private static int GetSurroundingAlignments(IList <PeakAlignment> alignList, PeakMatchData target, out PeakAlignment prev, out PeakAlignment next)
{
prev = next = null;
if (!alignList.Any())
{
return(0);
}
var insertPos = alignList.Select(align => align.ReferencePeak).ToList().BinarySearch(target, RT_COMPARER);
if (insertPos < 0)
{
insertPos = ~insertPos;
}
if (insertPos == 0)
{
next = alignList.First();
}
else if (insertPos != alignList.Count)
{
prev = alignList[insertPos - 1];
next = alignList[insertPos];
}
else
{
prev = alignList.Last();
}
return(insertPos);
}
private static PeakMatch MakePeakMatchBetween(float scale, PeakMatchData referenceTarget, PeakAlignment prev, PeakAlignment next)
{
if (prev == null && next == null)
{
return(null);
}
float startTime, endTime;
var range = scale * (referenceTarget.EndTime - referenceTarget.StartTime);
if (prev != null && next != null)
{
startTime = prev.AlignedPeak.RetentionTime + scale * (referenceTarget.StartTime - prev.ReferencePeak.RetentionTime);
endTime = next.AlignedPeak.RetentionTime - scale * (next.ReferencePeak.RetentionTime - referenceTarget.EndTime);
}
else if (next != null)
{
endTime = next.AlignedPeak.StartTime - scale * (next.ReferencePeak.StartTime - referenceTarget.EndTime);
startTime = endTime - range;
}
else
{
startTime = prev.AlignedPeak.EndTime + scale * (referenceTarget.StartTime - prev.ReferencePeak.EndTime);
endTime = startTime + range;
}
return(new PeakMatch(startTime + (referenceTarget.ShiftLeft * range), endTime + (referenceTarget.ShiftRight * range)));
}
public double GetMatchScore(PeakMatchData other)
{
var timeMin = Math.Min(MinTime, other.MinTime);
var timeMax = Math.Max(MaxTime, other.MaxTime);
return(SCORE_DOT_WEIGHT * Abundances.Dot(other.Abundances) +
SCORE_RT_WEIGHT * (1 - Math.Abs((RetentionTime - timeMin) - (other.RetentionTime - timeMin)) / (timeMax - timeMin)) +
SCORE_AREA_WEIGHT * (1 - Math.Abs(PercentArea - other.PercentArea)));
}
public PeakAlignment(PeakMatchData referencePeak, PeakMatchData alignedPeak)
{
ReferencePeak = referencePeak;
AlignedPeak = alignedPeak;
}
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 double GetMatchScore(PeakMatchData other)
{
var timeMin = Math.Min(MinTime, other.MinTime);
var timeMax = Math.Max(MaxTime, other.MaxTime);
return SCORE_DOT_WEIGHT * Abundances.Dot(other.Abundances) +
SCORE_RT_WEIGHT * (1 - Math.Abs((RetentionTime - timeMin) - (other.RetentionTime - timeMin)) / (timeMax - timeMin)) +
SCORE_AREA_WEIGHT * (1 - Math.Abs(PercentArea - other.PercentArea));
}
private static PeakMatch GetPeakMatch(SrmDocument doc, ChromatogramSet chromSet, IPathContainer fileInfo, TransitionGroupDocNode nodeTranGroup,
PeakMatchData referenceTarget, IEnumerable <PeakMatchData> referenceMatchData)
{
if (referenceTarget == null)
{
return(new PeakMatch(0, 0));
}
var mzMatchTolerance = (float)doc.Settings.TransitionSettings.Instrument.MzMatchTolerance;
ChromatogramGroupInfo[] loadInfos;
if (!nodeTranGroup.HasResults || !doc.Settings.MeasuredResults.TryLoadChromatogram(chromSet, null, nodeTranGroup, mzMatchTolerance, true, out loadInfos))
{
return(null);
}
var chromGroupInfo = loadInfos.FirstOrDefault(info => Equals(info.FilePath, fileInfo.FilePath));
if (chromGroupInfo == null || chromGroupInfo.NumPeaks == 0 || !chromGroupInfo.TimeIntensitiesGroup.HasAnyPoints)
{
return(null);
}
var matchData = new List <PeakMatchData>();
double totalArea = chromGroupInfo.TransitionPointSets.Sum(chromInfo => chromInfo.Peaks.Sum(peak => peak.Area));
for (int i = 0; i < chromGroupInfo.NumPeaks; i++)
{
matchData.Add(new PeakMatchData(nodeTranGroup, chromGroupInfo, mzMatchTolerance, i, totalArea, chromSet.OptimizationFunction));
}
// TODO: Try to improve this. Align peaks in area descending order until peaks do not match
var alignments = new List <PeakAlignment>();
bool referenceAligned = false;
using (var referenceIter = referenceMatchData.OrderByDescending(d => d.PercentArea).GetEnumerator())
