public static HlaFilter GetInstanceOrNull(string hlaFilterLine)
{
HlaFilter hlaFilter = new HlaFilter();
if (hlaFilterLine == null || hlaFilterLine == "")
{
return(null);
}
string supertypeKeyword = "Supertype";
if (hlaFilterLine.StartsWith(supertypeKeyword))
{
SpecialFunctions.CheckCondition(false, "Need code");
//string supertype = hlaFilterLine.Substring(supertypeKeyword.Length);
//hlaFilter.Name = hlaFilterLine;
//if (supertype == "Undefined")
//{
// hlaFilterLine = HlaToLength.SupertypeToListString("Not" + supertype);
// hlaFilter.direction = false;
//}
//else
//{
// hlaFilterLine = HlaToLength.SupertypeToListString(supertype);
//}
}
else
{
hlaFilter.Name = hlaFilterLine.Replace(",", "");
}
foreach (string hlaString in hlaFilterLine.Split(','))
{
hlaFilter.Add(HlaToLength.GetInstanceABMixed(hlaString));
}
return(hlaFilter);
}
public static void ReportRocCurve(List <RocRow> rocRowCollection, string fileName, bool isComplete, long lineLimit, HlaFilter hlaFilterOrNull)
{
if (hlaFilterOrNull != null)
{
fileName = fileName + "FilteredOn" + hlaFilterOrNull.Name;
rocRowCollection = hlaFilterOrNull.Filter(rocRowCollection);
}
Debug.WriteLine(fileName);
using (TextWriter evalStream = File.CreateText(fileName))
{
rocRowCollection.Sort(
delegate(RocRow x, RocRow y)
{
return(y.Prediction.CompareTo(x.Prediction));
});
long positiveTotal = CountPositives(rocRowCollection);
long negativeTotal = rocRowCollection.Count - positiveTotal;
long positiveSoFar = positiveTotal;
long negativeSoFar = 0;
double prevPrediction = 1.0;
if (!isComplete)
{
evalStream.WriteLine("WARNING: The weights files were incomplete");
}
evalStream.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}",
"CrossValIndex", "Label",
"Mer", "Hla",
"Prediction",
"FalsePositiveCount", "FalseNegativeCount",
rocRowCollection.Count > lineLimit ? "SampledFalsePositiveFraction" : "FalsePositiveFraction",
rocRowCollection.Count > lineLimit ? "SampledFalseNegativeFraction" : "FalseNegativeFraction");
evalStream.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}",
"", "",
"", "",
1.0,
positiveSoFar, negativeSoFar,
(double)positiveSoFar / (double)positiveTotal,
(double)negativeSoFar / (double)negativeTotal);
for (long iRocRow = 0; iRocRow < rocRowCollection.Count; ++iRocRow)
{
RocRow rocRow = rocRowCollection[(int)iRocRow];
Debug.Assert(prevPrediction >= rocRow.Prediction); // real assert
//if (prevPrediction > rocRow.Prediction)
//{
// Console.WriteLine("WARNING: There needs to be a code change for when there are predictions with ties. Consider switching to SpecialFunctions.Roc (but it doesn't currently have sampling or filtering)");
//}
prevPrediction = rocRow.Prediction;
if (rocRow.Label)
{
--positiveSoFar;
}
else
{
++negativeSoFar;
}
if (DoOutput(iRocRow, rocRowCollection.Count, lineLimit))
{
evalStream.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}",
rocRow.CrossValIndex, rocRow.Label,
rocRow.MerAndHlaToLength.Mer, rocRow.MerAndHlaToLength.HlaToLength,
rocRow.Prediction,
positiveSoFar, negativeSoFar,
(double)positiveSoFar / (double)positiveTotal,
(double)negativeSoFar / (double)negativeTotal);
}
}
Debug.Assert(positiveSoFar == 0); // real assert
Debug.Assert(negativeSoFar == negativeTotal);
}
}
