public double Dot(IonAbundances other)
{
var abundancesThis = new List <double>();
var abundancesOther = new List <double>();
foreach (var fragment in _abundances.Keys.Union(other._abundances.Keys))
{
abundancesThis.Add(_abundances.ContainsKey(fragment) ? _abundances[fragment] : 0);
abundancesOther.Add(other._abundances.ContainsKey(fragment) ? other._abundances[fragment] : 0);
}
var statisticsThis = new Statistics(abundancesThis);
var statisticsOther = new Statistics(abundancesOther);
return(statisticsThis.Angle(statisticsOther));
}
public PeakMatchData(TransitionGroupDocNode nodeTranGroup, ChromatogramGroupInfo chromGroupInfo,
float mzMatchTolerance, int peakIndex, double totalChromArea)
{
Abundances = new IonAbundances(nodeTranGroup, chromGroupInfo, mzMatchTolerance, peakIndex);
PercentArea = Abundances.Sum() / totalChromArea;
var peak = GetLargestPeak(nodeTranGroup, chromGroupInfo, peakIndex, mzMatchTolerance);
RetentionTime = peak.RetentionTime;
StartTime = peak.StartTime;
EndTime = peak.EndTime;
ShiftLeft = 0;
ShiftRight = 0;
MinTime = chromGroupInfo.Times.First();
MaxTime = chromGroupInfo.Times.Last();
}
public PeakMatchData(TransitionGroupDocNode nodeTranGroup, ChromatogramGroupInfo chromGroupInfo,
float mzMatchTolerance, int peakIndex, double totalChromArea,
OptimizableRegression regression)
{
Abundances = new IonAbundances(nodeTranGroup, chromGroupInfo, mzMatchTolerance, peakIndex, regression);
PercentArea = Abundances.Sum() / totalChromArea;
var peak = GetLargestPeak(nodeTranGroup, chromGroupInfo, peakIndex, mzMatchTolerance, regression);
RetentionTime = peak.RetentionTime;
StartTime = peak.StartTime;
EndTime = peak.EndTime;
ShiftLeft = 0;
ShiftRight = 0;
MinTime = chromGroupInfo.TimeIntensitiesGroup.MinTime;
MaxTime = chromGroupInfo.TimeIntensitiesGroup.MaxTime;
}
private static void GetReferenceData(SrmDocument doc, PeptideDocNode nodePep, TransitionGroupDocNode nodeTranGroup, int resultsIndex, ChromFileInfoId resultsFile,
out PeakMatchData referenceTarget, out PeakMatchData[] referenceMatchData, out DateTime?runTime)
{
referenceTarget = null;
referenceMatchData = new PeakMatchData[0];
runTime = null;
var referenceMatchDataList = new List <PeakMatchData>();
var mzMatchTolerance = (float)doc.Settings.TransitionSettings.Instrument.MzMatchTolerance;
if (!nodeTranGroup.HasResults || resultsIndex < 0 || resultsIndex >= nodeTranGroup.Results.Count)
{
return;
}
var tranGroupChromInfo = nodeTranGroup.GetChromInfo(resultsIndex, resultsFile);
if (tranGroupChromInfo == null)
{
return;
}
var chromSet = doc.Settings.MeasuredResults.Chromatograms[resultsIndex];
if (!doc.Settings.MeasuredResults.TryLoadChromatogram(chromSet, nodePep, nodeTranGroup, mzMatchTolerance, true, out var chromGroupInfos))
{
return;
}
var chromGroupInfo = chromGroupInfos.FirstOrDefault(info => Equals(chromSet.GetFileInfo(tranGroupChromInfo.FileId).FilePath, info.FilePath));
if (chromGroupInfo == null || chromGroupInfo.NumPeaks == 0 || !chromGroupInfo.TimeIntensitiesGroup.HasAnyPoints)
{
return;
}
runTime = chromGroupInfo.RunStartTime;
if (!tranGroupChromInfo.RetentionTime.HasValue || !tranGroupChromInfo.StartRetentionTime.HasValue || !tranGroupChromInfo.EndRetentionTime.HasValue)
{
return;
}
int peakIndex = -1;
foreach (var transition in chromGroupInfo.TransitionPointSets)
