public override void ReadXml(XmlReader reader)
{
base.ReadXml(reader);
AnnotationTargets = AnnotationTargetSet.Parse(reader.GetAttribute(Attr.targets));
// In older documents, it's possible for the "type" attribute value to be "-1".
Type = TypeSafeEnum.ValidateOrDefault(reader.GetEnumAttribute(Attr.type, AnnotationType.text),
AnnotationType.text);
Lookup = reader.GetAttribute(Attr.lookup);
var items = new List <string>();
if (reader.IsEmptyElement)
{
reader.Read();
}
else
{
reader.Read();
while (reader.IsStartElement(El.value))
{
items.Add(reader.ReadElementString());
}
reader.ReadEndElement();
}
_items = MakeReadOnly(items);
}
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();
}
public override void ReadXml(XmlReader reader)
{
base.ReadXml(reader);
AnnotationTargets = AnnotationTargetSet.Parse(reader.GetAttribute(Attr.targets));
Type = reader.GetEnumAttribute(Attr.type, AnnotationType.text);
var items = new List <string>();
if (reader.IsEmptyElement)
{
reader.Read();
}
else
{
reader.Read();
while (reader.IsStartElement(El.value))
{
items.Add(reader.ReadElementString());
}
reader.ReadEndElement();
}
_items = MakeReadOnly(items);
}
public static TAttr GetEnumAttribute <TAttr>(this XmlReader reader, string name, TAttr defaultValue)
{
return(reader.GetEnumAttribute(name, defaultValue, EnumCase.unkown));
}
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 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();
}
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();
}
