public void Save(XmlWriter w)
{
w.WriteStartElement("door");
w.WriteAttribute("x", Position.X);
w.WriteAttribute("y", Position.Y);
w.WriteAttribute("kind", Kind);
w.WriteAttribute("state", State);
w.WriteEndElement();
}
public void Save(XmlWriter w)
{
w.WriteStartElement("brush");
w.WriteAttribute("left", Bounds.Left);
w.WriteAttribute("top", Bounds.Top);
w.WriteAttribute("right", Bounds.Right);
w.WriteAttribute("bottom", Bounds.Bottom);
w.WriteAttribute("content", Content);
w.WriteEndElement();
}
public override void WriteXml(XmlWriter writer)
{
// Write tag attributes.
base.WriteXml(writer);
if (PrecursorRightFilter.HasValue)
{
writer.WriteAttributeNullable(ATTR.precursor_left_filter, PrecursorFilter);
writer.WriteAttributeNullable(ATTR.precursor_right_filter, PrecursorRightFilter);
}
else
{
writer.WriteAttributeNullable(ATTR.precursor_filter, PrecursorFilter);
}
if (!Equals(SpecialHandling, SpecialHandlingType.NONE))
writer.WriteAttribute(ATTR.special_handling, SpecialHandling);
writer.WriteAttributeNullable(ATTR.windows_per_scan, WindowsPerScan);
writer.WriteElements(_prespecifiedIsolationWindows);
}
public override void WriteXml(XmlWriter writer)
{
// Write tag attributes
base.WriteXml(writer);
if (IsTrained)
{
writer.WriteAttribute(ATTR.uses_decoys, UsesDecoys, true);
writer.WriteAttribute(ATTR.uses_false_targets, UsesSecondBest);
writer.WriteAttribute(ATTR.bias, Parameters.Bias);
// Write calculators
var calculators = new List<FeatureCalculator>(PeakFeatureCalculators.Count);
for (int i = 0; i < PeakFeatureCalculators.Count; i++)
calculators.Add(new FeatureCalculator(PeakFeatureCalculators[i].GetType(), Parameters.Weights[i]));
writer.WriteElements(calculators);
}
}
public void WriteXml(XmlWriter writer)
{
// Write tag attributes
writer.WriteAttribute(ATTR.symbol, IsotopeSymbol);
// Write element string
writer.WriteString(AtomPercentEnrichment.ToString(CultureInfo.InvariantCulture));
}
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
}
// instrument information
WriteInstrumentConfigList(writer, fileInfo.InstrumentInfoList);
writer.WriteEndElement();
}
SrmDocument.WriteAnnotations(writer, Annotations);
}
protected virtual void SaveAttributes(XmlWriter w)
{
w.WriteAttribute("class", GetType().ToString());
w.WriteAttribute("x", Position.X);
w.WriteAttribute("y", Position.Y);
w.WriteAttribute("dir", Direction);
w.WriteAttribute("name", Name);
}
public override void WriteXml(XmlWriter writer)
{
base.WriteXml(writer);
writer.WriteAttribute(Attr.library, Library);
}
protected override void SaveAttributes(XmlWriter w)
{
base.SaveAttributes(w);
w.WriteAttribute("numguards", NumGuards);
w.WriteAttribute("maxguards", MaxGuards);
w.WriteAttribute("respawnrate", RespawnRate);
}
public void WriteXml(XmlWriter writer)
{
// Write attibutes
writer.WriteAttribute(ATTR.max_variable_mods, MaxVariableMods);
writer.WriteAttribute(ATTR.max_neutral_losses, MaxNeutralLosses);
if (InternalStandardTypes.Count == 0)
{
writer.WriteAttribute(ATTR.internal_standard, IsotopeLabelType.NONE_NAME);
}
if (InternalStandardTypes.Count == 1)
{
var internalStandardType = InternalStandardTypes[0];
if (!ReferenceEquals(internalStandardType, IsotopeLabelType.heavy))
writer.WriteAttribute(ATTR.internal_standard, internalStandardType.Name);
}
else
{
foreach (var labelType in InternalStandardTypes)
{
writer.WriteStartElement(EL.internal_standard);
writer.WriteAttribute(ATTR.name, labelType.Name);
writer.WriteEndElement();
}
}
// Write child elements
if (StaticModifications.Count > 0)
writer.WriteElementList(EL.static_modifications, StaticModifications);
foreach (var heavyMods in GetHeavyModifications())
{
writer.WriteStartElement(EL.heavy_modifications);
if (!ReferenceEquals(heavyMods.LabelType, IsotopeLabelType.heavy))
writer.WriteAttribute(ATTR.isotope_label, heavyMods.LabelType);
writer.WriteElements(heavyMods.Modifications);
writer.WriteEndElement();
}
}
public void WriteXml(XmlWriter writer)
{
// Write attributes
writer.WriteAttribute(ATTR.pick, Pick);
if (RankId != null || _rankIdName != null)
{
// If libraries were never connected properly, then _rankIdName may still contain
// the rank ID.
