.Matching);
            if (string.IsNullOrEmpty(Formula))
            {
                writer.WriteAttributeNullable(ATTR.massdiff_monoisotopic, MonoisotopicMass);
                writer.WriteAttributeNullable(ATTR.massdiff_average, AverageMass);
            }
            if (!IsVariable)
                writer.WriteAttribute(ATTR.explicit_decl, IsExplicit);

            writer.WriteAttributeNullable(ATTR.unimod_id, UnimodId);

            writer.WriteAttributeIfString(ATTR.short_name, ShortName);

            if (Losses != null)
                writer.WriteElements(Losses);
        }
Exemple #4
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 public void WriteXml(XmlWriter writer)
 {
     if(PanoramaPublishUri != null)
         writer.WriteAttributeIfString(Attr.panorama_publish_uri, PanoramaPublishUri.ToString());
     //            Assume.IsFalse(string.IsNullOrEmpty(DocumentGuid)); // Should have a document GUID by this point
     if(!string.IsNullOrEmpty(DocumentGuid))
         writer.WriteAttributeString(Attr.document_guid, DocumentGuid);
     var elements = AnnotationDefs.Cast<IXmlSerializable>().Concat(GroupComparisonDefs);
     if (ViewSpecList.ViewSpecs.Any())
     {
         elements = elements.Concat(new[] {ViewSpecList});
     }
     writer.WriteElements(elements, GetElementHelpers());
 }
        public void WriteXml(XmlWriter writer)
        {
            // Write attibutes
            writer.WriteAttribute(ATTR.max_variable_mods, MaxVariableMods);
            writer.WriteAttribute(ATTR.max_neutral_losses, MaxNeutralLosses);
            if (InternalStandardTypes.Count == 0)
            {
                writer.WriteAttribute(ATTR.internal_standard, IsotopeLabelType.NONE_NAME);
            }
            if (InternalStandardTypes.Count == 1)
            {
                var internalStandardType = InternalStandardTypes[0];
                if (!ReferenceEquals(internalStandardType, IsotopeLabelType.heavy))
                    writer.WriteAttribute(ATTR.internal_standard, internalStandardType.Name);
            }
            else
            {
                foreach (var labelType in InternalStandardTypes)
                {
                    writer.WriteStartElement(EL.internal_standard);
                    writer.WriteAttribute(ATTR.name, labelType.Name);
                    writer.WriteEndElement();
                }
            }

            // Write child elements
            if (StaticModifications.Count > 0)
                writer.WriteElementList(EL.static_modifications, StaticModifications);
            foreach (var heavyMods in GetHeavyModifications())
            {
                writer.WriteStartElement(EL.heavy_modifications);
                if (!ReferenceEquals(heavyMods.LabelType, IsotopeLabelType.heavy))
                    writer.WriteAttribute(ATTR.isotope_label, heavyMods.LabelType);
                writer.WriteElements(heavyMods.Modifications);
                writer.WriteEndElement();
            }
        }
 public void WriteXml(XmlWriter writer)
 {
     writer.WriteElements(RetentionTimeSources.Values);
     writer.WriteElements(FileAlignments.Values);
 }
        public override void WriteXml(XmlWriter writer)
        {
            // Write tag attributes.
            base.WriteXml(writer);

            if (PrecursorRightFilter.HasValue)
            {
                writer.WriteAttributeNullable(ATTR.precursor_left_filter, PrecursorFilter);
                writer.WriteAttributeNullable(ATTR.precursor_right_filter, PrecursorRightFilter);
            }
            else
            {
                writer.WriteAttributeNullable(ATTR.precursor_filter, PrecursorFilter);
            }

            if (!Equals(SpecialHandling, SpecialHandlingType.NONE))
                writer.WriteAttribute(ATTR.special_handling, SpecialHandling);
            writer.WriteAttributeNullable(ATTR.windows_per_scan, WindowsPerScan);

            writer.WriteElements(_prespecifiedIsolationWindows);
        }