public PeakFeatureStatistics(PeakTransitionGroupFeatures features, IList <double> mprophetScores, IList <double> pValues, int bestScoreIndex, double?qValue)
{
Features = features;
MprophetScores = mprophetScores;
PValues = pValues;
BestScoreIndex = bestScoreIndex;
QValue = qValue;
}
public PeakFeatureStatistics(PeakTransitionGroupFeatures features, IList <float> mprophetScores, IList <float> pvalues,
int bestScoreIndex, float bestScore, float?qValue)
{
MprophetScores = mprophetScores; // May only be present for writing features
PValues = pvalues;
// Don't hold onto the features, because they hold a lot of memory
BestPeakIndex = features.PeakGroupFeatures[bestScoreIndex].OriginalPeakIndex;
BestScoreIndex = bestScoreIndex;
BestScore = bestScore;
QValue = qValue;
}
private static void WriteRow(TextWriter writer,
PeakTransitionGroupFeatures features,
PeakGroupFeatures peakGroupFeatures,
CultureInfo cultureInfo,
double mProphetScore,
double pValue,
double qValue)
{
char separator = TextUtil.GetCsvSeparator(cultureInfo);
string fileName = SampleHelp.GetFileName(features.Id.FilePath);
var fieldsArray = new List <string>
{
Convert.ToString(features.Id, cultureInfo),
Convert.ToString(features.Id.Run, cultureInfo),
fileName,
Convert.ToString(peakGroupFeatures.RetentionTime, cultureInfo),
Convert.ToString(peakGroupFeatures.StartTime, cultureInfo),
Convert.ToString(peakGroupFeatures.EndTime, cultureInfo),
features.Id.NodePep.RawUnmodifiedTextId, // Unmodified sequence, or custom ion name
features.Id.NodePep.RawTextId, // Modified sequence, or custom ion name
features.Id.NodePepGroup.Name,
Convert.ToString(features.Id.NodePep.IsDecoy ? 1 : 0, cultureInfo),
ToFieldString((float)mProphetScore, cultureInfo),
ToFieldString((float)pValue, cultureInfo),
ToFieldString((float)qValue, cultureInfo)
};
if (IsFilterTestData)
{
fieldsArray.Add(peakGroupFeatures.GetFilterPairsText(cultureInfo));
}
foreach (var name in fieldsArray)
{
writer.WriteDsvField(name, separator);
writer.Write(separator);
}
bool first = true;
foreach (float featureColumn in peakGroupFeatures.Features)
{
if (!first)
{
writer.Write(separator);
}
writer.WriteDsvField(ToFieldString(featureColumn, cultureInfo), separator);
first = false;
}
writer.WriteLine();
}
private static void WriteRow(TextWriter writer,
PeakTransitionGroupFeatures features,
PeakGroupFeatures peakGroupFeatures,
CultureInfo cultureInfo,
double mProphetScore,
double pValue,
double qValue)
{
char separator = TextUtil.GetCsvSeparator(cultureInfo);
string fileName = SampleHelp.GetFileName(features.Id.FilePath);
var fieldsArray = new List <string>
{
Convert.ToString(features.Id, cultureInfo),
Convert.ToString(features.Id.Run, cultureInfo),
fileName,
// CONSIDER: This impacts memory consumption for large-scale DIA, and it is not clear anyone uses these
Convert.ToString(peakGroupFeatures.RetentionTime, cultureInfo),
Convert.ToString(peakGroupFeatures.StartTime, cultureInfo),
Convert.ToString(peakGroupFeatures.EndTime, cultureInfo),
features.Id.RawUnmodifiedTextId, // Unmodified sequence, or custom ion name
features.Id.RawTextId, // Modified sequence, or custom ion name
features.Id.NodePepGroup.Name,
Convert.ToString(features.IsDecoy ? 1 : 0, cultureInfo),
ToFieldString((float)mProphetScore, cultureInfo),
ToFieldString((float)pValue, cultureInfo),
ToFieldString((float)qValue, cultureInfo)
};
foreach (var name in fieldsArray)
{
writer.WriteDsvField(name, separator);
writer.Write(separator);
}
bool first = true;
foreach (float featureColumn in peakGroupFeatures.Features)
{
if (!first)
{
writer.Write(separator);
}
writer.WriteDsvField(ToFieldString(featureColumn, cultureInfo), separator);
first = false;
}
writer.WriteLine();
}
private void WriteTransitionGroup(TextWriter writer,
PeakTransitionGroupFeatures features,
CultureInfo cultureInfo,
bool bestOnly,
bool includeDecoys)
{
var id = features.Key;
int bestScoresIndex = -1;
IList <float> mProphetScores = null;
IList <float> pValues = null;
