/// <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,
};
}
