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);
// 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)
{
base.ReadXml(reader);
ControlAnnotation = reader.GetAttribute(ATTR.control_annotation);
ControlValue = reader.GetAttribute(ATTR.control_value);
CaseValue = reader.GetAttribute(ATTR.case_value);
IdentityAnnotation = reader.GetAttribute(ATTR.identity_annotation);
AverageTechnicalReplicates = reader.GetBoolAttribute(ATTR.avg_tech_replicates, true);
NormalizationMethod = NormalizationMethod.FromName(reader.GetAttribute(ATTR.normalization_method));
IncludeInteractionTransitions = reader.GetBoolAttribute(ATTR.include_interaction_transitions, false);
SummarizationMethod = SummarizationMethod.FromName(reader.GetAttribute(ATTR.summarization_method));
ConfidenceLevelTimes100 = reader.GetDoubleAttribute(ATTR.confidence_level, 95);
PerProtein = reader.GetBoolAttribute(ATTR.per_protein, false);
UseZeroForMissingPeaks = reader.GetBoolAttribute(ATTR.use_zero_for_missing_peaks, false);
QValueCutoff = reader.GetNullableDoubleAttribute(ATTR.q_value_cutoff);
var colorRows = new List <MatchRgbHexColor>();
reader.Read();
while (reader.IsStartElement(MatchRgbHexColor.XML_ROOT))
{
var row = new MatchRgbHexColor();
row.ReadXml(reader);
colorRows.Add(row);
}
if (colorRows.Any())
{
reader.Read();
}
ColorRows = ImmutableList <MatchRgbHexColor> .ValueOf(colorRows);
}
public override void ReadXml(XmlReader reader)
{
// Read tag attributes
base.ReadXml(reader);
PeakArea = reader.GetDoubleAttribute(ATTR.peak_area);
// Consume tag
reader.Read();
}
public static CircleShape Load(XmlReader reader)
{
CircleShape circle = new CircleShape();
circle.Position = ManeuveringBoard.ParseXmlPoint(reader.GetStringAttribute("position"));
circle.Radius = reader.GetDoubleAttribute("radius");
return(circle);
}
public static BearingObservation Load(XmlReader reader, Dictionary <Observation, string> observers)
{
BearingObservation shape = new BearingObservation();
LoadPositionalData(shape, reader);
shape.Bearing = reader.GetDoubleAttribute("bearing");
observers.Add(shape, reader.GetAttribute("observer"));
return(shape);
}
protected virtual void ReadAttributes(XmlReader reader)
{
Formula = reader.GetAttribute(ATTR.formula);
if (!string.IsNullOrEmpty(Formula))
{
Formula = BioMassCalc.AddH(Formula); // Update this old style formula to current by adding the hydrogen we formerly left out due to assuming protonation
}
else
{
Formula = reader.GetAttribute(ATTR.ion_formula);
}
if (string.IsNullOrEmpty(Formula))
{
AverageMass = reader.GetDoubleAttribute(ATTR.mass_average);
MonoisotopicMass = reader.GetDoubleAttribute(ATTR.mass_monoisotopic);
}
Validate();
}
public static new UnitShape Load(XmlReader reader, Dictionary <Observation, string> observers, Dictionary <string, UnitShape> unitsById)
{
UnitShape shape = new UnitShape();
shape.Name = reader.GetAttribute("name");
shape.Position = ManeuveringBoard.ParseXmlPoint(reader.GetStringAttribute("position"));
shape.Direction = reader.GetDoubleAttribute("course");
shape.Speed = reader.GetDoubleAttribute("speed");
shape.Type = Utility.ParseEnum <UnitShapeType>(reader.GetStringAttribute("type", "unknown"), true);
string id = reader.GetAttribute("id");
if (!string.IsNullOrEmpty(id))
{
unitsById.Add(id, shape);
}
if (!reader.IsEmptyElement)
{
reader.Read();
while (reader.NodeType == XmlNodeType.Element)
{
if (reader.LocalName == "tmaSolution")
{
shape.TMASolution = TMASolution.Load(reader);
}
else if (reader.LocalName == "children" && !reader.IsEmptyElement)
{
reader.Read(); // move to either the first child or the end element
while (reader.NodeType == XmlNodeType.Element)
{
shape.Children.Add(Shape.Load(reader, observers, unitsById));
}
reader.ReadEndElement();
}
else
{
throw new InvalidDataException("Expected element " + reader.LocalName);
}
}
}
return(shape);
}
public void ReadXml(XmlReader reader)
{
// Read tag attributes
Start = reader.GetDoubleAttribute(ATTR.start);
End = reader.GetDoubleAttribute(ATTR.end);
