//!!!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);
}
internal static string GetAminoAcid(int position, bool treatHlaAsPrefix, Hla hla)
{
string sequence;
if (treatHlaAsPrefix)
{
sequence = null;
foreach (string hlaPrefix in EveryPrefixInclusiveDownToTwoDigits(hla.ToString()))
{
if (HlaNameToSequenceAsPrefix.TryGetValue(hlaPrefix, out sequence)) // Will also get a hit because empty string is included.
{
break;
}
}
SpecialFunctions.CheckCondition(null != sequence, "The hla, even trimmed two length 3 (class letter and two digits), not found in HlaToSequence file: '" + hla.ToString() + "'.");
}
else
{
sequence = HlaNameToSequenceExact[hla.ToString()];
}
char aminoAcidChar = sequence[position - 1];
string sAminoAcid = VirusCount.Biology.GetInstance().OneLetterAminoAcidAbbrevTo3Letter[aminoAcidChar];
return(sAminoAcid);
}
static public bool?HasHla(Hla hlaGoal, Dictionary <string, string> row, HlaResolution hlaResolution)
{
bool hasNull = false;
for (int i = 1; i <= 2; ++i)
{
string column = hlaGoal.ToString().Substring(0, 1) + i.ToString();
HlaToLength hlaToLengthOrNull = HlaAssignmentParams.GetHlaToLengthValueOrNull(row, column, hlaResolution);
if (hlaToLengthOrNull == null || hlaToLengthOrNull.HlaNumberToLength >= 9000)
{
hasNull = true;
continue;
}
if (hlaGoal.ToString() == hlaToLengthOrNull.ToString())
{
return(true);
}
}
if (hasNull)
{
return(null);
}
else
{
return(false);
}
}
////!!!same logic is elseware. Look for common heading
//private static Dictionary<string, Dictionary<string, double>> LoadReactTableUnfiltered(TextReader patientReader, out Set<string> cidsInReactTable)
//{
// cidsInReactTable = Set<string>.GetInstance();
// Dictionary<string, Dictionary<string, double>> reactTable = new Dictionary<string, Dictionary<string, double>>();
// string header = "peptide cid magnitude";
// foreach (Dictionary<string, string> row in SpecialFunctions.TabFileTable(patientReader, header, false))
// {
// string cid = row["cid"];
// cidsInReactTable.AddNewOrOld(cid);
// string peptide = row["peptide"];
// double amount = double.Parse(row["magnitude"]);
// Dictionary<string, double> peptideToAmount = SpecialFunctions.GetValueOrDefault(reactTable, peptide);
// peptideToAmount.Add(cid, amount);
// }
// return reactTable;
//}
private Dictionary <string, Set <Hla> > LoadKnownTable(DbDataReader datareader, string caseName)
{
//!!!code appears elsewhere. Look for common header
Dictionary <string, Set <Hla> > knownTable = new Dictionary <string, Set <Hla> >();
int indexPeptide = datareader.GetOrdinal("peptide");
int indexHLA = datareader.GetOrdinal("knownHLA");
int irecord = 0;
while (datareader.Read())
{
++irecord;
string peptide = datareader.GetString(indexPeptide).Trim();
string hlaName = datareader.GetString(indexHLA).Trim();
if (peptide.Length == 0 || hlaName.Length == 0)
{
continue;
}
Set <Hla> knownHlaSet = SpecialFunctions.GetValueOrDefault(knownTable, peptide);
Hla hla = HlaFactory.GetGroundInstance(hlaName);
SpecialFunctions.CheckCondition(!knownHlaSet.Contains(hla), string.Format("Hla {0} is duplicated in {1}known.txt, for peptide {2}", hla, caseName, peptide));
knownHlaSet.AddNew(hla); //!!!const
}
Console.WriteLine("{0}: number of records read: {1}", "Known table", irecord);
return(knownTable);
}
public static IsHla24 GetInstance(Hla hla)
{
IsHla24 isHla24 = new IsHla24();
isHla24.Hla24 = FindHla24(hla);
return(isHla24);
}
private static string FindHla24(Hla hla)
{
string hlaName = hla.ToString();
