public PeptideLabelRatio(IsotopeLabelType labelType, IsotopeLabelType standardType,
RatioValue ratio) : this()
{
LabelType = labelType;
StandardType = standardType;
Ratio = ratio;
}
public static float? GetRatio(RatioValue ratioValue)
{
return ratioValue == null ? (float?) null : ratioValue.Ratio;
}
protected bool Equals(RatioValue other)
{
return Ratio.Equals(other.Ratio) && StdDev.Equals(other.StdDev) && DotProduct.Equals(other.DotProduct);
}
private IList<PeptideLabelRatio> AddPeptideRatio(IList<PeptideLabelRatio> listRatios, int i,
IsotopeLabelType labelType, IsotopeLabelType standardType, RatioValue ratio)
{
if (_emptyPeptideRatios == null)
{
listRatios.Add(new PeptideLabelRatio(labelType, standardType, ratio));
}
else if (ratio != null)
{
if (listRatios == null)
listRatios = _emptyPeptideRatios.ToArray();
listRatios[i] = new PeptideLabelRatio(labelType, standardType, ratio);
}
return listRatios;
}
public static float? GetDotProduct(RatioValue ratioValue)
{
return ratioValue == null ? (float?) null : ratioValue.DotProduct;
}
public IList<TransitionGroupChromInfo> UpdateTransitonGroupRatios(TransitionGroupDocNode nodeGroup,
IList<TransitionGroupChromInfo> listInfo,
bool isMatching)
{
if (Calculators.Count == 0 || listInfo == null)
return null;
var listInfoNew = new List<TransitionGroupChromInfo>();
var standardTypes = Settings.PeptideSettings.Modifications.RatioInternalStandardTypes;
foreach (var info in listInfo)
{
PeptideChromInfoCalculator calc;
if (!Calculators.TryGetValue(info.FileIndex, out calc))
Assume.Fail(); // Should never happen
else
{
var infoNew = info;
var labelType = nodeGroup.TransitionGroup.LabelType;
int count = standardTypes.Count;
if (calc.HasGlobalArea)
count++;
var ratios = new RatioValue[count];
for (int i = 0; i < standardTypes.Count; i++)
{
ratios[i] = calc.CalcTransitionGroupRatio(nodeGroup, labelType, standardTypes[i]);
}
if (calc.HasGlobalArea)
ratios[count - 1] = calc.CalcTransitionGroupGlobalRatio(nodeGroup, labelType);
if (!ArrayUtil.EqualsDeep(ratios, info.Ratios))
infoNew = infoNew.ChangeRatios(ratios);
if (isMatching && calc.IsSetMatching && !infoNew.IsUserSetMatched)
infoNew = infoNew.ChangeUserSet(UserSet.MATCHED);
listInfoNew.Add(infoNew);
}
}
if (ArrayUtil.ReferencesEqual(listInfo, listInfoNew))
return listInfo;
return listInfoNew;
}
protected bool Equals(RatioValue other)
{
return(Ratio.Equals(other.Ratio) && StdDev.Equals(other.StdDev) && DotProduct.Equals(other.DotProduct));
}
public static float?GetDotProduct(RatioValue ratioValue)
{
return(ratioValue == null ? (float?)null : ratioValue.DotProduct);
}
public static float?GetRatio(RatioValue ratioValue)
{
return(ratioValue == null ? (float?)null : ratioValue.Ratio);
}
public RatioValue GetTransitionGroupRatioValue(NormalizationMethod.RatioToLabel ratioToLabel,
PeptideDocNode peptideDocNode,
TransitionGroupDocNode transitionGroupDocNode, TransitionGroupChromInfo transitionGroupChromInfo)
{
if (peptideDocNode == null || transitionGroupChromInfo == null)
{
return(null);
}
if (transitionGroupDocNode.LabelType.Name == ratioToLabel.IsotopeLabelTypeName)
{
return(null);
}
var otherTransitionGroup =
FindMatchingTransitionGroup(ratioToLabel, peptideDocNode, transitionGroupDocNode);
if (otherTransitionGroup == null)
{
return(null);
}
var numerators = new List <double>();
var denominators = new List <double>();
if (SimpleRatios)
{
foreach (var tran in transitionGroupDocNode.Transitions.Where(tran =>
tran.IsQuantitative(Document.Settings)))
{
var chromInfo = FindMatchingTransitionChromInfo(transitionGroupChromInfo.FileId,
transitionGroupChromInfo.OptimizationStep, tran);
if (chromInfo != null)
{
numerators.Add(chromInfo.Area);
}
}
foreach (var tran in otherTransitionGroup.Transitions.Where(tran =>
tran.IsQuantitative(Document.Settings)))
{
var chromInfo = FindMatchingTransitionChromInfo(transitionGroupChromInfo.FileId,
transitionGroupChromInfo.OptimizationStep, tran);
if (chromInfo != null)
{
denominators.Add(chromInfo.Area);
}
}
if (numerators.Count == 0 || denominators.Count == 0)
{
return(null);
}
return(RatioValue.ValueOf(numerators.Sum() / denominators.Sum()));
}
var transitionMap = GetTransitionMap(otherTransitionGroup);
foreach (var transition in transitionGroupDocNode.Transitions)
{
if (!transition.IsQuantitative(Document.Settings))
{
continue;
}
var targetKey = new PeptideDocNode.TransitionKey(transitionGroupDocNode, new TransitionLossKey(transitionGroupDocNode, transition, transition.Losses), otherTransitionGroup.LabelType);
if (!transitionMap.TryGetValue(
targetKey,
out TransitionDocNode otherTransition))
{
continue;
}
if (!otherTransition.IsQuantitative(Document.Settings))
{
continue;
}
var transitionChromInfo = FindMatchingTransitionChromInfo(transitionGroupChromInfo.FileId,
transitionGroupChromInfo.OptimizationStep, transition);
var otherTransitionChromInfo = FindMatchingTransitionChromInfo(transitionGroupChromInfo.FileId,
transitionGroupChromInfo.OptimizationStep, otherTransition);
if (transitionChromInfo == null || transitionChromInfo.IsEmpty || otherTransitionChromInfo == null || otherTransitionChromInfo.IsEmpty)
{
continue;
}
numerators.Add(transitionChromInfo.Area);
denominators.Add(otherTransitionChromInfo.Area);
}
return(RatioValue.Calculate(numerators, denominators));
}