{
peakIndex = transition.IndexOfPeak(tranGroupChromInfo.RetentionTime.Value);
if (peakIndex != -1)
{
break;
}
}
// Get time information
float timeMin = chromGroupInfo.TimeIntensitiesGroup.MinTime;
float timeMax = chromGroupInfo.TimeIntensitiesGroup.MaxTime;
float totalArea = chromGroupInfo.TransitionPointSets.Sum(chromInfo => chromInfo.Peaks.Sum(peak => peak.Area));
for (int i = 0; i < chromGroupInfo.NumPeaks; i++)
{
referenceMatchDataList.Add(new PeakMatchData(nodeTranGroup, chromGroupInfo, mzMatchTolerance, i, totalArea, chromSet.OptimizationFunction));
}
// Get ion abundance information
var abundances = new IonAbundances();
foreach (var nodeTran in nodeTranGroup.Transitions)
{
var chromInfoCached = chromGroupInfo.GetTransitionInfo(nodeTran, mzMatchTolerance, chromSet.OptimizationFunction);
if (chromInfoCached == null)
{
continue;
}
var tranChromInfo = nodeTran.Results[resultsIndex].First(r => r.FileIndex == tranGroupChromInfo.FileIndex);
float area;
if (peakIndex != -1)
{
// A peak exists here
var cachedPeak = chromInfoCached.GetPeak(peakIndex);
area = cachedPeak.Area;
if (cachedPeak.RetentionTime.Equals(tranGroupChromInfo.RetentionTime.Value))
{
var range = cachedPeak.EndTime - cachedPeak.StartTime;
referenceMatchDataList[peakIndex].ShiftLeft = (tranChromInfo.StartRetentionTime - cachedPeak.StartTime) / range;
referenceMatchDataList[peakIndex].ShiftRight = (tranChromInfo.EndRetentionTime - cachedPeak.EndTime) / range;
}
}
else
{
area = tranChromInfo.Area;
}
abundances.Add(nodeTran, area);
}
referenceTarget = peakIndex != -1
? referenceMatchDataList[peakIndex]
: new PeakMatchData(abundances, abundances.Sum() / totalArea, tranGroupChromInfo.RetentionTime.Value,
tranGroupChromInfo.StartRetentionTime.Value, tranGroupChromInfo.EndRetentionTime.Value, timeMin, timeMax);
referenceMatchData = referenceMatchDataList.ToArray();
}
public PeakMatchData(TransitionGroupDocNode nodeTranGroup, ChromatogramGroupInfo chromGroupInfo,
float mzMatchTolerance, int peakIndex, double totalChromArea)
{
Abundances = new IonAbundances(nodeTranGroup, chromGroupInfo, mzMatchTolerance, peakIndex);
PercentArea = Abundances.Sum()/totalChromArea;
var peak = GetLargestPeak(nodeTranGroup, chromGroupInfo, peakIndex, mzMatchTolerance);
RetentionTime = peak.RetentionTime;
StartTime = peak.StartTime;
EndTime = peak.EndTime;
ShiftLeft = 0;
ShiftRight = 0;
MinTime = chromGroupInfo.Times.First();
MaxTime = chromGroupInfo.Times.Last();
}
public PeakMatchData(IonAbundances abundances, double percentArea,
float rt, float rtStart, float rtEnd, float rtMin, float rtMax)
{
Abundances = abundances;
PercentArea = percentArea;
RetentionTime = rt;
StartTime = rtStart;
EndTime = rtEnd;
ShiftLeft = 0;
ShiftRight = 0;
MinTime = rtMin;
MaxTime = rtMax;
}
public double Dot(IonAbundances other)
{
var abundancesThis = new List<double>();
var abundancesOther = new List<double>();
foreach (var fragment in _abundances.Keys.Union(other._abundances.Keys))
{
abundancesThis.Add(_abundances.ContainsKey(fragment) ? _abundances[fragment] : 0);
abundancesOther.Add(other._abundances.ContainsKey(fragment) ? other._abundances[fragment] : 0);
}
var statisticsThis = new Statistics(abundancesThis);
var statisticsOther = new Statistics(abundancesOther);