hlaName = hlaName.Replace("*", "");
if (hlaName.StartsWith("HLA"))
{
hlaName = hlaName.Substring(3);
}
if (hlaName.StartsWith(" ") || hlaName.StartsWith("-"))
{
hlaName = hlaName.Substring(1);
}
SpecialFunctions.CheckCondition(hlaName.Length == 5, "Expect hla to contain a class letter and a 4-digit number. " + hla.ToString());
SpecialFunctions.CheckCondition(hlaName[0] == 'A' || hlaName[0] == 'B' || hlaName[0] == 'C', "Expect hla to contain a class letter: A,B, or C. " + hla.ToString());
int ignore;
SpecialFunctions.CheckCondition(int.TryParse(hlaName.Substring(1), out ignore), "Expect hla to contain a 4-digit number. " + hla.ToString());
string hla24;
if (hlaName.StartsWith("A68") || hlaName.StartsWith("B15"))
{
hla24 = hlaName;
}
else
{
hla24 = hlaName.Substring(0, 3);
}
return(hla24);
}
internal static IsSupertypeFromWorkingDirectory GetInstance(Hla hla)
{
IsSupertypeFromWorkingDirectory isSupertypeFromWorkingDirectory = new IsSupertypeFromWorkingDirectory();
isSupertypeFromWorkingDirectory.SupertypeFromWorkingDirectory = VirusCount.HlaToLength.ToSupertypeFromWorkingDirectoryString(hla.ToString());
return(isSupertypeFromWorkingDirectory);
}
//!!!very similar to other code
public static Dictionary <Pair <NEC, Hla>, bool> ReadTable(HlaFactory hlaFactory, string fileName, bool dedup)
{
Dictionary <Pair <NEC, Hla>, bool> table = new Dictionary <Pair <NEC, Hla>, bool>();
foreach (Dictionary <string, string> row in SpecialFunctions.TabFileTable(fileName, "N\tepitope\tC\thla\tlabel", false))
{
string n = row["N"];
string epitope = row["epitope"];
SpecialFunctions.CheckCondition(Biology.GetInstance().LegalPeptide(epitope), string.Format("Peptide, '{0}', contains illegal char.", epitope));
string c = row["C"];
NEC nec = NEC.GetInstance(n, epitope, c);
Hla hla = hlaFactory.GetGroundInstance(row["hla"]);
string labelString = row["label"];
SpecialFunctions.CheckCondition(labelString == "0" || labelString == "1", "Expect label to be '0' or '1'");
Pair <NEC, Hla> pair = new Pair <NEC, Hla>(nec, hla);
bool labelAsBool = (labelString == "1");
if (dedup && table.ContainsKey(pair))
{
SpecialFunctions.CheckCondition(table[pair] == labelAsBool, "The example " + pair.ToString() + " appears with contradictory labels.");
continue;
}
table.Add(pair, labelAsBool);
}
return(table);
}
internal static IsZero6SupertypeNoBlanks GetInstance(Hla hla)
{
IsZero6SupertypeNoBlanks isZero6SupertypeNoBlanks = new IsZero6SupertypeNoBlanks();
isZero6SupertypeNoBlanks.Zero6SupertypeNoBlanks = VirusCount.HlaToLength.ToZero6SupertypeNoBlanksString(hla.ToString());
return(isZero6SupertypeNoBlanks);
}
internal static IsZero6Supertype GetInstance(Hla hla)
{
IsZero6Supertype isZero6Supertype = new IsZero6Supertype();
isZero6Supertype.Zero6Supertype = VirusCount.HlaToLength.ToZero6SupertypeBlanksString(hla.ToString());
return(isZero6Supertype);
}
public static IsHla GetInstance(Hla hla)
{
IsHla isHla = new IsHla();
isHla.Hla = hla.ToString();
return(isHla);
}
public override Hla GetGroundOrAbstractInstance(string name)
{
Hla hla = new Hla();
hla.Name = name;
return(hla);
}
private void FlipListedBits(Set <Hla> assignmentAsSet, List <int> indexList)
{
foreach (int index in indexList)
{
Hla hlaOfRepondingPatients = QmmrModelOnePeptide.QmrrModelMissingAssignment.SwitchableHlasOfRespondingPatients[index];
BitFlip(assignmentAsSet, hlaOfRepondingPatients);
}
}
internal static IsSupertypeFromFile GetInstance(Hla hla, string filePrefix, Assembly assembly, string resourcePrefix)