Target = reader.GetNullableDoubleAttribute(ATTR.target);
StartMargin = reader.GetNullableDoubleAttribute(ATTR.margin);
if (StartMargin == null)
{
StartMargin = reader.GetNullableDoubleAttribute(ATTR.margin_left);
EndMargin = reader.GetNullableDoubleAttribute(ATTR.margin_right);
}
CERange = reader.GetNullableDoubleAttribute(ATTR.ce_range);
// Consume tag
reader.Read();
DoValidate();
}
public TypedMass ReadMonoisotopicMass(XmlReader reader)
{
var mass = reader.GetNullableDoubleAttribute(ATTR.mass_monoisotopic); // Pre-3.62 we wrote out massH for custom ions but not for reporter ions
if (mass.HasValue)
{
return(new TypedMass(mass.Value, (this is SettingsCustomIon) ? MassType.Monoisotopic : MassType.MonoisotopicMassH));
}
return(new TypedMass(reader.GetDoubleAttribute(ATTR.neutral_mass_monoisotopic), MassType.Monoisotopic));
}
public void ReadXml(XmlReader reader)
{
// Read tag attributes
Type = reader.GetTypeAttribute(ATTR2.type);
Weight = reader.GetDoubleAttribute(ATTR2.weight);
// Consume tag
reader.Read();
Validate();
}
public override void ReadXml(XmlReader reader)
{
base.ReadXml(reader);
ControlAnnotation = reader.GetAttribute(ATTR.control_annotation);
ControlValue = reader.GetAttribute(ATTR.control_value);
CaseValue = reader.GetAttribute(ATTR.case_value);
IdentityAnnotation = reader.GetAttribute(ATTR.identity_annotation);
AverageTechnicalReplicates = reader.GetBoolAttribute(ATTR.avg_tech_replicates, true);
SumTransitions = reader.GetBoolAttribute(ATTR.sum_transitions, true);
NormalizationMethod = NormalizationMethod.FromName(reader.GetAttribute(ATTR.normalization_method));
IncludeInteractionTransitions = reader.GetBoolAttribute(ATTR.include_interaction_transitions, false);
SummarizationMethod = SummarizationMethod.FromName(reader.GetAttribute(ATTR.summarization_method));
ConfidenceLevelTimes100 = reader.GetDoubleAttribute(ATTR.confidence_level, 95);
PerProtein = reader.GetBoolAttribute(ATTR.per_protein, false);
reader.Read();
}
public void ReadXml(XmlReader reader)
{
LogIndex = Interlocked.Increment(ref _logIndexCounter);
FormatVersion = new DocumentFormat(reader.GetDoubleAttribute(ATTR.format_version));
var time = DateTime.Parse(reader.GetAttribute(ATTR.time_stamp), CultureInfo.InvariantCulture);
TimeStamp = DateTime.SpecifyKind(time, DateTimeKind.Utc).ToLocalTime();
User = reader.GetAttribute(ATTR.user);
InsertUndoRedoIntoAllInfo = reader.GetBoolAttribute(ATTR.insert_undo_redo);
var countType = reader.GetAttribute(ATTR.count_type);
if (countType == null)
{
CountEntryType = null;
}
else
{
CountEntryType = (MessageType)Enum.Parse(typeof(MessageType), countType);
}
reader.ReadStartElement();
Reason = reader.IsStartElement(EL.reason) ? reader.ReadElementString() : string.Empty;
ExtraInfo = reader.IsStartElement(EL.extra_info) ? reader.ReadElementString().UnescapeNonPrintableChars() : string.Empty;
UndoRedo = reader.DeserializeElement <LogMessage>();
Summary = reader.DeserializeElement <LogMessage>();
var list = new List <LogMessage>();
while (reader.IsStartElement(EL.message))
{
list.Add(reader.DeserializeElement <LogMessage>());
}
AllInfo = list;
reader.ReadEndElement();
}
/// <summary>
/// Reads in an engine.xml file and turns it into a CaptionList, SpeakerSet and engine
/// Settings.
/// </summary>
/// <param name="path">The Path to the engine.xml file.</param>
/// <returns>A 3-Tuple containing a CaptionList, a SpeakerSet, and a Settings
/// object in that specific order.</returns>
public static Tuple <List <Caption>, Dictionary <string, Speaker>, SettingsXml> ParseEngineXml(string path)
{
var captionList = new List <Caption>();
var speakerSet = new Dictionary <string, Speaker>();
var settings = new SettingsXml();
XmlReaderSettings readerSettings = new XmlReaderSettings
{
IgnoreWhitespace = true,
IgnoreComments = true
};
using (XmlReader r = XmlReader.Create(path, readerSettings))
{
while (r.Read())
{
//Look for start elements only.
if (!r.IsStartElement())
{
continue;
}
// Get element name and switch on it.
