public override void ReadXml(XmlReader reader)
{
// Read tag attributes
base.ReadXml(reader);
// Earlier versions always used decoys only
UsesDecoys = reader.GetBoolAttribute(ATTR.uses_decoys, true);
UsesSecondBest = reader.GetBoolAttribute(ATTR.uses_false_targets, false);
double bias = reader.GetDoubleAttribute(ATTR.bias);
bool isEmpty = reader.IsEmptyElement;
// Consume tag
reader.Read();
if (!isEmpty)
{
// Read calculators
var calculators = new List<FeatureCalculator>();
reader.ReadElements(calculators);
var weights = new double[calculators.Count];
for (int i = 0; i < calculators.Count; i++)
{
if (calculators[i].Type != PeakFeatureCalculators[i].GetType())
throw new InvalidDataException(Resources.LegacyScoringModel_ReadXml_Invalid_legacy_model_);
weights[i] = calculators[i].Weight;
}
Parameters = new LinearModelParams(weights, bias);
reader.ReadEndElement();
}
DoValidate();
}
public override void ReadXml(XmlReader reader)
{
// Read tag attributes
base.ReadXml(reader);
// Consume tag
reader.ReadStartElement();
var list = new List<IsotopeEnrichmentItem>();
reader.ReadElements(list);
_isotopeEnrichments = MakeReadOnly(list);
reader.ReadEndElement();
DoValidate();
}
public override void ReadXml(XmlReader reader)
{
// Read tag attributes
base.ReadXml(reader);
ColinearWarning = reader.GetBoolAttribute(ATTR.colinear_warning);
// Earlier versions always used decoys only
UsesDecoys = reader.GetBoolAttribute(ATTR.uses_decoys, true);
UsesSecondBest = reader.GetBoolAttribute(ATTR.uses_false_targets);
double bias = reader.GetDoubleAttribute(ATTR.bias);
// Consume tag
reader.Read();
// Read calculators
var calculators = new List<FeatureCalculator>();
reader.ReadElements(calculators);
var peakFeatureCalculators = new List<IPeakFeatureCalculator>(calculators.Count);
var weights = new double[calculators.Count];
for (int i = 0; i < calculators.Count; i++)
{
weights[i] = calculators[i].Weight;
peakFeatureCalculators.Add(PeakFeatureCalculator.GetCalculator(calculators[i].Type));
}
SetPeakFeatureCalculators(peakFeatureCalculators);
Parameters = new LinearModelParams(weights, bias);
reader.ReadEndElement();
DoValidate();
}
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 override void ReadXml(XmlReader reader)
{
// Read tag attributes.
SpecialHandling = reader.GetAttribute(ATTR.special_handling) ?? SpecialHandlingType.NONE;
// Backward compatibility with v1.3: force all ions name to all ions (may be MSe)
if (!SpecialHandlingType.IsAllIons(SpecialHandling))
base.ReadXml(reader);
else
{
ReadXmlName(SpecialHandlingType.ALL_IONS);
SpecialHandling = SpecialHandlingType.ALL_IONS;
}
PrecursorFilter = reader.GetNullableDoubleAttribute(ATTR.precursor_filter);
if (!PrecursorFilter.HasValue)
{
PrecursorFilter = reader.GetNullableDoubleAttribute(ATTR.precursor_left_filter);
PrecursorRightFilter = reader.GetNullableDoubleAttribute(ATTR.precursor_right_filter);
}
WindowsPerScan = reader.GetNullableIntAttribute(ATTR.windows_per_scan);
if (reader.IsEmptyElement)
reader.Read();
else
{
// Consume tag
reader.ReadStartElement();
var list = new List<IsolationWindow>();
reader.ReadElements(list);
PrespecifiedIsolationWindows = list;
reader.ReadEndElement();
}
DoValidate();
}
