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 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);
Regex = reader.GetAttribute(ATTR.regex);
IsIncludeMatch = reader.GetBoolAttribute(ATTR.include);
IsMatchMod = reader.GetBoolAttribute(ATTR.match_mod_sequence);
// Consume tag
reader.Read();
Validate();
}
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
MaxMissedCleavages = reader.GetIntAttribute(ATTR.max_missed_cleavages);
ExcludeRaggedEnds = reader.GetBoolAttribute(ATTR.exclude_ragged_ends);
// Consume tag
reader.Read();
Validate();
}
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 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)
{
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();
}
public override void ReadXml(XmlReader reader)
{
// Read tag attributes
base.ReadXml(reader);
Fragment = reader.GetAttribute(ATTR.cut);
if (IsFragment)
{
Restrict = reader.GetAttribute(ATTR.no_cut);
Terminus = reader.GetAttribute(ATTR.sense, ToSeqTerminus);
MinFragmentLength = reader.GetNullableIntAttribute(ATTR.min_length) ??
DEFAULT_MIN_FRAGMENT_LENGTH;
}
else
{
var charges = TextUtil.ParseInts(reader.GetAttribute(ATTR.charges)); // Old version?
if (charges.Count() > 1)
throw new InvalidDataException(Resources.MeasuredIon_ReadXml_Multiple_charge_states_for_custom_ions_are_no_longer_supported_);
SettingsCustomIon = SettingsCustomIon.Deserialize(reader);
if (charges.Any()) // Old style - fix it up a little for our revised ideas about custom ion ionization
{
Charge = charges[0];
if (string.IsNullOrEmpty(SettingsCustomIon.Formula)) // Adjust the user-supplied masses
{
SettingsCustomIon = new SettingsCustomIon(SettingsCustomIon.Formula,
Math.Round(SettingsCustomIon.MonoisotopicMass + BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.H), SequenceMassCalc.MassPrecision), // Assume user provided neutral mass. Round new value easiest XML roundtripping.
Math.Round(SettingsCustomIon.AverageMass + BioMassCalc.AVERAGE.GetMass(BioMassCalc.H), SequenceMassCalc.MassPrecision), // Assume user provided neutral mass. Round new value easiest XML roundtripping.
SettingsCustomIon.Name);
}
}
else
{
Charge = reader.GetIntAttribute(ATTR.charge);
}
IsOptional = reader.GetBoolAttribute(ATTR.optional);
}
// Consume tag
reader.Read();
Validate();
}