using (var curIter = matchData.OrderByDescending(d => d.PercentArea).GetEnumerator())
{
while (referenceIter.MoveNext() && curIter.MoveNext())
{
var alignAttempt = new PeakAlignment(referenceIter.Current, curIter.Current);
if (!TryInsertPeakAlignment(alignments, alignAttempt))
{
break;
}
if (referenceTarget == alignAttempt.ReferencePeak)
{
// Reference target aligned
referenceAligned = true;
matchData = new List <PeakMatchData> {
alignAttempt.AlignedPeak
};
break;
}
}
}
PeakMatch manualMatch = null;
if (!referenceAligned)
{
PeakAlignment prev, next;
GetSurroundingAlignments(alignments, referenceTarget, out prev, out next);
if (prev != null || next != null)
{
// At least one alignment occurred
var chromGroupMinTime = chromGroupInfo.TimeIntensitiesGroup.MinTime;
var chromGroupMaxTime = chromGroupInfo.TimeIntensitiesGroup.MaxTime;
float scale = (chromGroupMaxTime - chromGroupMinTime) / (referenceTarget.MaxTime - referenceTarget.MinTime);
manualMatch = MakePeakMatchBetween(scale, referenceTarget, prev, next);
if (chromGroupMinTime >= manualMatch.EndTime || manualMatch.StartTime >= chromGroupMaxTime)
{
manualMatch = null;
}
float curMinTime = prev == null ? chromGroupMinTime : prev.AlignedPeak.RetentionTime;
float curMaxTime = next == null ? chromGroupMaxTime : next.AlignedPeak.RetentionTime;
matchData = matchData.Where(d => curMinTime < d.RetentionTime && d.RetentionTime < curMaxTime).ToList();
}
}
PeakMatchData bestMatch = null;
double bestScore = double.MinValue;
foreach (var other in matchData)
{
var score = referenceTarget.GetMatchScore(other);
if (bestMatch == null || score > bestScore)
{
bestScore = score;
bestMatch = other;
}
}
// If no matching peak with high enough score was found, but there is a matching
// peak or some peak with a low score.
if (bestMatch == null || (!referenceAligned && bestScore < INTEGRATE_SCORE_THRESHOLD && manualMatch != null))
{
return(manualMatch);
}
if (referenceTarget.ShiftLeft == 0 && referenceTarget.ShiftRight == 0)
{
return(new PeakMatch(bestMatch.RetentionTime));
}
var range = bestMatch.EndTime - bestMatch.StartTime;
var startTime = bestMatch.StartTime + (referenceTarget.ShiftLeft * range);
var endTime = bestMatch.EndTime + (referenceTarget.ShiftRight * range);
return(startTime <= bestMatch.RetentionTime && bestMatch.RetentionTime <= endTime
? new PeakMatch(startTime, endTime)
: new PeakMatch(bestMatch.RetentionTime)); // If the shifted boundaries exclude the peak itself, don't change the boundaries
}
public PeakAlignment(PeakMatchData referencePeak, PeakMatchData alignedPeak)
{
ReferencePeak = referencePeak;
AlignedPeak = alignedPeak;
}
private static PeakMatch MakePeakMatchBetween(float scale, PeakMatchData referenceTarget, PeakAlignment prev, PeakAlignment next)
{
if (prev == null && next == null)
return null;
float startTime, endTime;
var range = scale * (referenceTarget.EndTime - referenceTarget.StartTime);
if (prev != null && next != null)
{
startTime = prev.AlignedPeak.RetentionTime + scale*(referenceTarget.StartTime - prev.ReferencePeak.RetentionTime);
endTime = next.AlignedPeak.RetentionTime - scale*(next.ReferencePeak.RetentionTime - referenceTarget.EndTime);
}
else if (next != null)
{
endTime = next.AlignedPeak.StartTime - scale*(next.ReferencePeak.StartTime - referenceTarget.EndTime);
startTime = endTime - range;
}
else
{
startTime = prev.AlignedPeak.EndTime + scale*(referenceTarget.StartTime - prev.ReferencePeak.EndTime);
endTime = startTime + range;
}
return new PeakMatch(startTime + (referenceTarget.ShiftLeft*range), endTime + (referenceTarget.ShiftRight*range));
}
private static int GetSurroundingAlignments(IList<PeakAlignment> alignList, PeakMatchData target, out PeakAlignment prev, out PeakAlignment next)
{
prev = next = null;
if (!alignList.Any())
return 0;
var insertPos = alignList.Select(align => align.ReferencePeak).ToList().BinarySearch(target, RT_COMPARER);
if (insertPos < 0)
insertPos = ~insertPos;
if (insertPos == 0)
{
next = alignList.First();
}
