static public Set <Hla> HlaSetInternal(string parameter, Set <Hla> hlaSet, Dictionary <string, Set <Hla> > supertypeMap)
{
Hla hla = HlaFactoryNoConstraints.GetGroundInstance(parameter);
//SpecialFunctions.CheckCondition(hlaSet.Contains(hla), string.Format("Hla value of {0} is unknown", parameter));
return(Set <Hla> .GetInstance(hla));
}
private void LoadUpPredictor(string modelName, int eLength, int ncLength, Converter <Hla, Hla> hlaForNormalization)
{
//Load up the predictor
string featurerizerName;
switch (modelName.ToLower())
{
//!!!would be better not to have multiple of these switch statements around - looks like a job for a Class
case "lanliedb03062007":
featurerizerName = "[email protected]";
SampleNEC = NEC.GetInstance("", new string(' ', eLength), "");
HlaFactory = HlaFactory.GetFactory("MixedWithB15AndA68");
SourceDataFileName = "lanlIedb03062007.pos.source.txt";
NameList = new string[] { "LANL", "IEDB" };
break;
default:
SpecialFunctions.CheckCondition(false, "Don't know what featurerizer to use for the model");
featurerizerName = null;
SourceDataFileName = null;
NameList = null;
break;
}
Converter <object, Set <IHashableFeature> > featurizer = FeatureLib.CreateFeaturizer(featurerizerName);
//GeneratorType generatorType = GeneratorType.ComboAndZero6SuperType;
//FeatureSerializer featureSerializer = PositiveNegativeExperimentCollection.GetFeatureSerializer();
//KmerDefinition = kmerDefinition;
//HlaResolution hlaResolution = HlaResolution.ABMixed;
string resourceName = string.Format("maxentModel{0}{1}{2}{3}.xml", modelName.Split('.')[0], SampleNEC.N.Length, SampleNEC.E.Length, SampleNEC.C.Length);
EpitopeLearningDataList = new List <EpitopeLearningDataDupHlaOK>();
using (StreamReader streamReader = Predictor.OpenResource(resourceName))
{
Logistic = (Logistic)FeatureLib.FeatureSerializer.FromXmlStreamReader(streamReader);
//Logistic.FeatureGenerator = EpitopeFeatureGenerator.GetInstance(KmerDefinition, generatorType, featureSerializer).GenerateFeatureSet;
Logistic.FeatureGenerator = FeatureLib.CreateFeaturizer(featurerizerName);
foreach (string name in NameList)
{
EpitopeLearningData epitopeLearningDataX = EpitopeLearningData.GetDbWhole(HlaFactory, SampleNEC.E.Length, name, SourceDataFileName);
Debug.Assert(epitopeLearningDataX.Count > 0, "Expect given data to have some data");
//!!!combine with previous step
EpitopeLearningDataDupHlaOK epitopeLearningData = new EpitopeLearningDataDupHlaOK(epitopeLearningDataX.Name);
foreach (KeyValuePair <Pair <string, Hla>, bool> merAndHlaAndLabel in epitopeLearningDataX)
{
Hla hlaIn = merAndHlaAndLabel.Key.Second;
Hla hlaOut = hlaForNormalization(hlaIn);
Dictionary <Hla, Dictionary <Hla, bool> > hla2ToHlaToLabel = SpecialFunctions.GetValueOrDefault(epitopeLearningData, merAndHlaAndLabel.Key.First);
Dictionary <Hla, bool> hlaToLabel = SpecialFunctions.GetValueOrDefault(hla2ToHlaToLabel, hlaOut);
hlaToLabel.Add(hlaIn, merAndHlaAndLabel.Value);
}
EpitopeLearningDataList.Add(epitopeLearningData);
}
}
HlaForNormalization = hlaForNormalization;
}
private static string SetSupertypeAny(Hla hla, SupertypeSpec hasBlanks)
{
switch (hasBlanks)
{
case SupertypeSpec.HasBlanksTrue:
{
HlaToLength hlaToLength = HlaToLength.GetInstanceABMixed(hla.Name);
string supertypeAny = hlaToLength.ToZero6SupertypeBlanksString();
return(supertypeAny);
}
case SupertypeSpec.HasBlanksFalse:
{
HlaToLength hlaToLength = HlaToLength.GetInstanceABMixed(hla.Name);
string supertypeAny = hlaToLength.ToZero6SupertypeNoBlanksString();
return(supertypeAny);
}
case SupertypeSpec.None:
return("none"); //!!!const
default:
SpecialFunctions.CheckCondition(false, "unknown SupertypeSpec: " + hasBlanks.ToString());
return(null);
}
}
private void AddToHlaToPriorLogOdds(Hla hla, Dictionary <int, int> lengthToSmoothedCount, int smoothedTotal, int k)
{
double relFreq = (double)lengthToSmoothedCount[k] / (double)smoothedTotal;
Dictionary <Hla, double> hlaToPriorLogOdds = SpecialFunctions.GetValueOrDefault(KToHlaToPriorLogOdds, k);
hlaToPriorLogOdds.Add(hla, SpecialFunctions.LogOdds((relFreq / .25) * RatioOfTrueToFalseTrainingExample));
}
static public Hla TrimToHla2(Hla hlaIn)
{
string hlaName = hlaIn.ToString();
SpecialFunctions.CheckCondition(hlaName.Length >= 3, string.Format("Expected hla name to have length of at least 3 (a class and two digits), but it is '{0}'.", hlaName));
Hla hlaOut = SingletonSpecification.HlaFactoryNoConstraints.GetGroundInstance(hlaName.Substring(0, 3));
return(hlaOut);
}
private void AddToSupertypeMap(Hla hla)
{
string supertypeAny = SetSupertypeAny(hla, HasBlanks);
if (supertypeAny != "unknown" && supertypeAny != "none") //!!!"unknown" is a misnomer. Should be "none" or null, but don't want to change it because it is already in useful models.
