public static void ReadElements <TItem>(this XmlReader reader, List <TItem> list,
params IXmlElementHelper <TItem>[] helpers)
{
IXmlElementHelper <TItem> helper;
while ((helper = reader.FindHelper(helpers)) != null)
{
list.Add(helper.Deserialize(reader));
}
}
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 override void ReadXml(XmlReader reader)
{
// Read tag attributes
base.ReadXml(reader);
UseForRetentionTimeFilter = reader.GetBoolAttribute(ATTR.use_for_retention_time_prediction, false);
AnalyteConcentration = reader.GetNullableDoubleAttribute(ATTR.analyte_concentration);
SampleType = SampleType.FromName(reader.GetAttribute(ATTR.sample_type));
// Consume tag
reader.Read();
// Check if there is an optimization function element, and read
// if if there is.
IXmlElementHelper <OptimizableRegression> helper =
reader.FindHelper(OPTIMIZATION_HELPERS);
if (helper != null)
{
OptimizationFunction = helper.Deserialize(reader);
}
var chromFileInfos = new List <ChromFileInfo>();
var fileLoadIds = new List <string>();
while (reader.IsStartElement(EL.sample_file) ||
reader.IsStartElement(EL.replicate_file) ||
reader.IsStartElement(EL.chromatogram_file))
{
// Note that the file path is actually be a URI that encodes things like lockmass correction as well as filename
ChromFileInfo chromFileInfo = new ChromFileInfo(MsDataFileUri.Parse(reader.GetAttribute(ATTR.file_path)));
chromFileInfo = chromFileInfo.ChangeHasMidasSpectra(reader.GetBoolAttribute(ATTR.has_midas_spectra, false));
chromFileInfos.Add(chromFileInfo);
string id = reader.GetAttribute(ATTR.id) ?? GetOrdinalSaveId(fileLoadIds.Count);
fileLoadIds.Add(id);
reader.Read();
if (reader.IsStartElement(EL.instrument_info_list))
{
reader.Skip();
reader.Read();
}
}
Annotations = SrmDocument.ReadAnnotations(reader);
MSDataFileInfos = chromFileInfos;
_fileLoadIds = fileLoadIds.ToArray();
// Consume end tag
reader.ReadEndElement();
}
public override void ReadXml(XmlReader reader)
{
// Read tag attributes
base.ReadXml(reader);
UseForRetentionTimeFilter = reader.GetBoolAttribute(ATTR.use_for_retention_time_prediction, false);
AnalyteConcentration = reader.GetNullableDoubleAttribute(ATTR.analyte_concentration);
SampleType = SampleType.FromName(reader.GetAttribute(ATTR.sample_type));
// Consume tag
reader.Read();
// Check if there is an optimization function element, and read
// if if there is.
IXmlElementHelper<OptimizableRegression> helper =
reader.FindHelper(OPTIMIZATION_HELPERS);
if (helper != null)
OptimizationFunction = helper.Deserialize(reader);
var msDataFilePaths = new List<MsDataFileUri>();
var fileLoadIds = new List<string>();
while (reader.IsStartElement(EL.sample_file) ||
reader.IsStartElement(EL.replicate_file) ||
reader.IsStartElement(EL.chromatogram_file))
{
// Note that the file path is actually be a URI that encodes things like lockmass correction as well as filename
msDataFilePaths.Add(MsDataFileUri.Parse(reader.GetAttribute(ATTR.file_path)));
string id = reader.GetAttribute(ATTR.id) ?? GetOrdinalSaveId(fileLoadIds.Count);
fileLoadIds.Add(id);
reader.Read();
if (reader.IsStartElement(EL.instrument_info_list))
{
reader.Skip();
reader.Read();
}
}
Annotations = SrmDocument.ReadAnnotations(reader);
MSDataFileInfos = msDataFilePaths.ConvertAll(path => new ChromFileInfo(path));
_fileLoadIds = fileLoadIds.ToArray();
// Consume end tag
reader.ReadEndElement();
}
public void ReadXml(XmlReader reader)
{
// Consume tag
if (reader.IsEmptyElement)
reader.Read();
else
{
reader.ReadStartElement();
// Read child element
var helperSpec = reader.FindHelper(PEAK_SCORING_MODEL_SPEC_HELPERS);
if (helperSpec != null)
PeakScoringModel = helperSpec.Deserialize(reader);
reader.ReadEndElement();
}
}
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();
}