switch (r.Name)
{
case XmlElements.Enact: break;
case XmlElements.Settings:
r.Read();
r.AssertNode(XmlElements.Meta);
settings.Base = r.GetNonNullAttribute(XmlAttributes.Base);
settings.Spacing = r.GetNonNullAttribute(XmlAttributes.WordSpacing);
settings.SeparateEmotionWords = r.GetNonNullAttribute(XmlAttributes.SeparateEmotionWords);
r.Read();
r.AssertNode(XmlElements.Playback);
settings.Playback.AutoPlay = r.GetBoolAttribute(XmlAttributes.AutoPlay);
settings.Playback.AutoRewind = r.GetBoolAttribute(XmlAttributes.AutoRewind);
settings.Playback.Seek = r.GetNonNullAttribute(XmlAttributes.Seek);
settings.Playback.AutoSize = r.GetBoolAttribute(XmlAttributes.AutoSize);
settings.Playback.Scale = r.GetIntAttribute(XmlAttributes.Scale);
settings.Playback.Volume = r.GetIntAttribute(XmlAttributes.Volume);
settings.Playback.ShowCaptions = r.GetBoolAttribute(XmlAttributes.ShowCaptions);
r.Read();
r.AssertNode(XmlElements.Skin);
settings.Skin.Source = r.GetNonNullAttribute(XmlAttributes.Source);
settings.Skin.AutoHide = r.GetBoolAttribute(XmlAttributes.AutoHide);
settings.Skin.FadeTime = r.GetIntAttribute(XmlAttributes.FadeTime);
settings.Skin.BackGroundAlpha = r.GetIntAttribute(XmlAttributes.BackgroundAlpha);
settings.Skin.BackgroundColour = r.GetNonNullAttribute(XmlAttributes.BackgroundColour);
r.Read();
r.AssertNode(XmlElements.Video);
settings.VideoSource = r.GetNonNullAttribute(XmlAttributes.Source);
r.Read();
r.AssertNode(XmlElements.Emotions);
r.Read();
r.AssertNode(XmlElements.Happy);
settings.Happy.Fps = r.GetNonNullAttribute(XmlAttributes.FPS);
settings.Happy.Duration = r.GetNonNullAttribute(XmlAttributes.Duration);
settings.Happy.AlphaBegin = r.GetNonNullAttribute(XmlAttributes.AlphaBegin);
settings.Happy.AlphaFinish = r.GetNonNullAttribute(XmlAttributes.AlphaFinish);
settings.Happy.ScaleBegin = r.GetNonNullAttribute(XmlAttributes.ScaleBegin);
settings.Happy.ScaleFinish = r.GetNonNullAttribute(XmlAttributes.ScaleFinish);
settings.Happy.YFinish = r.GetNonNullAttribute(XmlAttributes.YFinish);
r.Read();
r.AssertNode(XmlElements.Sad);
settings.Sad.Fps = r.GetNonNullAttribute(XmlAttributes.FPS);
settings.Sad.Duration = r.GetNonNullAttribute(XmlAttributes.Duration);
settings.Sad.AlphaBegin = r.GetNonNullAttribute(XmlAttributes.AlphaBegin);
settings.Sad.AlphaFinish = r.GetNonNullAttribute(XmlAttributes.AlphaFinish);
settings.Sad.ScaleBegin = r.GetNonNullAttribute(XmlAttributes.ScaleBegin);
settings.Sad.ScaleFinish = r.GetNonNullAttribute(XmlAttributes.ScaleFinish);
settings.Sad.YFinish = r.GetNonNullAttribute(XmlAttributes.YFinish);
r.Read();
r.AssertNode(XmlElements.Fear);
settings.Fear.Fps = r.GetNonNullAttribute(XmlAttributes.FPS);
settings.Fear.Duration = r.GetNonNullAttribute(XmlAttributes.Duration);
settings.Fear.ScaleBegin = r.GetNonNullAttribute(XmlAttributes.ScaleBegin);
settings.Fear.ScaleFinish = r.GetNonNullAttribute(XmlAttributes.ScaleFinish);
settings.Fear.VibrateX = r.GetNonNullAttribute(XmlAttributes.VibrateX);
settings.Fear.VibrateY = r.GetNonNullAttribute(XmlAttributes.VibrateY);
r.Read();
r.AssertNode(XmlElements.Anger);
settings.Anger.Fps = r.GetNonNullAttribute(XmlAttributes.FPS);
settings.Anger.Duration = r.GetNonNullAttribute(XmlAttributes.Duration);
settings.Anger.ScaleBegin = r.GetNonNullAttribute(XmlAttributes.ScaleBegin);
settings.Anger.ScaleFinish = r.GetNonNullAttribute(XmlAttributes.ScaleFinish);
settings.Anger.VibrateX = r.GetNonNullAttribute(XmlAttributes.VibrateX);
settings.Anger.VibrateY = r.GetNonNullAttribute(XmlAttributes.VibrateY);
break;
case XmlElements.Speakers: break; //Do Nothing
case XmlElements.Speaker:
r.AssertNode(XmlElements.Speaker);
string name = r.GetNonNullAttribute(XmlAttributes.Name);
Speaker s = new Speaker(name);
