Example #1
0
        public void ReadXml(XmlReader reader)
        {
            // Read tag attributes
            MonoisotopicMass = reader.GetNullableDoubleAttribute(ATTR.massdiff_monoisotopic) ?? 0;
            AverageMass = reader.GetNullableDoubleAttribute(ATTR.massdiff_average) ?? 0;
            Formula = reader.GetAttribute(ATTR.formula);
            Inclusion = reader.GetEnumAttribute(ATTR.inclusion, LossInclusion.Library);

            // Consume tag
            reader.Read();

            Validate();
        }
Example #2
0
        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();
        }
Example #3
0
        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();
        }