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);
}
private bool Equals(NormalizationMethod other)
{
if (null == IsotopeLabelTypeName)
{
return(ReferenceEquals(this, other));
}
return(Equals(IsotopeLabelTypeName, other.IsotopeLabelTypeName));
}
public static bool Matches(NormalizationMethod normalizationMethod, IsotopeLabelType isotopeLabelType)
{
if (isotopeLabelType == null)
{
return(false);
}
RatioToLabel ratioToLabel = normalizationMethod as RatioToLabel;
return(ratioToLabel != null && Equals(ratioToLabel.Name, isotopeLabelType.Name));
}
private bool Equals(NormalizationMethod other)
{
if (null == other)
{
return(false);
}
if (ReferenceEquals(this, other))
{
return(true);
}
return(Name.Equals(other.Name));
}
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 override int GetHashCode()
{
unchecked
{
int hashCode = base.GetHashCode();
hashCode = (hashCode * 397) ^ (ControlAnnotation != null ? ControlAnnotation.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (ControlValue != null ? ControlValue.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CaseValue != null ? CaseValue.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (IdentityAnnotation != null ? IdentityAnnotation.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ AverageTechnicalReplicates.GetHashCode();
hashCode = (hashCode * 397) ^ SumTransitions.GetHashCode();
hashCode = (hashCode * 397) ^ NormalizationMethod.GetHashCode();
hashCode = (hashCode * 397) ^ IncludeInteractionTransitions.GetHashCode();
hashCode = (hashCode * 397) ^ SummarizationMethod.GetHashCode();
hashCode = (hashCode * 397) ^ ConfidenceLevel.GetHashCode();
hashCode = (hashCode * 397) ^ PerProtein.GetHashCode();
return(hashCode);
}
}
public override int GetHashCode()
{
unchecked
{
int hashCode = base.GetHashCode();
hashCode = (hashCode * 397) ^ (ControlAnnotation != null ? ControlAnnotation.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (ControlValue != null ? ControlValue.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (CaseValue != null ? CaseValue.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (IdentityAnnotation != null ? IdentityAnnotation.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ AverageTechnicalReplicates.GetHashCode();
hashCode = (hashCode * 397) ^ (NormalizationMethod != null ? NormalizationMethod.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ IncludeInteractionTransitions.GetHashCode();
hashCode = (hashCode * 397) ^ (SummarizationMethod != null ? SummarizationMethod.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ ConfidenceLevelTimes100.GetHashCode();
hashCode = (hashCode * 397) ^ PerProtein.GetHashCode();
hashCode = (hashCode * 397) ^ UseZeroForMissingPeaks.GetHashCode();
hashCode = (hashCode * 397) ^ QValueCutoff.GetHashCode();
hashCode = (hashCode * 397) ^ (ColorRows != null ? ColorRows.GetHashCode() : 0);
return(hashCode);
}
}
public static double? SumQuantities(IEnumerable<Quantity> quantities, NormalizationMethod normalizationMethod)
{
double numerator = 0;
double denominator = 0;
int count = 0;
foreach (var quantity in quantities)
{
numerator += quantity.Intensity;
denominator += quantity.Denominator;
count++;
}
if (count == 0)
{
return null;
}
if (!string.IsNullOrEmpty(normalizationMethod.IsotopeLabelTypeName))
{
return numerator/denominator;
}
return numerator/denominator*count;
}
public static double?SumQuantities(IEnumerable <Quantity> quantities, NormalizationMethod normalizationMethod, bool simpleRatios)
{
double numerator = 0;
double denominator = 0;
int count = 0;
foreach (var quantity in quantities)
{
numerator += quantity.Intensity;
denominator += quantity.Denominator;
count++;
}
if (count == 0)
{
return(null);
}
if (!simpleRatios && normalizationMethod is NormalizationMethod.RatioToLabel)
{
return(numerator / denominator);
}
return(numerator / denominator * count);
}