writer.WriteAttribute(ATTR.rank_type, RankId != null ? RankId.Value : _rankIdName);
writer.WriteAttributeNullable(ATTR.peptide_count, PeptideCount);
}
writer.WriteAttribute(ATTR.document_library, HasDocumentLibrary);
// Write child elements
var libraries = (_libraries.Count > 0 || _disconnectedLibraries == null ?
_libraries : _disconnectedLibraries);
if (libraries.Count > 0)
{
// writer.WriteElements(_libraries, LIBRARY_HELPERS);
for (int i = 0; i < libraries.Count; i++)
{
// First make sure it's not the document library
var spec = (!ReferenceEquals(libraries, _disconnectedLibraries) ? _librarySpecs[i] : null);
if (spec == null || !spec.IsDocumentLibrary)
{
// If there is a library, write it. Otherwise, write the
// library spec.
var item = libraries[i];
if (item == null)
{
if (spec != null && !spec.IsDocumentLocal)
{
IXmlElementHelper<LibrarySpec> helper = XmlUtil.FindHelper(spec, LIBRARY_SPEC_HELPERS);
if (helper == null)
throw new InvalidOperationException(
Resources.
PeptideLibraries_WriteXml_Attempt_to_serialize_list_containing_invalid_type);
writer.WriteElement(helper.ElementNames[0], spec);
}
}
else
{
IXmlElementHelper<Library> helper = XmlUtil.FindHelper(item, LIBRARY_HELPERS);
if (helper == null)
throw new InvalidOperationException(
Resources.
PeptideLibraries_WriteXml_Attempt_to_serialize_list_containing_invalid_type);
writer.WriteElement(helper.ElementNames[0], item);
}
}
}
}
}
public void WriteXml(XmlWriter writer)
{
// Write tag attributes
writer.WriteAttribute(ATTR2.type, Type);
writer.WriteAttribute(ATTR2.weight, Weight);
}
public override void WriteXml(XmlWriter writer)
{
// Write tag attributes
base.WriteXml(writer);
if (IsFragment)
{
writer.WriteAttributeString(ATTR.cut, Fragment);
writer.WriteAttributeIfString(ATTR.no_cut, Restrict);
writer.WriteAttributeNullable(ATTR.sense, Terminus);
writer.WriteAttributeNullable(ATTR.min_length, MinFragmentLength);
}
else
{
writer.WriteAttributeIfString(ATTR.ion_formula, SettingsCustomIon.Formula);
// Masses are information only, if their is a formula, but Panorama may need these
writer.WriteAttribute(ATTR.mass_monoisotopic, SettingsCustomIon.MonoisotopicMass);
writer.WriteAttribute(ATTR.mass_average, SettingsCustomIon.AverageMass);
writer.WriteAttributeString(ATTR.charge, Charge.ToString(CultureInfo.InvariantCulture));
writer.WriteAttribute(ATTR.optional, IsOptional);
}
}
public override void WriteXml(XmlWriter writer)
{
// Write tag attributes
base.WriteXml(writer);
writer.WriteAttribute(ATTR.count_measured, SpectrumCount);
}
public override void WriteXml(XmlWriter writer)
{
// Write tag attributes
base.WriteXml(writer);
writer.WriteAttribute(ATTR.revision, Revision);
}
public override void WriteXml(XmlWriter writer)
{
// Write tag attributes
base.WriteXml(writer);
writer.WriteAttributeString(ATTR.regex, Regex);
writer.WriteAttribute(ATTR.include, IsIncludeMatch);
writer.WriteAttribute(ATTR.match_mod_sequence, IsMatchMod);
}
public override void WriteXml(XmlWriter writer)
{
base.WriteXml(writer);
