/// <summary>
/// Align retention times with a target.
/// For the MS2 Id's that are found in both the target and the timesToAlign, the MS2 id's
/// are plotted against each other, and a linear regression is performed.
/// In cases where there is more than one MS2 id in either file, only the earliest MS2 id from
/// each file is used.
/// </summary>
public static AlignedRetentionTimes AlignLibraryRetentionTimes(IDictionary <Target, double> target, IDictionary <Target, double> originalTimes, double refinementThreshhold, RegressionMethodRT regressionMethod,
Func <bool> isCanceled)
{
var calculator = new DictionaryRetentionScoreCalculator("alignment", originalTimes); // Not L10N
var targetTimesList = new List <MeasuredRetentionTime>();
foreach (var entry in calculator.RetentionTimes)
{
double targetTime;
if (!target.TryGetValue(entry.Key, out targetTime))
{
continue;
}
MeasuredRetentionTime measuredRetentionTime;
try
{
measuredRetentionTime = new MeasuredRetentionTime(entry.Key, targetTime);
}
catch
{
continue;
}
targetTimesList.Add(measuredRetentionTime);
}
RetentionTimeStatistics regressionStatistics;
var regression = RetentionTimeRegression.CalcRegression(XmlNamedElement.NAME_INTERNAL, new[] { calculator }, regressionMethod, targetTimesList, out regressionStatistics);
if (regression == null)
{
return(null);
}
RetentionTimeRegression regressionRefined;
RetentionTimeStatistics regressionRefinedStatistics = regressionStatistics;
HashSet <int> outIndexes = new HashSet <int>();
if (regressionStatistics.R >= refinementThreshhold)
{
regressionRefined = regression;
}
else
{
var cache = new RetentionTimeScoreCache(new[] { calculator }, new MeasuredRetentionTime[0], null);
regressionRefined = regression.FindThreshold(refinementThreshhold, null, 0,
targetTimesList.Count, new MeasuredRetentionTime[0], targetTimesList, null, regressionStatistics,
calculator, regressionMethod, cache, isCanceled, ref regressionRefinedStatistics,
ref outIndexes);
}
return(new AlignedRetentionTimes
{
TargetTimes = target,
OriginalTimes = originalTimes,
Regression = regression,
RegressionStatistics = regressionStatistics,
RegressionRefined = regressionRefined,
RegressionRefinedStatistics = regressionRefinedStatistics,
OutlierIndexes = outIndexes,
Calculator = calculator
});
}
/// <summary>
/// Align retention times with a target.
/// For the MS2 Id's that are found in both the target and the timesToAlign, the MS2 id's
/// are plotted against each other, and a linear regression is performed.
/// In cases where there is more than one MS2 id in either file, only the earliest MS2 id from
/// each file is used.
/// </summary>
public static AlignedRetentionTimes AlignLibraryRetentionTimes(IDictionary<string, double> target, IDictionary<string, double> originalTimes, double refinementThreshhold, Func<bool> isCanceled)
{
var calculator = new DictionaryRetentionScoreCalculator("alignment", originalTimes); // Not L10N
var targetTimesList = new List<MeasuredRetentionTime>();
foreach (var entry in calculator.RetentionTimes)
{
double targetTime;
if (!target.TryGetValue(entry.Key, out targetTime))
{
continue;
}
MeasuredRetentionTime measuredRetentionTime;
try
{
measuredRetentionTime = new MeasuredRetentionTime(entry.Key, targetTime);
}
catch
{
continue;
}
targetTimesList.Add(measuredRetentionTime);
}
RetentionTimeStatistics regressionStatistics;
var regression = RetentionTimeRegression.CalcRegression(XmlNamedElement.NAME_INTERNAL, new[] {calculator}, targetTimesList, out regressionStatistics);
if (regression == null)
{
return null;
}
RetentionTimeRegression regressionRefined;
RetentionTimeStatistics regressionRefinedStatistics = regressionStatistics;
HashSet<int> outIndexes = new HashSet<int>();
if (regressionStatistics.R >= refinementThreshhold)
{
regressionRefined = regression;
}
else
{
var cache = new RetentionTimeScoreCache(new[] {calculator}, new MeasuredRetentionTime[0], null);
regressionRefined = regression.FindThreshold(refinementThreshhold, null, 0,
targetTimesList.Count, new MeasuredRetentionTime[0], targetTimesList, regressionStatistics,
calculator, cache, isCanceled, ref regressionRefinedStatistics,
ref outIndexes);
}
return new AlignedRetentionTimes
{
TargetTimes = target,
OriginalTimes = originalTimes,
Regression = regression,
RegressionStatistics = regressionStatistics,
RegressionRefined = regressionRefined,
RegressionRefinedStatistics = regressionRefinedStatistics,
OutlierIndexes = outIndexes,
};
}
public GraphData(SrmDocument document, GraphData dataPrevious,
int resultIndex, double threshold, int?thresholdPrecision, bool refine, bool bestResult, PointsTypeRT pointsType)
{
_document = document;
_resultIndex = resultIndex;
_bestResult = bestResult;
_threshold = threshold;
_thresholdPrecision = thresholdPrecision;
_pointsType = pointsType;
_peptidesIndexes = new List <PeptideDocumentIndex>();
_peptidesTimes = new List <MeasuredRetentionTime>();
int index = -1;
var standards = new HashSet <string>();
if (RTGraphController.PointsType == PointsTypeRT.standards)
{
standards = document.GetRetentionTimeStandards();
}
// CONSIDER: Retention time prediction for small molecules?