return statisticsThis.Angle(statisticsOther);
}
private static void GetReferenceData(SrmDocument doc, PeptideDocNode nodePep, TransitionGroupDocNode nodeTranGroup, int resultsIndex, int? resultsFile,
out PeakMatchData referenceTarget, out PeakMatchData[] referenceMatchData, out DateTime? runTime)
{
referenceTarget = null;
referenceMatchData = new PeakMatchData[0];
runTime = null;
var referenceMatchDataList = new List<PeakMatchData>();
var mzMatchTolerance = (float) doc.Settings.TransitionSettings.Instrument.MzMatchTolerance;
if (!nodeTranGroup.HasResults || resultsIndex < 0 || resultsIndex >= nodeTranGroup.Results.Count)
return;
var tranGroupChromInfo = nodeTranGroup.Results[resultsIndex][resultsFile ?? 0];
if (tranGroupChromInfo == null)
return;
var chromSet = doc.Settings.MeasuredResults.Chromatograms[resultsIndex];
ChromatogramGroupInfo[] chromGroupInfos;
if (!doc.Settings.MeasuredResults.TryLoadChromatogram(chromSet, nodePep, nodeTranGroup, mzMatchTolerance, true, out chromGroupInfos))
return;
var chromGroupInfo = chromGroupInfos.FirstOrDefault(info => Equals(chromSet.GetFileInfo(tranGroupChromInfo.FileId).FilePath, info.FilePath));
if (chromGroupInfo == null || chromGroupInfo.NumPeaks == 0 || !chromGroupInfo.Times.Any())
return;
runTime = chromGroupInfo.RunStartTime;
if (!tranGroupChromInfo.RetentionTime.HasValue || !tranGroupChromInfo.StartRetentionTime.HasValue || !tranGroupChromInfo.EndRetentionTime.HasValue)
return;
int peakIndex = -1;
foreach (var transition in chromGroupInfo.TransitionPointSets)
{
peakIndex = transition.IndexOfPeak(tranGroupChromInfo.RetentionTime.Value);
if (peakIndex != -1)
break;
}
// Get time information
float timeMin = chromGroupInfo.Times.First();
float timeMax = chromGroupInfo.Times.Last();
float totalArea = chromGroupInfo.TransitionPointSets.Sum(chromInfo => chromInfo.Peaks.Sum(peak => peak.Area));
for (int i = 0; i < chromGroupInfo.NumPeaks; i++)
referenceMatchDataList.Add(new PeakMatchData(nodeTranGroup, chromGroupInfo, mzMatchTolerance, i, totalArea));
// Get ion abundance information
var abundances = new IonAbundances();
foreach (var nodeTran in nodeTranGroup.Transitions)
{
var chromInfoCached = chromGroupInfo.GetTransitionInfo((float) nodeTran.Mz, mzMatchTolerance);
if (chromInfoCached == null)
continue;
var tranChromInfo = nodeTran.Results[resultsIndex].First(r => r.FileIndex == tranGroupChromInfo.FileIndex);
float area;
if (peakIndex != -1)
{
// A peak exists here
var cachedPeak = chromInfoCached.GetPeak(peakIndex);
area = cachedPeak.Area;
if (cachedPeak.RetentionTime.Equals(tranGroupChromInfo.RetentionTime.Value))
{
var range = cachedPeak.EndTime - cachedPeak.StartTime;
referenceMatchDataList[peakIndex].ShiftLeft = (tranChromInfo.StartRetentionTime - cachedPeak.StartTime)/range;
referenceMatchDataList[peakIndex].ShiftRight = (tranChromInfo.EndRetentionTime - cachedPeak.EndTime)/range;
}
}
else
{
area = tranChromInfo.Area;
}
abundances.Add(nodeTran, area);
}
referenceTarget = peakIndex != -1
? referenceMatchDataList[peakIndex]
: new PeakMatchData(abundances, abundances.Sum()/totalArea, tranGroupChromInfo.RetentionTime.Value,
tranGroupChromInfo.StartRetentionTime.Value, tranGroupChromInfo.EndRetentionTime.Value, timeMin, timeMax);
referenceMatchData = referenceMatchDataList.ToArray();
}