public static double?SumQuantities(IEnumerable <Quantity> quantities, NormalizationMethod normalizationMethod)
{
double numerator = 0;
double denominator = 0;
int count = 0;
foreach (var quantity in quantities)
{
numerator += quantity.Intensity;
denominator += quantity.Denominator;
count++;
}
if (count == 0)
{
return(null);
}
if (!string.IsNullOrEmpty(normalizationMethod.IsotopeLabelTypeName))
{
return(numerator / denominator);
}
return(numerator / denominator * count);
}
private Quantity GetTransitionQuantity(
SrmSettings srmSettings,
IDictionary <PeptideDocNode.TransitionKey, TransitionChromInfo> peptideStandards,
NormalizationMethod normalizationMethod,
int replicateIndex,
TransitionGroupDocNode transitionGroup, TransitionDocNode transition,
bool treatMissingAsZero)
{
if (null == transition.Results)
{
return(null);
}
if (replicateIndex >= transition.Results.Count)
{
return(null);
}
var chromInfos = transition.Results[replicateIndex];
if (chromInfos.IsEmpty)
{
return(null);
}
var chromInfo = GetTransitionChromInfo(transition, replicateIndex);
if (null == chromInfo)
{
return(null);
}
double?normalizedArea = GetArea(treatMissingAsZero, QValueCutoff, IncludeTruncatedPeaks, transitionGroup, transition, replicateIndex, chromInfo);
if (!normalizedArea.HasValue)
{
return(null);
}
double denominator = 1.0;
if (null != peptideStandards)
{
if (QuantificationSettings.SimpleRatios)
{
if (peptideStandards.Count == 0)
{
return(null);
}
denominator = peptideStandards.Values.Sum(value => value.Area);
}
else
{
TransitionChromInfo chromInfoStandard;
if (!peptideStandards.TryGetValue(GetRatioTransitionKey(transitionGroup, transition), out chromInfoStandard))
{
return(null);
}
else
{
denominator = chromInfoStandard.Area;
}
}
}
else
{
if (chromInfo.IsTruncated.GetValueOrDefault())
{
return(null);
}
if (Equals(normalizationMethod, NormalizationMethod.GLOBAL_STANDARDS))
{
var fileInfo = srmSettings.MeasuredResults.Chromatograms[replicateIndex]
.GetFileInfo(chromInfo.FileId);
if (fileInfo == null)
{
return(null);
}
denominator = srmSettings.CalcGlobalStandardArea(replicateIndex, fileInfo);
}
else if (normalizationMethod is NormalizationMethod.RatioToSurrogate)
{
denominator = ((NormalizationMethod.RatioToSurrogate)NormalizationMethod)
.GetStandardArea(srmSettings, replicateIndex, chromInfo.FileId);
}
else if (Equals(normalizationMethod, NormalizationMethod.EQUALIZE_MEDIANS))
{
var normalizationData = GetNormalizationData();
if (null == normalizationData)
{
throw new InvalidOperationException(string.Format(@"Normalization method '{0}' is not supported here.", NormalizationMethod));
}
double?medianAdjustment = normalizationData.GetMedian(chromInfo.FileId, transitionGroup.TransitionGroup.LabelType)
- normalizationData.GetMedianMedian(srmSettings.MeasuredResults.Chromatograms[replicateIndex].SampleType, transitionGroup.TransitionGroup.LabelType);
if (!medianAdjustment.HasValue)
{
return(null);
}
normalizedArea /= Math.Pow(2.0, medianAdjustment.Value);
}
else if (Equals(normalizationMethod, NormalizationMethod.TIC))
{
var factor = srmSettings.GetTicNormalizationDenominator(replicateIndex, chromInfo.FileId);
if (!factor.HasValue)
{
return(null);
}
denominator = factor.Value;
}
}
return(new Quantity(normalizedArea.Value, denominator));
}
public GroupComparisonDef ChangeNormalizationMethod(NormalizationMethod value)
{
return(ChangeProp(ImClone(this), im => im.NormalizationMethod = value));
}
private bool Equals(NormalizationMethod other)
{
if (null == IsotopeLabelTypeName)
{
return ReferenceEquals(this, other);
}
return Equals(IsotopeLabelTypeName, other.IsotopeLabelTypeName);
}
public GroupComparisonDef ChangeNormalizationMethod(NormalizationMethod value)
{
return ChangeProp(ImClone(this), im => im.NormalizationMethod = value);
}
public QuantificationSettings ChangeNormalizationMethod(NormalizationMethod normalizationMethod)
{
return ChangeProp(ImClone(this), im => im.NormalizationMethod = normalizationMethod);
}