foreach (var nodePeptide in document.Peptides)
{
index++;
switch (RTGraphController.PointsType)
{
default:
if (nodePeptide.IsDecoy)
{
continue;
}
break;
case PointsTypeRT.standards:
if (!standards.Contains(document.Settings.GetModifiedSequence(nodePeptide)))
{
continue;
}
break;
case PointsTypeRT.decoys:
if (!nodePeptide.IsDecoy)
{
continue;
}
break;
}
float?rt = null;
if (!bestResult)
{
rt = nodePeptide.GetSchedulingTime(resultIndex);
}
else
{
int iBest = nodePeptide.BestResult;
if (iBest != -1)
{
rt = nodePeptide.GetSchedulingTime(iBest);
}
}
if (!rt.HasValue)
{
rt = 0;
}
_peptidesIndexes.Add(new PeptideDocumentIndex(nodePeptide, index));
string modSeq = _document.Settings.GetSourceTextId(nodePeptide);
_peptidesTimes.Add(new MeasuredRetentionTime(modSeq, rt.Value));
}
_calculatorName = Settings.Default.RTCalculatorName;
RetentionScoreCalculatorSpec calc = !string.IsNullOrEmpty(_calculatorName)
? Settings.Default.GetCalculatorByName(Settings.Default.RTCalculatorName)
: null;
if (calc == null)
{
// Initialize all calculators
Settings.Default.RTScoreCalculatorList.Initialize(null);
//This call will pick the best calculator, disqualifying any iRT Calcs that do not have
//connected databases
_regressionAll = RetentionTimeRegression.CalcRegression(XmlNamedElement.NAME_INTERNAL,
Settings.Default.RTScoreCalculatorList,
_peptidesTimes,
_scoreCache,
true,
out _statisticsAll,
out _calculator);
}
else
{
// Initialize the one calculator
calc = Settings.Default.RTScoreCalculatorList.Initialize(null, calc);
_regressionAll = RetentionTimeRegression.CalcRegression(XmlNamedElement.NAME_INTERNAL,
new[] { calc },
_peptidesTimes,
_scoreCache,
true,
out _statisticsAll,
out _calculator);
//If _regressionAll is null, it is safe to assume that the calculator is an iRT Calc with
//its database disconnected.
if (_regressionAll == null)
{
var tryIrtCalc = calc as RCalcIrt;
//Only show an error message if the user specifically chooses this calculator.