{
Set <Hla> hlaSet = SpecialFunctions.GetValueOrDefault(_supertypeMap, supertypeAny);
hlaSet.AddNewOrOld(hla);
}
}
public override bool Equals(object obj)
{
Hla other = obj as Hla;
if (null == other)
{
return(false);
}
else
{
return(this == other);
}
}
public static Prediction GetInstance(string inputPeptide, Hla hla, double posteriorProbability, double weightOfEvidence, NEC nec, int eStartPosition, int eLastPosition, string source)
{
Prediction prediction = new Prediction();
prediction.InputPeptide = inputPeptide;
prediction.Hla = hla;
prediction.PosteriorProbability = posteriorProbability;
prediction.WeightOfEvidence = weightOfEvidence;
prediction.NEC = nec;
prediction.EStartPosition = eStartPosition;
prediction.ELastPosition = eLastPosition;
prediction.Source = source;
return(prediction);
}
public override bool IsMoreGeneralThan(Hla hla)
{
Debug.Assert(!IsGround); // real assert
SpecialFunctions.CheckCondition(hla.IsGround); //We only have code for this
foreach (string subHlaName in Name.Split('/'))
{
if (subHlaName == hla.Name)
{
return(true);
}
}
return(false);
}
//static PatchPatternFactory PatchPatternFactory = PatchPatternFactory.GetFactory("strings");
//private static PatchPattern CreateStringPatchPattern(string peptide)
//{
// PatchPatternBuilder aPatchPatternBuilder = PatchPatternFactory.GetBuilder();
// aPatchPatternBuilder.AppendGroundDisjunct(peptide);
// PatchPattern patchPattern = aPatchPatternBuilder.ToPatchPattern();
// return patchPattern;
//}
public double Predict(NEC nec, Hla hla, bool modelOnly, out string source)
{
Debug.Assert(HlaFactory.IsGroundOrAbstractInstance(hla.ToString())); // real assert
SpecialFunctions.CheckCondition(nec.N.Length == SampleNEC.N.Length && nec.E.Length == SampleNEC.E.Length && nec.C.Length == SampleNEC.C.Length,
string.Format("Length of peptide must be {0},{1},{2}", SampleNEC.N.Length, SampleNEC.E.Length, SampleNEC.C.Length));
Pair <NEC, Hla> necAndHla = new Pair <NEC, Hla>(nec, hla);
List <Pair <string, Hla> > sourceAndOriginalHlaCollection = ListAllSourcesContainingThisMerAndHlaToLength(necAndHla);
source = SpecialFunctions.Join("+", sourceAndOriginalHlaCollection); //Will be "" if list is empty
double probability = (sourceAndOriginalHlaCollection.Count == 0 || modelOnly) ? probability = (double)Logistic.EvaluateViaCache(necAndHla) : 1.0;
return(probability);
}
public double Predict(List <Dictionary <string, string> > patientTable, NEC nec, bool modelOnly)
{
double predictedPTotal = 0.0;
foreach (Dictionary <string, string> patientRow in patientTable)
{
double product = 1.0;
foreach (KeyValuePair <string, string> columnAndValue in patientRow)
{
Hla hla = HlaFactory.GetGroundInstance(columnAndValue.Key.Substring(0, 1) + columnAndValue.Value);
Debug.Assert(nec.N.Length == SampleNEC.N.Length && nec.E.Length == SampleNEC.E.Length && nec.C.Length == SampleNEC.C.Length); // real assert
string sourceIgnore;
double probability = Predict(nec, hla, modelOnly, out sourceIgnore);
product *= 1.0 - probability;
}
double noiseyOrForThisPatient = 1.0 - product;
predictedPTotal += noiseyOrForThisPatient;
}
double predictedP = predictedPTotal / (double)patientTable.Count;
return(predictedP);
}
////!!! this could be moved into a class
//private object CreateKey(Prediction prediction, Best display)
//{
// switch (display)
// {
// case Best.overall:
// return "best";
// case Best.perHla:
// return prediction.Hla;
// case Best.perPrediction:
// return prediction;
// case Best.perLength:
// return prediction.K;
// case Best.perHlaAndLength:
// return new Pair<Hla, int>(prediction.Hla, prediction.K);
// default:
// SpecialFunctions.CheckCondition(false, "Don't know how to display " + display.ToString());
// return null;
// }
//}
/// <summary>
/// HlaSetSpecification class choices:
/// HlaSetSpecification.Singleton – Means that an Hla will be given and it is the only hla to be considered
/// HlaSetSpecification.Supertype – Means that a supertype will be given and it’s hlas should be considered
/// HlaSetSpecification.All – Means to consider all known hlas
/// </summary>
/// <param name="inputPeptide">a string of amino acids</param>
/// <param name="merLength">A value from the MerLength enum, which includes MerLength.scan, MerLength.given, MerLength.Eight, etc</param>
/// <param name="hlaSetSpecification">A predefined HlaSetSpecification class.</param>
/// <param name="hlaOrSupertypeOrNull">The hla or supertype required by HlaSetSpecification, or null for HlaSetSpecification.All</param>
/// <param name="modelOnly">If should report the probability from the model, even when the epitope is on a source list.</param>
/// <returns></returns>
public IEnumerable <Prediction> PredictionEnumeration(string inputPeptide, MerLength merLength, int?dOfCenter, HlaSetSpecification hlaSetSpecification, string hlaOrSupertypeOrNull, bool modelOnly)
{
Set <Hla> hlaSet = HlaSet(hlaSetSpecification, hlaOrSupertypeOrNull);
foreach (int eLength in KEnumeration(merLength, inputPeptide.Length))
{
Predictor predictor = KToPredictor[eLength];
Dictionary <Hla, double> hlaToPriorLogOdds = KToHlaToPriorLogOdds[eLength];
int necLength = NCLength + eLength + NCLength;
foreach (int startIndex in StartIndexEnumeration(inputPeptide.Length, necLength, dOfCenter))
{
string peptide = inputPeptide.Substring(startIndex, necLength);
NEC nec = NEC.GetInstance(peptide, NCLength, eLength, NCLength);
foreach (Hla hla in hlaSet)
{
Hla hlaForNormalization = HlaForNormalization(hla);
double priorLogOddsOfThisLengthAndHla;
if (!hlaToPriorLogOdds.TryGetValue(hlaForNormalization, out priorLogOddsOfThisLengthAndHla))
{
SpecialFunctions.CheckCondition(!RaiseErrorIfNotFoundInNormalizationTable, string.Format("Hla '{0}' (which is '{1}' for the purposes of normalization) and is not found in the normalization table", hla, hlaForNormalization));
priorLogOddsOfThisLengthAndHla = SpecialFunctions.LogOdds(RatioOfTrueToFalseTrainingExample);
}
string source;
double originalP = predictor.Predict(nec, hla, modelOnly, out source);
double originalLogOdds = SpecialFunctions.LogOdds(originalP);
double correctedLogOdds = originalLogOdds + priorLogOddsOfThisLengthAndHla;
double posteriorProbability = SpecialFunctions.InverseLogOdds(correctedLogOdds);
double weightOfEvidence = correctedLogOdds - SpecialFunctions.LogOdds(RatioOfTrueToFalseTrainingExample);
Prediction prediction = Prediction.GetInstance(inputPeptide, hla, posteriorProbability, weightOfEvidence, nec, startIndex + NCLength + 1, startIndex + NCLength + eLength, source);
yield return(prediction);
}
}
}
}
private List <Pair <string, Hla> > ListAllSourcesContainingThisMerAndHlaToLength(Pair <NEC, Hla> necAndHlaIn)
{
string peptide = necAndHlaIn.First.E;
Hla hlaNorm = HlaForNormalization(necAndHlaIn.Second);
List <Pair <string, Hla> > sourceAndOriginalHlaCollection = new List <Pair <string, Hla> >();
foreach (EpitopeLearningDataDupHlaOK epitopeLearningData in EpitopeLearningDataList)
{
if (null != epitopeLearningData && epitopeLearningData.ContainsKey(peptide))
{
Dictionary <Hla, Dictionary <Hla, bool> > hlaNormToHlaOriToLabel = epitopeLearningData[peptide];
if (hlaNormToHlaOriToLabel.ContainsKey(hlaNorm))
{
foreach (KeyValuePair <Hla, bool> hlaOriAndLabel in hlaNormToHlaOriToLabel[hlaNorm])
{
Debug.Assert(hlaOriAndLabel.Value); // real assert
sourceAndOriginalHlaCollection.Add(new Pair <string, Hla>(epitopeLearningData.Name, hlaOriAndLabel.Key));
}
}
}
}
return(sourceAndOriginalHlaCollection);
}
public virtual bool IsMoreGeneralThan(Hla possibleCause)
{
throw new Exception("The method or operation is not implemented.");
}
static public Hla Identity(Hla hla)
{
return(hla);
}