{
IsSupertypeFromFile isSupertypeFromFile = new IsSupertypeFromFile();
isSupertypeFromFile.FilePrefix = filePrefix;
isSupertypeFromFile.Supertype = LookupSupertypeFromFile(hla.ToString(), filePrefix, assembly, resourcePrefix);
isSupertypeFromFile.Assembly = assembly;
isSupertypeFromFile.ResourcePrefix = resourcePrefix;
return(isSupertypeFromFile);
}
private static void BitFlip(Set <Hla> assignmentAsSet, Hla hlaOfRepondingPatients)
{
if (assignmentAsSet.Contains(hlaOfRepondingPatients))
{
assignmentAsSet.Remove(hlaOfRepondingPatients);
}
else
{
assignmentAsSet.AddNew(hlaOfRepondingPatients);
}
}
public override bool IsMoreGeneralThan(Hla hla)
{
SpecialFunctions.CheckCondition(!IsGround && hla.IsGround, "IsMoreGeneralThan is only defined between an abstract and ground hla");
foreach (var nameAndOri in NameAndOriList)
{
if (IsMoreGeneralOrEqualThan(nameAndOri.Key, hla.Name))
{
return(true);
}
}
return(false);
}
internal static HlaAssignmentWithResponses GetInstance(Quickscore <Hla, int> quickscore, List <Hla> hlaListFromRepondingPatients, List <int> indexCollection,
Dictionary <Hla, List <int> > hlaToRespondingPatients)
{
List <Hla> trueCollection = new List <Hla>();
foreach (int index in indexCollection)
{
Hla hla = hlaListFromRepondingPatients[index];
trueCollection.Add(hla);
}
return(HlaAssignmentWithResponses.GetInstance(trueCollection, quickscore, hlaListFromRepondingPatients, hlaToRespondingPatients));
}
private static void CreateAndAddHlaFeature(bool subtractHlaFeatures, Hla hla, Pair <NEC, Hla> necAndHla, ref Set <IHashableFeature> hlaishEnumeration)
{
if (subtractHlaFeatures)
{
return;
}
IsHla featureHla = IsHla.GetInstance(hla);
hlaishEnumeration.AddNew(featureHla);
Debug.Assert((bool)featureHla.Evaluate(necAndHla)); // real assert - must only generate true features
}
public static Dictionary <Hla, List <int> > Filter9xs(Dictionary <Hla, List <int> > hlaToRespondingPatientsUnfiltered)
{
Debug.Fail("Confirm that is function is still useful after the 'string'->Qmrr.String conversion");
Dictionary <Hla, List <int> > filtered = new Dictionary <Hla, List <int> >();
foreach (KeyValuePair <Hla, List <int> > hlaAndPatientList in hlaToRespondingPatientsUnfiltered)
{
Hla hla = hlaAndPatientList.Key;
if (!nineXs.IsMatch(hla.ToString()))
{
filtered.Add(hla, hlaAndPatientList.Value);
}
}
return(filtered);
}
internal override Dictionary <Hla, PValueDetails> CreateHlaToPValueDetails(int nullIndex, string peptide, Dictionary <string, Set <Hla> > pidToHlaSetAll, Set <Hla> setOfHlasToConsiderAdding, TextWriter writer)
{
Dictionary <Hla, PValueDetails> hlaToPValueDetails = new Dictionary <Hla, PValueDetails>();
if (setOfHlasToConsiderAdding.Count == 0)
{
return(hlaToPValueDetails);
}
Dictionary <string, double> pidToReactValue = ReactTableUnfiltered[peptide];
Set <Hla> knownHlaSet = KnownTable(peptide);
SpecialFunctions.CheckCondition(setOfHlasToConsiderAdding.Intersection(knownHlaSet).Count == 0);
Set <Hla> bestHlaSetSoFar = Set <Hla> .GetInstance();
while (setOfHlasToConsiderAdding.Count > 0)
{
BestSoFar <PValueDetails, Hla> bestHlaToAddSoFar = BestSoFar <PValueDetails, Hla> .GetInstance(delegate(PValueDetails pValueDetails1, PValueDetails pValueDetails2) { return(pValueDetails1.Diff.CompareTo(pValueDetails2.Diff)); });
foreach (Hla hla in setOfHlasToConsiderAdding) //!!!only look at hla's of patients with reactivity to this peptide (how effects nulls?)