double qValue = double.NaN;
PeakFeatureStatistics peakFeatureStatistics;
if (_featureDictionary.TryGetValue(id, out peakFeatureStatistics))
{
bestScoresIndex = peakFeatureStatistics.BestScoreIndex;
mProphetScores = peakFeatureStatistics.MprophetScores;
pValues = peakFeatureStatistics.PValues;
qValue = peakFeatureStatistics.QValue ?? double.NaN;
}
if (features.IsDecoy && !includeDecoys)
{
return;
}
int j = 0;
foreach (var peakGroupFeatures in features.PeakGroupFeatures)
{
if (!bestOnly || j == bestScoresIndex)
{
double mProphetScore = mProphetScores != null ? mProphetScores[j] : double.NaN;
double pValue = pValues != null ? pValues[j] : double.NaN;
WriteRow(writer, features, peakGroupFeatures, cultureInfo, mProphetScore,
pValue, qValue);
}
++j;
}
}
private static bool IsUnknownScore(PeakTransitionGroupFeatures features, int selectedCalculator)
{
return(features.PeakGroupFeatures.Any(groupFeatures => double.IsNaN(groupFeatures.Features[selectedCalculator])));
}
private static bool IsUnknownScore(PeakTransitionGroupFeatures features, int selectedCalculator)
{
return features.PeakGroupFeatures.Any(groupFeatures => double.IsNaN(groupFeatures.Features[selectedCalculator]));
}
public PeakFeatureStatistics(PeakTransitionGroupFeatures features, IList<double> mprophetScores, IList<double> pValues, int bestScoreIndex, double? qValue)
{
Features = features;
MprophetScores = mprophetScores;
PValues = pValues;
BestScoreIndex = bestScoreIndex;
QValue = qValue;
}
private void WriteTransitionGroup(TextWriter writer,
PeakTransitionGroupFeatures features,
CultureInfo cultureInfo,
bool bestOnly,
bool includeDecoys)
{
var id = features.Id.Key;
int bestScoresIndex = -1;
IList<double> mProphetScores = null;
IList<double> pValues = null;
double qValue = double.NaN;
PeakFeatureStatistics peakFeatureStatistics;
if (_featureDictionary.TryGetValue(id, out peakFeatureStatistics))
{
bestScoresIndex = peakFeatureStatistics.BestScoreIndex;
mProphetScores = peakFeatureStatistics.MprophetScores;
pValues = peakFeatureStatistics.PValues;
qValue = peakFeatureStatistics.QValue ?? double.NaN;
}
if (features.Id.NodePep.IsDecoy && !includeDecoys)
return;
int j = 0;
foreach (var peakGroupFeatures in features.PeakGroupFeatures)
{
if (!bestOnly || j == bestScoresIndex)
{
double mProphetScore = mProphetScores != null ? mProphetScores[j] : double.NaN;
double pValue = pValues != null ? pValues[j] : double.NaN;
WriteRow(writer, features, peakGroupFeatures, cultureInfo, mProphetScore,
pValue, qValue);
}
++j;
}
}
private static void WriteRow(TextWriter writer,
PeakTransitionGroupFeatures features,
PeakGroupFeatures peakGroupFeatures,
CultureInfo cultureInfo,
double mProphetScore,
double pValue,
double qValue)
{
char separator = TextUtil.GetCsvSeparator(cultureInfo);
string fileName = SampleHelp.GetFileName(features.Id.FilePath);
var fieldsArray = new List<string>
{
Convert.ToString(features.Id, cultureInfo),
Convert.ToString(features.Id.Run, cultureInfo),
fileName,
Convert.ToString(peakGroupFeatures.RetentionTime, cultureInfo),
Convert.ToString(peakGroupFeatures.StartTime, cultureInfo),
Convert.ToString(peakGroupFeatures.EndTime, cultureInfo),
features.Id.NodePep.RawUnmodifiedTextId, // Unmodified sequence, or custom ion name
features.Id.NodePep.RawTextId, // Modified sequence, or custom ion name
features.Id.NodePepGroup.Name,
Convert.ToString(features.Id.NodePep.IsDecoy ? 1 : 0, cultureInfo),
ToFieldString((float) mProphetScore, cultureInfo),
ToFieldString((float) pValue, cultureInfo),
ToFieldString((float) qValue, cultureInfo)
};
if (IsFilterTestData)
{
fieldsArray.Add(peakGroupFeatures.GetFilterPairsText(cultureInfo));
}
foreach (var name in fieldsArray)
{
writer.WriteDsvField(name, separator);
writer.Write(separator);
}
bool first = true;
foreach (float featureColumn in peakGroupFeatures.Features)
{
if (!first)
writer.Write(separator);
writer.WriteDsvField(ToFieldString(featureColumn, cultureInfo), separator);
first = false;
}
writer.WriteLine();
}