public SpecificFragment(LipidClass lipidClass, LipidType lipidType, string fragmentDescription, FragmentationMode fragmentationMode, FragmentationType fragmentationType)
{
LipidClass = lipidClass;
LipidType = lipidType;
FragmentDescription = fragmentDescription;
FragmentationMode = fragmentationMode;
FragmentationType = fragmentationType;
}
private double ScoreSingleFragmentationTypeDissimilarity(
IEnumerable <MsMsSearchResult> searchResultList,
List <ScoreModelUnit> relatedScoreModelUnits,
FragmentationType fragmentationType,
double maxIntensity)
{
double fragmentationTypeScore = 0;
foreach (var result in searchResultList)
{
var fragment = result.TheoreticalPeak.Description;
double intensity = 0;
if (result.ObservedPeak != null)
{
intensity = Math.Log10(result.ObservedPeak.Intensity) / Math.Log10(maxIntensity);
}
var scoreUnits = relatedScoreModelUnits.Where(x => x.FragmentationType == fragmentationType && x.FragmentDescription.Equals(fragment));
var found = false;
foreach (var scoreUnit in scoreUnits)
{
double fragmentScore;
var inverseProbability = 1 - scoreUnit.Probability;
// Observed
if (!found && intensity <= scoreUnit.IntensityMax)
{
fragmentScore = Math.Log(inverseProbability / scoreUnit.Probability) - Math.Log(inverseProbability);
found = true;
}
// Not Observed
else
{
fragmentScore = -Math.Log(inverseProbability);
}
fragmentationTypeScore += fragmentScore;
}
}
return(fragmentationTypeScore);
}
public int CompareTo(ScoreModelUnit other)
{
if (!LipidClass.Equals(other.LipidClass))
{
return(LipidClass.CompareTo(other.LipidClass));
}
if (!LipidType.Equals(other.LipidType))
{
return(LipidType.CompareTo(other.LipidType));
}
if (!FragmentDescription.Equals(other.FragmentDescription))
{
return(String.Compare(FragmentDescription, other.FragmentDescription, StringComparison.Ordinal));
}
if (!FragmentationMode.Equals(other.FragmentationMode))
{
return(FragmentationMode.CompareTo(other.FragmentationMode));
}
if (!FragmentationType.Equals(other.FragmentationType))
{
return(FragmentationType.CompareTo(other.FragmentationType));
}
return(IntensityMax.CompareTo(other.IntensityMax));
}
public MsMsAnnotation(FragmentationType fragmentationType)
{
FragmentionType = fragmentationType;
}