{
PValueDetails pValueDetails = CreateAPValueDetail(nullIndex, peptide, pidToHlaSetAll, knownHlaSet, bestHlaSetSoFar, hla);
bestHlaToAddSoFar.Compare(pValueDetails, hla);
}
//Debug.WriteLine("");
PValueDetails bestPValueDetails = bestHlaToAddSoFar.ChampsScore; //!!!weird that PValue details is the score and the object
if (bestPValueDetails.PValue() > PValueCutOff)
{
break;
}
Hla hlaToAdd = bestHlaToAddSoFar.Champ;
setOfHlasToConsiderAdding.Remove(hlaToAdd);
bestHlaSetSoFar = bestHlaSetSoFar.Union(hlaToAdd);
hlaToPValueDetails.Add(hlaToAdd, bestPValueDetails);
writer.WriteLine(bestPValueDetails);
//Debug.WriteLine(bestPValueDetails);
writer.Flush();
}
return(hlaToPValueDetails);
}
public static void UnitTest()
{
HlaMsr1Factory hlaMsr1Factory = HlaMsr1Factory.GetFactory(new int[] { 4, 4, 4 });
HashSet <string> warningSet = new HashSet <string>();
SpecialFunctions.CheckCondition(hlaMsr1Factory.GetGroundOrAbstractInstance("B*1234/B23", ref warningSet).ToString() == "B1234/B23");
hlaMsr1Factory.GetGroundOrAbstractInstance("BND", ref warningSet);
Hla hla5 = hlaMsr1Factory.GetGroundOrAbstractInstance("B", ref warningSet);
SpecialFunctions.CheckCondition(hla5.ToString() == "B");
Hla hla3 = hlaMsr1Factory.GetGroundOrAbstractInstance("C1234", ref warningSet);
SpecialFunctions.CheckCondition(hla3.ToString() == "C1234");
SpecialFunctions.CheckCondition(hlaMsr1Factory.GetGroundOrAbstractInstance("B*1234", ref warningSet).ToString() == "B1234");
SpecialFunctions.CheckCondition(hlaMsr1Factory.GetGroundOrAbstractInstance("C1234/C12/C", ref warningSet).ToString() == "C");
Hla hla7 = hlaMsr1Factory.GetGroundOrAbstractInstance("C1234N", ref warningSet);
SpecialFunctions.CheckCondition(hla7.ToString() == "C1234");
Hla hla6 = hlaMsr1Factory.GetGroundOrAbstractInstance("C12", ref warningSet);
SpecialFunctions.CheckCondition(hla6.ToString() == "C12");
Hla hla1 = hlaMsr1Factory.GetGroundOrAbstractInstance("A74", ref warningSet);
SpecialFunctions.CheckCondition(hla1.ToString() == "A74");
Hla hla2 = hlaMsr1Factory.GetGroundOrAbstractInstance("A7412", ref warningSet);
SpecialFunctions.CheckCondition(hla2.ToString() == "A74");
SpecialFunctions.CheckCondition(hla6.IsMoreGeneralThan(hla7)); // assert
SpecialFunctions.CheckCondition(!hla6.IsMoreGeneralThan(hla2)); // assert
SpecialFunctions.CheckCondition(hlaMsr1Factory.GetGroundOrAbstractInstance("A12345678", ref warningSet).ToString() == "A1234");
SpecialFunctions.CheckCondition(hlaMsr1Factory.GetGroundOrAbstractInstance("B95", ref warningSet).ToString() == "B15");
SpecialFunctions.CheckCondition(hlaMsr1Factory.GetGroundOrAbstractInstance("B15/B9512", ref warningSet).ToString() == "B15");
Hla hla4 = hlaMsr1Factory.GetGroundOrAbstractInstance("A02/A9299", ref warningSet);
SpecialFunctions.CheckCondition(hla4.ToString() == "A02");
SpecialFunctions.CheckCondition(hla3.IsGround); // assert
SpecialFunctions.CheckCondition(hla1.IsGround); // assert
SpecialFunctions.CheckCondition(!hla4.IsGround); // assert
