public void ReadXml(XmlReader reader)
{
Title = reader.GetAttribute(ATTR.title);
Command = reader.GetAttribute(ATTR.command);
Arguments = reader.GetAttribute(ATTR.arguments) ?? string.Empty;
InitialDirectory = reader.GetAttribute(ATTR.initial_directory) ?? string.Empty;
OutputToImmediateWindow = reader.GetBoolAttribute(ATTR.output_to_immediate_window);
ReportTitle = reader.GetAttribute(ATTR.report_title);
PreviousCommandLineArgs = reader.GetAttribute(ATTR.argument_generated) ?? string.Empty;
ArgsCollectorDllPath = reader.GetAttribute(ATTR.argscollector_dll_path) ?? string.Empty;
ArgsCollectorClassName = reader.GetAttribute(ATTR.argscollector_class_name) ?? string.Empty;
ToolDirPath = reader.GetAttribute(ATTR.tool_dir_path) ?? string.Empty;
PackageVersion = reader.GetAttribute(ATTR.package_version) ?? string.Empty;
PackageIdentifier = reader.GetAttribute(ATTR.package_identifier) ?? string.Empty;
PackageName = reader.GetAttribute(ATTR.package_name) ?? string.Empty;
UpdateAvailable = reader.GetBoolAttribute(ATTR.update_available);
Annotations = new List <AnnotationDef>();
if (!reader.IsEmptyElement)
{
reader.ReadStartElement();
reader.ReadElementList(EL.annotation, Annotations);
reader.ReadEndElement();
}
else
{
reader.Read();
}
Validate();
}
public static void ReadElementList <TItem>(this XmlReader reader, Enum name, List <TItem> list)
{
reader.ReadElementList(name, list, new XmlElementHelper <TItem>());
}
public void ReadXml(XmlReader reader)
{
// Read start tag attributes
ExcludeNTermAAs = reader.GetIntAttribute(ATTR.start);
MinPeptideLength = reader.GetIntAttribute(ATTR.min_length);
MaxPeptideLength = reader.GetIntAttribute(ATTR.max_length);
AutoSelect = reader.GetBoolAttribute(ATTR.auto_select);
var list = new List<PeptideExcludeRegex>();
// Consume tag
if (reader.IsEmptyElement)
reader.Read();
else
{
reader.ReadStartElement();
// Read child elements
reader.ReadElementList(EL.peptide_exclusions, list);
reader.ReadEndElement();
}
Exclusions = list;
DoValidate();
}
public void ReadXml(XmlReader reader)
{
var list = new List<TypedModifications>();
var internalStandardTypes = new[] {IsotopeLabelType.heavy};
MaxVariableMods = reader.GetIntAttribute(ATTR.max_variable_mods, DEFAULT_MAX_VARIABLE_MODS);
MaxNeutralLosses = reader.GetIntAttribute(ATTR.max_neutral_losses, DEFAULT_MAX_NEUTRAL_LOSSES);
// Consume tag
if (reader.IsEmptyElement)
{
list.Add(new TypedModifications(IsotopeLabelType.light, new StaticMod[0]));
reader.Read();
}
else
{
var internalStandardNames = new List<string>();
string internalStandardName = reader.GetAttribute(ATTR.internal_standard);
reader.ReadStartElement();
if (internalStandardName != null)
{
if (internalStandardName == IsotopeLabelType.NONE_NAME)
internalStandardTypes = new IsotopeLabelType[0];
else
internalStandardNames.Add(internalStandardName);
}
else
{
while (reader.IsStartElement(EL.internal_standard))
{
internalStandardNames.Add(reader.GetAttribute(ATTR.name));
reader.Read();
}
}
if (internalStandardNames.Count > 0)
internalStandardTypes = new IsotopeLabelType[internalStandardNames.Count];
SetInternalStandardType(IsotopeLabelType.light, internalStandardNames, internalStandardTypes);
// Read child elements
var listMods = new List<StaticMod>();
reader.ReadElementList(EL.static_modifications, listMods);
list.Add(new TypedModifications(IsotopeLabelType.light, listMods));
int typeOrder = IsotopeLabelType.FirstHeavy;
while (reader.IsStartElement(EL.heavy_modifications))
{
// If first heavy tag has no isotope_label attribute, use the default heavy type
var labelType = IsotopeLabelType.heavy;
string typeName = reader.GetAttribute(ATTR.isotope_label);
if (!string.IsNullOrEmpty(typeName))
{
labelType = new IsotopeLabelType(typeName, typeOrder);
if (Equals(labelType, IsotopeLabelType.heavy))
labelType = IsotopeLabelType.heavy;
// If the created label type is going to be used and there are serialization
// context modifications, try to use the label types from the context.
else if (_serializationContext != null)
{
var modsContext = _serializationContext.GetModificationsByName(typeName);
if (modsContext != null)
{
// CONSIDER: Should this require full equality, including order?
labelType = modsContext.LabelType;
}
}
}
else if (typeOrder > IsotopeLabelType.FirstHeavy)
{
throw new InvalidDataException(
string.Format(Resources.PeptideModifications_ReadXml_Heavy_modifications_found_without__0__attribute,
ATTR.isotope_label));
}
typeOrder++;
SetInternalStandardType(labelType, internalStandardNames, internalStandardTypes);
// If no internal standard type was given, use the first heavy type.
if (internalStandardNames.Count == 0 && internalStandardTypes.Length != 0)
{
internalStandardNames.Add(labelType.Name);
internalStandardTypes = new[] {labelType};
}
listMods = new List<StaticMod>();
reader.ReadElementList(EL.heavy_modifications, listMods);
list.Add(new TypedModifications(labelType, listMods));
}
int iMissingType = internalStandardTypes.IndexOf(labelType => labelType == null);
if (iMissingType != -1)
{
throw new InvalidDataException(string.Format(Resources.PeptideModifications_ReadXml_Internal_standard_type__0__not_found,
internalStandardNames[iMissingType]));
}
reader.ReadEndElement();
}
if (list.Count < 2)
list.Add(new TypedModifications(IsotopeLabelType.heavy, new StaticMod[0]));
_modifications = MakeReadOnly(list.ToArray());
InternalStandardTypes = internalStandardTypes;
DoValidate();
}