else if (insertPos != alignList.Count)
{
prev = alignList[insertPos - 1];
next = alignList[insertPos];
}
else
{
prev = alignList.Last();
}
return insertPos;
}
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();
}
private static PeakMatch GetPeakMatch(SrmDocument doc, ChromatogramSet chromSet, IPathContainer fileInfo, TransitionGroupDocNode nodeTranGroup,
PeakMatchData referenceTarget, IEnumerable<PeakMatchData> referenceMatchData)
{
if (referenceTarget == null)
return new PeakMatch(0, 0);
var mzMatchTolerance = (float) doc.Settings.TransitionSettings.Instrument.MzMatchTolerance;
ChromatogramGroupInfo[] loadInfos;
if (!nodeTranGroup.HasResults || !doc.Settings.MeasuredResults.TryLoadChromatogram(chromSet, null, nodeTranGroup, mzMatchTolerance, true, out loadInfos))
return null;
var chromGroupInfo = loadInfos.FirstOrDefault(info => Equals(info.FilePath, fileInfo.FilePath));
if (chromGroupInfo == null || chromGroupInfo.NumPeaks == 0 || !chromGroupInfo.Times.Any())
return null;
var matchData = new List<PeakMatchData>();
double totalArea = chromGroupInfo.TransitionPointSets.Sum(chromInfo => chromInfo.Peaks.Sum(peak => peak.Area));
for (int i = 0; i < chromGroupInfo.NumPeaks; i++)
matchData.Add(new PeakMatchData(nodeTranGroup, chromGroupInfo, mzMatchTolerance, i, totalArea));
// TODO: Try to improve this. Align peaks in area descending order until peaks do not match
var alignments = new List<PeakAlignment>();
bool referenceAligned = false;
var referenceIter = referenceMatchData.OrderByDescending(d => d.PercentArea).GetEnumerator();
var curIter = matchData.OrderByDescending(d => d.PercentArea).GetEnumerator();
while (referenceIter.MoveNext() && curIter.MoveNext())
{
var alignAttempt = new PeakAlignment(referenceIter.Current, curIter.Current);
if (!TryInsertPeakAlignment(alignments, alignAttempt))
break;
if (referenceTarget == alignAttempt.ReferencePeak)
{
// Reference target aligned
referenceAligned = true;
matchData = new List<PeakMatchData> {alignAttempt.AlignedPeak};
break;
}
}
PeakMatch manualMatch = null;
if (!referenceAligned)
{
PeakAlignment prev, next;
GetSurroundingAlignments(alignments, referenceTarget, out prev, out next);
if (prev != null || next != null)
{
// At least one alignment occurred
var chromGroupMinTime = chromGroupInfo.Times.First();
var chromGroupMaxTime = chromGroupInfo.Times.Last();
float scale = (chromGroupMaxTime - chromGroupMinTime)/(referenceTarget.MaxTime - referenceTarget.MinTime);
manualMatch = MakePeakMatchBetween(scale, referenceTarget, prev, next);
if (chromGroupMinTime >= manualMatch.EndTime || manualMatch.StartTime >= chromGroupMaxTime)
manualMatch = null;
float curMinTime = prev == null ? chromGroupMinTime : prev.AlignedPeak.RetentionTime;
float curMaxTime = next == null ? chromGroupMaxTime : next.AlignedPeak.RetentionTime;
matchData = matchData.Where(d => curMinTime < d.RetentionTime && d.RetentionTime < curMaxTime).ToList();
}
}
PeakMatchData bestMatch = null;
double bestScore = double.MinValue;
foreach (var other in matchData)
{
var score = referenceTarget.GetMatchScore(other);
if (bestMatch == null || score > bestScore)
{
bestScore = score;
bestMatch = other;
}
}
// If no matching peak with high enough score was found, but there is a matching
// peak or some peak with a low score.
if (bestMatch == null || (!referenceAligned && bestScore < INTEGRATE_SCORE_THRESHOLD && manualMatch != null))
return manualMatch;
if (referenceTarget.ShiftLeft == 0 && referenceTarget.ShiftRight == 0)
return new PeakMatch(bestMatch.RetentionTime);
var range = bestMatch.EndTime - bestMatch.StartTime;
var startTime = bestMatch.StartTime + (referenceTarget.ShiftLeft*range);
var endTime = bestMatch.EndTime + (referenceTarget.ShiftRight*range);
return startTime <= bestMatch.RetentionTime && bestMatch.RetentionTime <= endTime
? new PeakMatch(startTime, endTime)
: new PeakMatch(bestMatch.RetentionTime); // If the shifted boundaries exclude the peak itself, don't change the boundaries
}