r.Read();
r.AssertNode(XmlElements.Background);
//Create background colour based on xml paramaters
bool visible = r.GetBoolAttribute(XmlAttributes.Visible);
double alphaD = r.GetDoubleAttribute(XmlAttributes.Alpha);
int colourCode = r.GetHexAttribute(XmlAttributes.Colour);
int alpha = (int)((visible) ? alphaD * 0xFF : 0x00);
// Bitshift alpha to the most significant byte of the integer
s.Font.BackgroundColour = Color.FromArgb(alpha << 24 | colourCode);
r.Read();
r.AssertNode(XmlElements.Font);
s.Font.Family = r.GetNonNullAttribute(XmlAttributes.Name);
s.Font.Size = r.GetIntAttribute(XmlAttributes.Size);
s.Font.ForegroundColour = Color.FromArgb(SpeakerFont.ForegroundAlphaValue << 24
| r.GetHexAttribute(XmlAttributes.Colour));
s.Font.Bold = r.GetIntAttribute(XmlAttributes.Bold);
r.ReadStartElement(XmlElements.Font);
//Add to speakerSet
speakerSet[s.Name] = s;
break;
case XmlElements.Captions: break; //Do Nothing
case XmlElements.Caption:
r.AssertNode(XmlElements.Caption);
Caption c = new Caption
{
Begin = r.GetNonNullAttribute(XmlAttributes.Begin),
End = r.GetNonNullAttribute(XmlAttributes.End),
Speaker = speakerSet[r.GetNonNullAttribute(XmlAttributes.Speaker)],
Location = (ScreenLocation)r.GetIntAttribute(XmlAttributes.Location),
Alignment = (Alignment)r.GetIntAttribute(XmlAttributes.Align)
};
List <CaptionWord> wordList = new List <CaptionWord>();
while (r.Read())
{
//If the Node is an end element, then the reader has parsed
//through all of this caption's words.
if (r.NodeType == XmlNodeType.EndElement && r.Name.Equals(XmlElements.Caption))
{
break;
}
if (r.NodeType == XmlNodeType.Element && r.Name.Equals(XmlElements.Word))
{
r.AssertNode(XmlElements.Word); //Doublecheck, it's the only way to be sure.
Emotion e = (Emotion)r.GetIntAttribute(XmlAttributes.Emotion);
Intensity i = (Intensity)r.GetIntAttribute(XmlAttributes.Intensity);
//Get word from node and add it to the list
CaptionWord word = new CaptionWord(e, i, r.ReadString(), 0);
wordList.Add(word);
}
}
c.Words.SetWordList(wordList);
captionList.Add(c);
break;
default: throw new ArgumentException("Value '" + r.Name + "' is not a valid node", r.Name);
}
}//Enact
}
return(Tuple.Create(captionList, speakerSet, settings));
}
public void ReadXml(XmlReader reader)
{
// Read tag attributes
Start = reader.GetDoubleAttribute(ATTR.start);
End = reader.GetDoubleAttribute(ATTR.end);
Target = reader.GetNullableDoubleAttribute(ATTR.target);
StartMargin = reader.GetNullableDoubleAttribute(ATTR.margin);
if (StartMargin == null)
{
StartMargin = reader.GetNullableDoubleAttribute(ATTR.margin_left);
EndMargin = reader.GetNullableDoubleAttribute(ATTR.margin_right);
}
CERange = reader.GetNullableDoubleAttribute(ATTR.ce_range);
// Consume tag
reader.Read();
DoValidate();
}
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();
}
protected virtual void ReadAttributes(XmlReader reader)
{
Formula = reader.GetAttribute(ATTR.formula);
if (!string.IsNullOrEmpty(Formula))
{
Formula = BioMassCalc.AddH(Formula); // Update this old style formula to current by adding the hydrogen we formerly left out due to assuming protonation
}
else
{
Formula = reader.GetAttribute(ATTR.ion_formula);
}
if (string.IsNullOrEmpty(Formula))
{
AverageMass = reader.GetDoubleAttribute(ATTR.mass_average);
MonoisotopicMass = reader.GetDoubleAttribute(ATTR.mass_monoisotopic);
}
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 static double GetDoubleAttribute(this XmlReader reader, string name)
{
return(reader.GetDoubleAttribute(name, 0.0));
}
public void ReadXml(XmlReader reader)
{
// Read tag attributes
Type = reader.GetTypeAttribute(ATTR2.type);
Weight = reader.GetDoubleAttribute(ATTR2.weight);
// Consume tag
reader.Read();
Validate();
}
