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 WriteXml(XmlWriter writer)
{
// Write tag attributes
base.WriteXml(writer);
writer.WriteAttribute(ATTR.use_for_retention_time_prediction, false);
writer.WriteAttributeNullable(ATTR.analyte_concentration, AnalyteConcentration);
if (null != SampleType && !Equals(SampleType, SampleType.DEFAULT))
{
writer.WriteAttribute(ATTR.sample_type, SampleType.Name);
}
// Write optimization element, if present
if (OptimizationFunction != null)
{
IXmlElementHelper <OptimizableRegression> helper = XmlUtil.FindHelper(
OptimizationFunction, OPTIMIZATION_HELPERS);
if (helper == null)
{
throw new InvalidOperationException(Resources.ChromatogramSet_WriteXml_Attempt_to_serialize_list_containing_invalid_type);
}
writer.WriteElement(helper.ElementNames[0], OptimizationFunction);
}
int i = 0;
foreach (var fileInfo in MSDataFileInfos)
{
writer.WriteStartElement(EL.sample_file);
writer.WriteAttribute(ATTR.id, GetOrdinalSaveId(i++));
writer.WriteAttribute(ATTR.file_path, fileInfo.FilePath);
writer.WriteAttribute(ATTR.sample_name, fileInfo.FilePath.GetSampleOrFileName());
if (fileInfo.RunStartTime != null)
{
writer.WriteAttribute(ATTR.acquired_time, XmlConvert.ToString((DateTime)fileInfo.RunStartTime, "yyyy-MM-ddTHH:mm:ss")); // Not L10N
}
if (fileInfo.FileWriteTime != null)
{
writer.WriteAttribute(ATTR.modified_time, XmlConvert.ToString((DateTime)fileInfo.FileWriteTime, "yyyy-MM-ddTHH:mm:ss")); // Not L10N
}
writer.WriteAttribute(ATTR.has_midas_spectra, fileInfo.HasMidasSpectra, false);
// instrument information
WriteInstrumentConfigList(writer, fileInfo.InstrumentInfoList);
writer.WriteEndElement();
}
SrmDocument.WriteAnnotations(writer, Annotations);
}
public static void WriteElements <TItem>(this XmlWriter writer, IEnumerable <TItem> list,
params IXmlElementHelper <TItem>[] helpers)
where TItem : IXmlSerializable
{
foreach (TItem item in list)
{
if (Equals(item, default(TItem)))
{
throw new InvalidDataException(Resources.XmlUtil_WriteElements_Attempt_to_serialize_list_missing_an_element);
}
IXmlElementHelper <TItem> helper = FindHelper(item, helpers);
if (helper == null)
{
throw new InvalidOperationException(string.Format(Resources.XmlUtil_WriteElements_Attempt_to_serialize_list_containing_invalid_type__0__, typeof(TItem)));
}
writer.WriteElement(helper.ElementNames[0], item);
}
}
