private static List <string> ProcessLine(ShowBy showBy, PredictorCollection predictorCollection, string line,
MerLength merLength, int?dOfCenter, HlaSetSpecification hlaSetSpecification, bool modelOnly)
{
try
{
string hlaOrSupertypeOrNull;
string inputPeptide = ExtractInputs(hlaSetSpecification, line, predictorCollection, out hlaOrSupertypeOrNull);
List <string> output = new List <string>();
foreach (List <Prediction> predictionList in predictorCollection.MaxProbabilityPredictions(showBy, inputPeptide, merLength, dOfCenter, hlaSetSpecification, hlaOrSupertypeOrNull, modelOnly).Values)
{
string outputLine = InsertMaterial(line, hlaSetSpecification.InputHeaderCollection().Length, Prediction.CollectionToString(predictionList, false, hlaSetSpecification.IncludeHlaInOutput()));
output.Add(outputLine);
}
return(output);
}
catch (Exception exception)
{
string errorString = SpecialFunctions.CreateTabString(
line,
string.Format("Error: {0}{1}", exception.Message, exception.InnerException == null ? "" : string.Format(" ({0})", exception.InnerException)));
List <string> output = new List <string>();
output.Add(errorString);
return(output);
}
}
private static void ReadInputCreatingOutput(ShowBy showBy, string modelName,
bool inputHasHeader, MerLength merLength, int?dOfCenter,
HlaSetSpecification hlaSetSpecification, bool modelOnly, string inputFileName, string outputFileName)
{
using (TextReader textReader = File.OpenText(inputFileName))
{
using (TextWriter textWriter = File.CreateText(outputFileName))
{
string header = CreateHeader(hlaSetSpecification, textReader, inputHasHeader);
textWriter.WriteLine(header);
PredictorCollection predictorCollection = PredictorCollection.GetInstance(modelName);
foreach (string line in SpecialFunctions.ReadEachLine(textReader))
{
foreach (string outputLine in ProcessLine(showBy, predictorCollection, line, merLength, dOfCenter, hlaSetSpecification, modelOnly))
{
textWriter.WriteLine(outputLine);
textWriter.Flush();
}
}
}
}
}
static public string ExtractInputs(HlaSetSpecification hlaSetSpecification, string line, PredictorCollection predictorCollection, out string hlaOrSupertypeOrNull)
{
List <string> fieldCollection = SpecialFunctions.Split(line, '\t');
int inputLength = hlaSetSpecification.InputHeaderCollection().Length;
SpecialFunctions.CheckCondition(inputLength <= fieldCollection.Count, string.Format("Expected input to have at least {0} columns", inputLength));
string inputPeptide = fieldCollection[0];
hlaOrSupertypeOrNull = (inputLength > 1) ? fieldCollection[1] : null;
return(inputPeptide);
}
