//!!!Yikes tons of repeated code and stuff re-run
internal static HlaAssignmentWithResponses CreateHlaAssignment(Quickscore <Hla, int> quickscore, string hlaListAsString, ICollection <int> patientsWhoRespond)
{
Qmrr.HlaFactory hlaFactory = Qmrr.HlaFactory.GetFactory("noConstraint");
//!!!this code is repeated elsewhere
Dictionary <Hla, List <int> > hlaToRespondingPatientsUnfiltered = quickscore.CreateCauseToSubsetOfEffects(patientsWhoRespond);
Dictionary <Hla, List <int> > hlaToRespondingPatients = Filter9xs(hlaToRespondingPatientsUnfiltered);
List <Hla> hlaListFromRepondingPatients = new List <Hla>(hlaToRespondingPatients.Keys);
Dictionary <Hla, bool> hlaAssignmentDicationary = new Dictionary <Hla, bool>();
foreach (string hlaName in hlaListAsString.Split(';'))
{
Hla hla = hlaFactory.GetGroundInstance(hlaName);
hlaAssignmentDicationary[hla] = true;
}
List <int> indexCollection = new List <int>();
for (int hlaIndex = 0; hlaIndex < hlaListFromRepondingPatients.Count; ++hlaIndex)
{
Hla hla = hlaListFromRepondingPatients[hlaIndex];
if (hlaAssignmentDicationary.ContainsKey(hla))
{
indexCollection.Add(hlaIndex);
}
}
HlaAssignmentWithResponses hlaAssignment = HlaAssignmentWithResponses.GetInstance(quickscore, hlaListFromRepondingPatients,
indexCollection, hlaToRespondingPatients);
return(hlaAssignment);
}
public static Hla GetHlaValue(Dictionary <string, string> row, string column, HlaResolution hlaResolution)
{
HlaToLength hlaToLength = GetHlaToLengthValueOrNull(row, column, hlaResolution);
SpecialFunctions.CheckCondition(hlaToLength != null);
return(HlaFactory.GetGroundInstance(hlaToLength.ToString()));
}
private void ReadKnownTable()
{
_knownTable = new Dictionary <string, Set <Hla> >();
if (OptimizationParameterList["useKnownList"].Value == 1)
{
foreach (Dictionary <string, string> row in SpecialFunctions.TabFileTable(KnownFileName, "peptide knownHLA", false)) //!!!const
{
string peptide = row["peptide"]; //!!!const
Set <Hla> knownHlaSet = SpecialFunctions.GetValueOrDefault(_knownTable, peptide);
knownHlaSet.AddNew(HlaFactory.GetGroundInstance(row["knownHLA"])); //!!!const
}
}
}
private static Hla GetHlaFromRow(Dictionary <string, string> causeAssignmentRow, HlaResolution hlaResolution)
{
Qmrr.HlaFactory hlaFactory = Qmrr.HlaFactory.GetFactory("noConstraint");
string hla = causeAssignmentRow["HLA"];
if (hla.Length == 4 || hla.Length == 2) //!!!should this be moved to GetHlaLengthInstance so doesn't appear twice?
{
hla = hla.Substring(0, 1) + "0" + hla.Substring(1);
}
HlaToLength hlaToLength = hlaResolution.GetHlaLengthInstance(hla);
SpecialFunctions.CheckCondition(hlaToLength != null);
return(hlaFactory.GetGroundInstance(hlaToLength.ToString()));
}
private void ReadPatientTable()
{
Qmrr.HlaFactory hlaFactory = Qmrr.HlaFactory.GetFactory("noConstraint");
PatientList = new Dictionary <string, Set <Hla> >();
foreach (Dictionary <string, string> row in SpecialFunctions.TabFileTable(PatientFileName, "pid a1 a2 b1 b2 c1 c2", false)) //!!!const
{
string patientId = row["pid"];
Set <Hla> hlaList = new Set <Hla>();
foreach (string columnName in new string[] { "a1", "a2", "b1", "b2", "c1", "c2" }) //!!!const
{
hlaList.AddNewOrOld(hlaFactory.GetGroundInstance(row[columnName]));
}
PatientList.Add(patientId, hlaList);
}
}
public static Quickscore <Hla, int> CreateQuickscore(string fileName, string header, double causePrior, double linkProbability, double leakProbability, HlaResolution hlaResolution)
{
Qmrr.HlaFactory hlaFactory = Qmrr.HlaFactory.GetFactory("noConstraint");
Quickscore <Hla, int> quickscore = Quickscore <Hla, int> .GetInstance(hlaFactory.GetGroundInstance(""));
foreach (Dictionary <string, string> row in QuickScoreOptimalsTable(fileName, header))
{
foreach (string column in CreateHlaColumns(header))
{
Hla hla = GetHlaValue(row, column, hlaResolution);
int patient = GetPatient(row);
quickscore.SetCause(hla, causePrior);
quickscore.SetLeak(patient, leakProbability);
quickscore.SetLink(hla, patient, linkProbability);
}
}
return(quickscore);
}
internal void SetPeptideToFitUniverse(string dataset)
{
Qmrr.HlaFactory hlaFactory = Qmrr.HlaFactory.GetFactory("noConstraint");
PeptideToFitUniverse = new Dictionary <string, Set <Hla> >();
string filename = dataset + "supertypefit.txt";
string line = null;
//!!!would be nice to read as a tab table, to remove redundent lines, to check that HLAs are of the right form
using (StreamReader streamReader = File.OpenText(filename))
{
while (null != (line = streamReader.ReadLine()))
{
string[] fields = line.Split('\t');
SpecialFunctions.CheckCondition(fields.Length == 2);
string peptide = fields[0];
Hla hla = hlaFactory.GetGroundInstance(fields[1]);
Set <Hla> fitUniverse = SpecialFunctions.GetValueOrDefault(PeptideToFitUniverse, peptide);
fitUniverse.AddNewOrOld(hla);
}
}
}
static public IEnumerable <Hla> FindAllHla(List <Dictionary <string, string> > expandedTable, HlaResolution hlaResolution, string header)
{
Qmrr.HlaFactory hlaFactory = Qmrr.HlaFactory.GetFactory("noConstraint");
Dictionary <Hla, bool> seenIt = new Dictionary <Hla, bool>();
foreach (Dictionary <string, string> row in expandedTable)
{
foreach (string column in HlaAssignmentParams.CreateHlaColumns(header))
{
HlaToLength hlaToLengthOrNull = HlaAssignmentParams.GetHlaToLengthValueOrNull(row, column, hlaResolution);
if (hlaToLengthOrNull == null || hlaToLengthOrNull.HlaNumberToLength >= 9000)
{
continue;
}
Hla hla = hlaFactory.GetGroundInstance(hlaToLengthOrNull.ToString());
if (!seenIt.ContainsKey(hla))
{
seenIt.Add(hla, true);
yield return(hla);
}
}
}
}