public static Leaf GetLeafInstance(StreamReader streamreader)
{
StringBuilder sb = new StringBuilder();
while (true)
{
char peek = Peek(streamreader);
if (peek == ':')
{
break;
}
SpecialFunctions.CheckCondition(!("()".Contains(peek.ToString())));
sb.Append(Read(streamreader));
}
Leaf leaf = new Leaf();
leaf.CaseName = sb.ToString();
if (leaf.CaseName.Contains("->")) //!!!const
{
int pos = leaf.CaseName.IndexOf("->");
Debug.Assert(pos >= 0); // real assert
int nodeId = int.Parse(leaf.CaseName.Substring(0, pos));
leaf.CaseName = leaf.CaseName.Substring(pos + 2);
Debug.WriteLine(SpecialFunctions.CreateTabString("NodeId", nodeId));
}
return(leaf);
}
private static void BinarySearchForNonInfiniteEvaluation(
double nonInfInput, double nonInfOutput,
double infInput, double infOutput,
out double bestInput, out double bestOutput,
//FuncEval nonInfiniteEval, FuncEval infiniteEval,
Converter <double, double> oneDRealFunctionInSearchSpace, double inputTol, double outputTol)
{
SpecialFunctions.CheckCondition(!double.IsInfinity(nonInfOutput));
double mid = (nonInfInput + infInput) / 2.0;
double fOfMid = oneDRealFunctionInSearchSpace(mid);
//FuncEval mid = new FuncEval((nonInfiniteEval.X + infiniteEval.X) / 2, oneDRealFunctionInSearchSpace);
Debug.WriteLine(string.Format("Binary search: f({0}) = {1}, f({2}) = {3}", nonInfInput, nonInfOutput, infInput, infOutput));
if (Math.Abs(fOfMid - nonInfOutput) < outputTol)
{
Debug.Assert(!double.IsInfinity(fOfMid));
bestInput = mid;
bestOutput = fOfMid;
}
else if (Math.Abs(mid - nonInfInput) < inputTol)
{
bestInput = nonInfInput;
bestOutput = nonInfOutput;
}
else if (double.IsInfinity(fOfMid))
{
BinarySearchForNonInfiniteEvaluation(nonInfInput, nonInfOutput, mid, fOfMid, out bestInput, out bestOutput, oneDRealFunctionInSearchSpace, inputTol, outputTol);
}
else
{
BinarySearchForNonInfiniteEvaluation(mid, fOfMid, infInput, infOutput, out bestInput, out bestOutput, oneDRealFunctionInSearchSpace, inputTol, outputTol);
}
}
internal static KeyValuePair <MerAndHlaToLength, bool> GetRandomInstance(MerAndHlaToLength[] originalTrainingKeysAsArray, bool label, Random random)
{
MerAndHlaToLength hlaModel = originalTrainingKeysAsArray[random.Next(originalTrainingKeysAsArray.Length)];
MerAndHlaToLength aMerAndHlaToLength = new MerAndHlaToLength();
aMerAndHlaToLength.HlaToLength = hlaModel.HlaToLength;
//aMerAndHlaToLength.Study = hlaModel.Study;
aMerAndHlaToLength.KmerDefinition = hlaModel.KmerDefinition;
int merLength = hlaModel.Mer.Length;
char[] rgchMer = new char[hlaModel.Mer.Length];
for (int iMer = 0; iMer < rgchMer.Length; ++iMer)
{
MerAndHlaToLength merModel = originalTrainingKeysAsArray[random.Next(originalTrainingKeysAsArray.Length)];
SpecialFunctions.CheckCondition(merLength == merModel.Mer.Length); //!!!raise error - the selection will not be uniform unless all are off the same length
rgchMer[iMer] = merModel.Mer[random.Next(merLength)];
}
aMerAndHlaToLength.Mer = new string(rgchMer);
KeyValuePair <MerAndHlaToLength, bool> aMerAndHlaToLengthWithLabel
= new KeyValuePair <MerAndHlaToLength, bool>(aMerAndHlaToLength, label);
return(aMerAndHlaToLengthWithLabel);
}
private bool CoreIsMoreGeneralThan(AASet c1, AASet c2)
{
SpecialFunctions.CheckCondition(IsCore(c1) && IsCore(c2)); //!!!raise error
bool b = ((c1 & (~c2)) != AASet.Empty);
return(b);
}
private static bool ExtractFlankSize(out int flankSize, string featurerizerName, params string[] mainNameCollection)
{
//!!!should use Regex
foreach (string mainName in mainNameCollection)
{
if (featurerizerName.Equals(mainName))
{
flankSize = 0;
return(true);
}
if (featurerizerName.StartsWith(mainName))
{
string rest = featurerizerName.Substring(mainName.Length);
if (!rest.StartsWith("."))