writer.WriteAttributeIfString(ATTR.control_annotation, ControlAnnotation);
writer.WriteAttributeIfString(ATTR.control_value, ControlValue);
writer.WriteAttributeIfString(ATTR.case_value, CaseValue);
writer.WriteAttributeIfString(ATTR.identity_annotation, IdentityAnnotation);
writer.WriteAttribute(ATTR.avg_tech_replicates, AverageTechnicalReplicates, true);
writer.WriteAttribute(ATTR.sum_transitions, SumTransitions, true);
writer.WriteAttributeIfString(ATTR.normalization_method, NormalizationMethod.Name);
writer.WriteAttribute(ATTR.include_interaction_transitions, IncludeInteractionTransitions, false);
writer.WriteAttribute(ATTR.summarization_method, SummarizationMethod.Name);
writer.WriteAttribute(ATTR.confidence_level, ConfidenceLevelTimes100);
writer.WriteAttribute(ATTR.per_protein, PerProtein, false);
}
public void WriteXml(XmlWriter writer)
{
// Write this bool whether it is true or false, to allow its absence
// as a marker of needing default values.
writer.WriteAttribute(ATTR.use_measured_rts, UseMeasuredRTs, !UseMeasuredRTs);
writer.WriteAttributeNullable(ATTR.measured_rt_window, MeasuredRTWindow);
writer.WriteAttribute(ATTR.use_spectral_library_drift_times, UseLibraryDriftTimes, !UseLibraryDriftTimes);
writer.WriteAttributeNullable(ATTR.spectral_library_drift_times_resolving_power, LibraryDriftTimesResolvingPower);
// Write child elements
if (RetentionTime != null)
writer.WriteElement(RetentionTime);
if (DriftTimePredictor != null)
writer.WriteElement(DriftTimePredictor);
}
public void WriteXml(XmlWriter writer)
{
// Write tag attributes
writer.WriteAttributeIfString(ATTR.formula, Formula);
writer.WriteAttribute(ATTR.massdiff_monoisotopic, MonoisotopicMass);
writer.WriteAttribute(ATTR.massdiff_average, AverageMass);
writer.WriteAttribute(ATTR.inclusion, Inclusion, LossInclusion.Library);
}
public void WriteXml(XmlWriter writer)
{
// Write attributes
writer.WriteAttribute(ATTR.start, ExcludeNTermAAs);
writer.WriteAttribute(ATTR.min_length, MinPeptideLength);
writer.WriteAttribute(ATTR.max_length, MaxPeptideLength);
writer.WriteAttribute(ATTR.auto_select, AutoSelect);
// Write child elements
writer.WriteElementList(EL.peptide_exclusions, Exclusions);
}
public override void WriteXml(XmlWriter writer)
{
// Write tag attributes
base.WriteXml(writer);
writer.WriteAttributeIfString(ATTR.aminoacid, AAs);
writer.WriteAttributeNullable(ATTR.terminus, Terminus);
writer.WriteAttribute(ATTR.variable, IsVariable);
writer.WriteAttributeIfString(ATTR.formula, Formula);
writer.WriteAttribute(ATTR.label_13C, Label13C);
writer.WriteAttribute(ATTR.label_15N, Label15N);
writer.WriteAttribute(ATTR.label_18O, Label18O);
writer.WriteAttribute(ATTR.label_2H, Label2H);
writer.WriteAttribute(ATTR.relative_rt, RelativeRT, RelativeRT.Matching);
if (string.IsNullOrEmpty(Formula))
{
writer.WriteAttributeNullable(ATTR.massdiff_monoisotopic, MonoisotopicMass);
writer.WriteAttributeNullable(ATTR.massdiff_average, AverageMass);
}
if (!IsVariable)
writer.WriteAttribute(ATTR.explicit_decl, IsExplicit);
