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 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 double GetScore(LinearModelParams parameters, PeakGroupFeatures peakGroupFeatures)
{
return GetScore(parameters.Weights, peakGroupFeatures, parameters.Bias);
}
/// <summary>
/// Calculate the score of a set of features given an array of weighting coefficients.
/// </summary>
private static double GetScore(IList<double> weights, PeakGroupFeatures peakGroupFeatures, double bias)
{
return LinearModelParams.Score(peakGroupFeatures.Features, weights, bias);
}