SpecialFunctions.CheckCondition(!hla5.IsGround); // assert
SpecialFunctions.CheckCondition(hlaMsr1Factory.GetGroundOrAbstractInstance("A1200", ref warningSet).ToString() == "A12");
SpecialFunctions.CheckCondition(!hlaMsr1Factory.GetGroundOrAbstractInstance("B*1234/B23", ref warningSet).IsGround);
}
//private Dictionary<string, bool> GetAList(Dictionary<string, string> row)
//{
// Dictionary<string, bool> alist = new Dictionary<string, bool>();
// string alistValue = row["HLA In Fixed List"];
// foreach (string hla in alistValue.Split(' '))
// {
// Debug.Assert((hla.Length == 3 && !hla.StartsWith("B15")) || (hla.Length == 5 && hla.StartsWith("B15")));
// alist.Add(hla, true);
// }
// return alist;
//}
public static HlaAssignmentWithResponses CreateHlaAssignment(List <Dictionary <string, string> > rowsOfThisPeptide, IEnumerable <Hla> hlaList, HlaResolution hlaResolution, Quickscore <Hla, int> quickscore, List <int> patientsWhoRespond)
{
//!!!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 (Dictionary <string, string> causeAssignmentRow in rowsOfThisPeptide)
{
Hla hla = GetHlaFromRow(causeAssignmentRow, hlaResolution);
hlaAssignmentDicationary[hla] = true;
}
HlaAssignmentWithResponses hlaAssignment = HlaAssignmentWithResponses.GetInstance(hlaAssignmentDicationary.Keys, quickscore, hlaListFromRepondingPatients,
hlaToRespondingPatients);
return(hlaAssignment);
}
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 static PValueDetails GetInstance(
string selectionName,
int nullIndex, string peptide, Hla hla,
double score1, double score2, Set <Hla> knownHlas, Set <Hla> bestHlaSetSoFar, double leakProbability, double linkProbability, OptimizationParameterList previousParams)
{
PValueDetails pValueDetails = new PValueDetails();
pValueDetails.SelectionName = selectionName;
pValueDetails.NullIndex = nullIndex;
pValueDetails.Peptide = peptide;
pValueDetails.Hla = hla;
pValueDetails.Score1 = score1;
pValueDetails.Score2 = score2;
pValueDetails.Diff = score1 - score2;
pValueDetails.KnownHlas = knownHlas;
pValueDetails.BestHlaSetSoFar = bestHlaSetSoFar;
pValueDetails.LeakProbability = leakProbability;
pValueDetails.LinkProbability = linkProbability;
pValueDetails.PreviousParams = previousParams;
return(pValueDetails);
}
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);
}
}
}
public override bool IsMoreGeneralThan(Hla hla)
{
Debug.Assert(!IsGround); // real assert
SpecialFunctions.CheckCondition(hla.IsGround); //We only have code for this
Debug.Assert(hla.Name.Length != 0 && Name.Length != 0);
if (Name[0] != hla.Name[0])
{
return(false);
}
string otherRest = hla.Name.Substring(1);
foreach (string rest in Name.Substring(1).Split('/'))
{
bool thisMatch = true;
foreach (KeyValuePair <char, char> abstractCharAndGroundChar in SpecialFunctions.EnumerateTwo(rest, otherRest))
{
char abstractChar = abstractCharAndGroundChar.Key;
char groundChar = abstractCharAndGroundChar.Value;
if (abstractChar != '?')
