public RegressionWithOutliers RegressTimes(MsDataFile target, out IList <String> modifiedPeptideSequences)
{
var targetDict = target.GetRetentionTimesByModifiedSequence();
var myTimes = new List <double>();
var targetTimes = new List <double>();
modifiedPeptideSequences = new List <string>();
using (var myEnumerator = GetRetentionTimesByModifiedSequence().GetEnumerator())
{
using (var targetEnumerator = target.GetRetentionTimesByModifiedSequence().GetEnumerator())
{
bool bContinue = myEnumerator.MoveNext() && targetEnumerator.MoveNext();
while (bContinue)
{
int compare = targetDict.KeyComparer.Compare(myEnumerator.Current.Key, targetEnumerator.Current.Key);
if (compare == 0)
{
myTimes.Add(myEnumerator.Current.Value);
targetTimes.Add(targetEnumerator.Current.Value);
modifiedPeptideSequences.Add(myEnumerator.Current.Key);
bContinue = myEnumerator.MoveNext() && targetEnumerator.MoveNext();
}
else if (compare < 0)
{
bContinue = myEnumerator.MoveNext();
}
else
{
bContinue = targetEnumerator.MoveNext();
}
}
}
}
return(new RegressionWithOutliers(myTimes, targetTimes));
}
public RetentionTimeAlignment GetRetentionTimeAlignment(MsDataFile other)
{
var key = new RetentionTimeAlignments.AlignmentKey(Id, other.Id);
var alignmentValue = Workspace.RetentionTimeAlignments.GetAlignment(key);
if (null != alignmentValue)
{
return(alignmentValue);
}
RetentionTimeAlignment result;
IList <string> regressedPeptides;
var regressionWithOutliers = RegressTimes(other, out regressedPeptides);
var refined = regressionWithOutliers.Refine();
if (refined != null)
{
result = new RetentionTimeAlignment(refined.Slope, refined.Intercept);
}
else
{
result = RetentionTimeAlignment.Invalid;
}
Workspace.RetentionTimeAlignments.AddAlignment(key, result);
return(result);
}
private static KeyValuePair <double, double> DecideChromatogramStartEndTime(MsDataFile msDataFile, ILookup <long, double> psmTimesByDataFileId)
{
var workspace = msDataFile.Workspace;
var chromTimeAroundMs2Id = workspace.GetChromTimeAroundMs2Id();
var timesInThisFile = psmTimesByDataFileId[msDataFile.Id].ToArray();
if (timesInThisFile.Length > 0)
{
return(new KeyValuePair <double, double>(timesInThisFile.Min() - chromTimeAroundMs2Id,
timesInThisFile.Max() + chromTimeAroundMs2Id));
}
var alignedTimes = new List <double>();
foreach (var grouping in psmTimesByDataFileId)
{
MsDataFile otherFile;
if (!workspace.MsDataFiles.TryGetValue(grouping.Key, out otherFile))
{
continue;
}
var alignment = otherFile.GetRetentionTimeAlignment(msDataFile);
if (alignment.IsInvalid)
{
continue;
}
alignedTimes.Add(alignment.GetTargetTime(grouping.Min()));
alignedTimes.Add(alignment.GetTargetTime(grouping.Max()));
}
if (alignedTimes.Count > 0)
{
return(new KeyValuePair <double, double>(alignedTimes.Min() - chromTimeAroundMs2Id,
alignedTimes.Max() + chromTimeAroundMs2Id));
}
var extraTime = workspace.GetExtraChromTimeWithoutMs2Id();
var minTime = psmTimesByDataFileId.SelectMany(grouping => grouping).Min();
var maxTime = psmTimesByDataFileId.SelectMany(grouping => grouping).Max();
return(new KeyValuePair <double, double>(minTime - chromTimeAroundMs2Id - extraTime, maxTime + chromTimeAroundMs2Id + extraTime));
}
public bool IsRejected(MsDataFile msDataFile)
{
return(_rejectedMsDataFileIds.Contains(msDataFile.Id));
}
public void RejectMsDataFile(MsDataFile msDataFile)
{
_rejectedMsDataFileIds.Add(msDataFile.Id);
}
public static PeptideFileAnalysis EnsurePeptideFileAnalysis(PeptideAnalysis peptideAnalysis, MsDataFile msDataFile)
{
var workspace = peptideAnalysis.Workspace;
using (var session = workspace.OpenSession())
{
var criteria = session.CreateCriteria(typeof(DbPeptideFileAnalysis))
.Add(Restrictions.Eq("PeptideAnalysis", session.Load <DbPeptideAnalysis>(peptideAnalysis.Id)))
.Add(Restrictions.Eq("MsDataFile", session.Load <DbMsDataFile>(msDataFile.Id)));
var dbPeptideAnalysis = (DbPeptideFileAnalysis)criteria.UniqueResult();
if (dbPeptideAnalysis != null)
{
return(GetPeptideFileAnalysis(peptideAnalysis, dbPeptideAnalysis));
}
}
if (!msDataFile.HasTimes())
{
return(null);
}
using (var session = workspace.OpenWriteSession())
{
var dbPeptideAnalysis = session.Load <DbPeptideAnalysis>(peptideAnalysis.Id);
var psmTimesByDataFileId = dbPeptideAnalysis.Peptide.PsmTimesByDataFileId(session);
var dbPeptideFileAnalysis = CreatePeptideFileAnalysis(session, msDataFile, dbPeptideAnalysis, psmTimesByDataFileId);
if (dbPeptideFileAnalysis == null)
{
return(null);
}
session.BeginTransaction();
session.Save(dbPeptideFileAnalysis);
dbPeptideAnalysis.FileAnalysisCount++;
session.Update(dbPeptideAnalysis);
session.Save(new DbChangeLog(peptideAnalysis));
session.Transaction.Commit();
workspace.ChromatogramGenerator.SetRequeryPending();
workspace.DatabasePoller.LoadAndMergeChanges(null);
return(workspace.PeptideAnalyses.FindByKey(dbPeptideAnalysis.GetId())
.FileAnalyses.FindByKey(dbPeptideFileAnalysis.GetId()));
}
}
public static DbPeptideFileAnalysis CreatePeptideFileAnalysis(ISession session, MsDataFile msDataFile, DbPeptideAnalysis dbPeptideAnalysis, ILookup <long, double> psmTimesByDataFileId)
{
var dbMsDataFile = session.Load <DbMsDataFile>(msDataFile.Id);
var startEndTime = DecideChromatogramStartEndTime(msDataFile, psmTimesByDataFileId);
return(new DbPeptideFileAnalysis
{
ChromatogramStartTime = startEndTime.Key,
ChromatogramEndTime = startEndTime.Value,
MsDataFile = dbMsDataFile,
PeptideAnalysis = dbPeptideAnalysis,
AutoFindPeak = true,
PsmCount = psmTimesByDataFileId[msDataFile.Id].Count(),
});
}