if (dataPrevious != null && !ReferenceEquals(calc, dataPrevious.Calculator) && tryIrtCalc != null)
{
throw new DatabaseNotConnectedException(tryIrtCalc);
}
}
}
if (_regressionAll != null)
{
_scoreCache = new RetentionTimeScoreCache(new[] { _calculator }, _peptidesTimes,
dataPrevious != null ? dataPrevious._scoreCache : null);
if (dataPrevious != null && !ReferenceEquals(_calculator, dataPrevious._calculator))
{
_scoreCache.RecalculateCalcCache(_calculator);
}
_scoresRefined = _statisticsAll.ListHydroScores.ToArray();
_timesRefined = _statisticsAll.ListRetentionTimes.ToArray();
}
_regressionPredict = document.Settings.PeptideSettings.Prediction.RetentionTime;
if (_regressionPredict != null)
{
if (!Equals(_calculator, _regressionPredict.Calculator))
{
_regressionPredict = null;
}
else
{
IDictionary <string, double> scoreCache = null;
if (_regressionAll != null && ReferenceEquals(_regressionAll.Calculator, _regressionPredict.Calculator))
{
scoreCache = _statisticsAll.ScoreCache;
}
_statisticsPredict = _regressionPredict.CalcStatistics(_peptidesTimes, scoreCache);
}
}
// Only refine, if not already exceeding the threshold
_refine = refine && !IsRefined();
}
public GraphData(SrmDocument document, GraphData dataPrevious,
int resultIndex, double threshold, int? thresholdPrecision, bool refine, bool bestResult)
{
_document = document;
_resultIndex = resultIndex;
_bestResult = bestResult;
_threshold = threshold;
_thresholdPrecision = thresholdPrecision;
_peptidesIndexes = new List<PeptideDocumentIndex>();
_peptidesTimes = new List<MeasuredRetentionTime>();
int index = -1;
// CONSIDER: Retention time prediction for small molecules?
foreach (var nodePeptide in document.Peptides)
{
index++;
float? rt = null;
if (!bestResult)
rt = nodePeptide.GetSchedulingTime(resultIndex);
else
{
int iBest = nodePeptide.BestResult;
if (iBest != -1)
rt = nodePeptide.GetSchedulingTime(iBest);
}
if (!rt.HasValue)
rt = 0;
_peptidesIndexes.Add(new PeptideDocumentIndex(nodePeptide, index));
string modSeq = _document.Settings.GetSourceTextId(nodePeptide);
_peptidesTimes.Add(new MeasuredRetentionTime(modSeq, rt.Value));
}
_calculatorName = Settings.Default.RTCalculatorName;
RetentionScoreCalculatorSpec calc = !string.IsNullOrEmpty(_calculatorName)
? Settings.Default.GetCalculatorByName(Settings.Default.RTCalculatorName)
: null;
if (calc == null)
{
// Initialize all calculators
Settings.Default.RTScoreCalculatorList.Initialize(null);
//This call will pick the best calculator, disqualifying any iRT Calcs that do not have
//connected databases
_regressionAll = RetentionTimeRegression.CalcRegression(XmlNamedElement.NAME_INTERNAL,
Settings.Default.RTScoreCalculatorList,
_peptidesTimes,
_scoreCache,
true,
out _statisticsAll,
out _calculator);
}
else
{
// Initialize the one calculator
calc = Settings.Default.RTScoreCalculatorList.Initialize(null, calc);
_regressionAll = RetentionTimeRegression.CalcRegression(XmlNamedElement.NAME_INTERNAL,
new[] {calc},
_peptidesTimes,
_scoreCache,
true,
out _statisticsAll,
out _calculator);
//If _regressionAll is null, it is safe to assume that the calculator is an iRT Calc with
//its database disconnected.
if(_regressionAll == null)
{
var tryIrtCalc = calc as RCalcIrt;
//Only show an error message if the user specifically chooses this calculator.
if (dataPrevious != null && !ReferenceEquals(calc, dataPrevious.Calculator) && tryIrtCalc != null)
{
throw new DatabaseNotConnectedException(tryIrtCalc);
}
}
}
if (_regressionAll != null)
{
_scoreCache = new RetentionTimeScoreCache(new[] { _calculator }, _peptidesTimes,
dataPrevious != null ? dataPrevious._scoreCache : null);
if (dataPrevious != null && !ReferenceEquals(_calculator, dataPrevious._calculator))
_scoreCache.RecalculateCalcCache(_calculator);
_scoresRefined = _statisticsAll.ListHydroScores.ToArray();
_timesRefined = _statisticsAll.ListRetentionTimes.ToArray();
}
_regressionPredict = document.Settings.PeptideSettings.Prediction.RetentionTime;
if (_regressionPredict != null)
{
if (!Equals(_calculator, _regressionPredict.Calculator))
_regressionPredict = null;
else
{
IDictionary<string, double> scoreCache = null;
if (_regressionAll != null && ReferenceEquals(_regressionAll.Calculator, _regressionPredict.Calculator))
scoreCache = _statisticsAll.ScoreCache;
_statisticsPredict = _regressionPredict.CalcStatistics(_peptidesTimes, scoreCache);
}
}
// Only refine, if not already exceeding the threshold
_refine = refine && !IsRefined();
}