{
if (abstractChar != groundChar)
{
thisMatch = false;
break;
}
}
}
if (thisMatch)
{
return(true);
}
}
return(false);
}
//!!!Yikes tons of repeated code and stuff re-run
public static HlaAssignmentWithResponses CreateHlaAssignment(List <Dictionary <string, string> > rowsOfThisPeptide, IEnumerable <Hla> hlaList, HlaResolution hlaResolution, Quickscore <Hla, int> quickscore, List <int> patientsWhoRespond, Hla hlaToReplace, Hla hlaWithWhichToReplaceItOrNull)
{
//!!!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 (Dictionary <string, string> causeAssignmentRow in rowsOfThisPeptide)
{
Hla hla = GetHlaFromRow(causeAssignmentRow, hlaResolution);
hlaAssignmentDicationary[hla] = true;
}
hlaAssignmentDicationary.Remove(hlaToReplace);
if (hlaWithWhichToReplaceItOrNull != null)
{
hlaAssignmentDicationary.Add(hlaWithWhichToReplaceItOrNull, 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);
}
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);
}
}
}
}
public void OnReceiveUpdateAttributeValues(Hla.Rti1516.IObjectInstanceHandle instanceHandle, string methodName, object newValue)
{
name = methodName;
val = newValue;
Sxta.Rti1516.HLAAttributes.HLAobjectRoot obj = registedObjects[instanceHandle] as Sxta.Rti1516.HLAAttributes.HLAobjectRoot;
if (log.IsDebugEnabled)
{
log.Debug("The method " + methodName + " has been called; new value:" + newValue + "; parameter type = " + newValue.GetType());
log.Debug("The object is " + obj);
}
}
public void OnReceiveUpdateAttributeValues(Hla.Rti1516.IObjectInstanceHandle instanceHandle, string methodName, object newValue)
{
name = methodName;
val = newValue;
if (log.IsDebugEnabled)
log.Debug("The method " + methodName + " has been called; new value:" + newValue + "; parameter type = " + newValue.GetType());
}
public object RegistedObject(Hla.Rti1516.IObjectInstanceHandle handle)
{
return registedObjects[handle];
}
private PValueDetails CreateAPValueDetail(int nullIndex, string peptide, Dictionary <string, Set <Hla> > pidToHlaSetAll, Set <Hla> knownHlaSet, Set <Hla> bestHlaSetSoFar, Hla hla)
{
//Dictionary<string, Dictionary<string, double>> reactTableCustom;
Dictionary <string, Set <Hla> > pidToHlaSetCustom =
CreatePidToHlaSetCustom(pidToHlaSetAll, bestHlaSetSoFar, hla, knownHlaSet);
//out pidToHlaSetCustom, out reactTableCustom);
//!!!could cache both calls to FindBestParams
double scoreBase;
OptimizationParameterList baseParams = FindBestParams(peptide, bestHlaSetSoFar, Set <Hla> .GetInstance(), pidToHlaSetCustom, out scoreBase);
double scoreWithOneMore;
OptimizationParameterList withMoreMoreParams = FindBestParams(peptide, bestHlaSetSoFar.Union(hla), Set <Hla> .GetInstance(), pidToHlaSetCustom, out scoreWithOneMore);
PValueDetails pValueDetails = PValueDetails.GetInstance(SelectionName, nullIndex, peptide, hla,
scoreWithOneMore, scoreBase, knownHlaSet, bestHlaSetSoFar, withMoreMoreParams["leakProbability"].Value, withMoreMoreParams["link" + hla].Value, withMoreMoreParams);
//Debug.Write(String.Format("{0}/{1}\t", hla, scoreWithOneMore));
return(pValueDetails);
}
//!!!this could be made faster by keeping track of patients with no abstract hlas
private Dictionary <string, Set <Hla> > CreatePidToHlaSetCustom(Dictionary <string, Set <Hla> > pidToHlaSetAll, Set <Hla> bestHlaSetSoFar, Hla hla, Set <Hla> knownHlaSet
//out Dictionary<string, Set<Hla>> pidToHlaSetCustom,
//out Dictionary<string, Dictionary<string, double>> reactTableCustom
)
{
Set <Hla> possibleCauses = bestHlaSetSoFar.Union(knownHlaSet);
possibleCauses.AddNewOrOld(hla);
#if DEBUG
foreach (Hla hlaPossibleCause in possibleCauses)
{
Debug.Assert(hlaPossibleCause.IsGround); // real assert
}
#endif
Dictionary <string, Set <Hla> > pidToHlaSetCustom = new Dictionary <string, Set <Hla> >();
//reactTableCustom = new Dictionary<string, Dictionary<string, double>>();
foreach (string pid in pidToHlaSetAll.Keys)
{
Set <Hla> patientHlaSet = pidToHlaSetAll[pid];
//bestSoFar/known Hla PidContains ExcludePid?
//B23 B25 B15?? No
//B23 B1511 B15?? Yes
if (!ThisPatientContainsAnAbstractHlaThatGeneralizesAPossibleCause(patientHlaSet, possibleCauses))
{
pidToHlaSetCustom.Add(pid, patientHlaSet);
// reactTableCustom.Add(pid, ReactTableUnfiltered[pid]);
}
else
{
//Debug.WriteLine(SpecialFunctions.CreateTabString(patientHlaSet, possibleCauses));
}
}
return(pidToHlaSetCustom);
}