writer.WriteAttributeNullable(ATTR.unimod_id, UnimodId);
writer.WriteAttributeIfString(ATTR.short_name, ShortName);
if (Losses != null)
writer.WriteElements(Losses);
}
public override void WriteXml(XmlWriter writer)
{
base.WriteXml(writer);
foreach (var column in Columns)
{
writer.WriteStartElement(El.grid_column);
writer.WriteAttribute(Attr.name, column.Name);
writer.WriteAttribute(Attr.visible, column.Visible);
writer.WriteAttribute(Attr.width, column.Width);
writer.WriteEndElement();
}
}
protected override void SaveAttributes(XmlWriter w)
{
base.SaveAttributes(w);
w.WriteAttribute("target", Target);
}
public void WriteXml(XmlWriter writer)
{
if (Formula != null)
{
writer.WriteAttribute(ATTR.ion_formula, Formula);
writer.WriteAttributeNullable(ATTR.mass_average, AverageMass);
writer.WriteAttributeNullable(ATTR.mass_monoisotopic, MonoisotopicMass);
}
else
{
// Without a formula we can't rederive masses, so write at higher precision
writer.WriteAttributeNullableRoundTrip(ATTR.mass_average, AverageMass);
writer.WriteAttributeNullableRoundTrip(ATTR.mass_monoisotopic, MonoisotopicMass);
}
if (Name != null)
writer.WriteAttribute(ATTR.custom_ion_name, Name);
}
public override void WriteXml(XmlWriter writer)
{
base.WriteXml(writer);
writer.WriteAttribute(ATTR.database_path, DatabasePath);
}
public void WriteXml(XmlWriter writer)
{
// Write tag attributes
writer.WriteAttribute(ATTR.max_missed_cleavages, MaxMissedCleavages);
writer.WriteAttribute(ATTR.exclude_ragged_ends, ExcludeRaggedEnds);
}
public override void WriteXml(XmlWriter writer)
{
// Write tag attributes
base.WriteXml(writer);
writer.WriteAttribute(ATTR.peak_area, PeakArea);
}
public override void WriteXml(XmlWriter writer)
{
// Write tag attributes
base.WriteXml(writer);
// If not cleavage both directions, then write the enzyme out the old way
if (IsBothTerm)
{
writer.WriteAttributeString(ATTR.cut_c, CleavageC);
writer.WriteAttributeString(ATTR.no_cut_c, RestrictC);
writer.WriteAttributeString(ATTR.cut_n, CleavageN);
writer.WriteAttributeString(ATTR.no_cut_n, RestrictN);
}
else if (IsCTerm)
{
writer.WriteAttributeString(ATTR.cut, CleavageC);
writer.WriteAttributeString(ATTR.no_cut, RestrictC);
writer.WriteAttribute(ATTR.sense, SequenceTerminus.C);
}
else
{
writer.WriteAttributeString(ATTR.cut, CleavageN);
writer.WriteAttributeString(ATTR.no_cut, RestrictN);
writer.WriteAttribute(ATTR.sense, SequenceTerminus.N);
}
}
public override void WriteXml(XmlWriter writer)
{
writer.WriteAttribute(Attr.revision, RevisionIndex);
base.WriteXml(writer);
}
public void WriteXml(XmlWriter writer)
{
writer.WriteAttribute(ATTR.start, Start);
writer.WriteAttribute(ATTR.end, End);
writer.WriteAttributeNullable(ATTR.target, Target);
if (StartMargin != null)
{
if (EndMargin != null)
{
writer.WriteAttributeNullable(ATTR.margin_left, StartMargin);
writer.WriteAttributeNullable(ATTR.margin_right, EndMargin);
}
else
{
writer.WriteAttributeNullable(ATTR.margin, StartMargin);
}
}
writer.WriteAttributeNullable(ATTR.ce_range, CERange);
}