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); }