{
continue;
}
SpecialFunctions.CheckCondition(rest.Length >= 2, "Expect '.NUMBER' after main name of featurizer");
flankSize = int.Parse(rest.Substring(1));
return(true);
}
}
flankSize = int.MinValue;
return(false);
}
public GeneticCodeMapping(string codon, string aminoAcid, bool normal)
{
SpecialFunctions.CheckCondition(codon.Length == 3); //!!!raise error
Codon = codon;
AminoAcid = aminoAcid;
Normal = normal;
}
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);
}
}
static HlaAssignMain CreateProgramFromArguments(string[] args)
{
ArgCollection argCollection = ArgCollection.GetInstance(args);
if (argCollection.ExtractOptionalFlag("help"))
{
Console.WriteLine();
Console.WriteLine(UsageMessage);
Console.WriteLine(HelpMessage);
return(null);
}
bool bExcel = argCollection.ExtractOptionalFlag("EXCEL");
argCollection.CheckNoMoreOptions();
double?leakProbabilityOrNull = argCollection.ExtractNext <double?>("leakProbabilityOrNull");
double pValue = argCollection.ExtractNext <double>("pValue");
string directoryName = argCollection.ExtractNext <string>("directory");
string caseName = argCollection.ExtractNext <string>("caseName");
string hlaFactoryName = argCollection.ExtractNext <string>("hlaFactory");
RangeCollection pieceIndexRange = argCollection.ExtractNext <RangeCollection>("pieceIndexRange");
int pieceCount = argCollection.ExtractNext <int>("pieceCount");
SpecialFunctions.CheckCondition(0 <= pieceIndexRange.FirstElement && pieceIndexRange.LastElement < pieceCount, "The pieceIndexRange must be a subrange of " + RangeCollection.GetInstance(0, pieceCount - 1).ToString());
RangeCollection nullIndexRange = argCollection.ExtractNext <RangeCollection>("nullIndexRange");
argCollection.CheckThatEmpty();
return(new HlaAssignMain(bExcel, leakProbabilityOrNull, pValue, directoryName, caseName, hlaFactoryName, pieceIndexRange, pieceCount, nullIndexRange));
}
public HlaMsr1 GetGroundInstance(string name, ref HashSet <string> warningSet)
{
HlaMsr1 hla = (HlaMsr1)GetGroundOrAbstractInstance(name, ref warningSet);
SpecialFunctions.CheckCondition(hla.IsGround, "Hla is not ground. " + name);
return(hla);
}
private IEnumerable <int> KEnumeration(MerLength merLength, int inputPeptideLength)
{
switch (merLength)
{
case MerLength.scan:
for (int k = (int)MerLength.firstLength; k <= (int)MerLength.lastLength; ++k)
{
yield return(k);
}
break;
case MerLength.given:
int inputEpitopeLength = inputPeptideLength - NCLength - NCLength;
SpecialFunctions.CheckCondition((int)MerLength.firstLength <= inputEpitopeLength && inputEpitopeLength <= (int)MerLength.lastLength,
string.Format("Given peptide length {0} is out of range", inputPeptideLength));
yield return(inputEpitopeLength);
break;
default:
SpecialFunctions.CheckCondition(MerLength.firstLength <= merLength && merLength <= MerLength.lastLength,
string.Format("Given peptide length {0} is out of range", (int)merLength));
yield return((int)merLength);
break;
}
}
internal IEnumerable <HlaMsr1> GeneralizationList(HlaMsr1Factory hlaMsr1Factory)
{
HashSet <string> warningSetToIgnore = new HashSet <string>();
SpecialFunctions.CheckCondition(IsGround, "Can only get generalization list for ground hlas");
if (Name.Length == 5)
{
yield return(this);
}
if (Name.Length >= 3)
{
string twoDigit = Name.Substring(0, 3);
if (HlaMsr1Factory.MoreThan100.ContainsKey(twoDigit))
{
twoDigit = ClassName + HlaMsr1Factory.MoreThan100[twoDigit];
}
yield return((HlaMsr1)hlaMsr1Factory.GetGroundOrAbstractInstance(twoDigit, ref warningSetToIgnore));
Debug.Assert(warningSetToIgnore.Count == 0); // real assert
}
yield return((HlaMsr1)hlaMsr1Factory.GetGroundOrAbstractInstance(ClassName, ref warningSetToIgnore));
Debug.Assert(warningSetToIgnore.Count == 0); // real assert
}
static public PatchPatternFactory GetFactory(string language)
{
SpecialFunctions.CheckCondition(language == "strings", "patch language must be 'strings'");
PatchPatternFactory patchPatternFactory = new PatchStringFactory();
return(patchPatternFactory);
}
static public AASet UnifyOrEmpty(AASet c1, AASet c2)
{
SpecialFunctions.CheckCondition(!AASetSequence.IsOptional(c1) && !AASetSequence.IsOptional(c2)); //!!!raise error
AASet result = c1 & c2;
return(result);
}
static public HlaFactory GetFactory(string name)
{
HlaFactory hlaFactory;
//!!!switch to switch
if (name == "noConstraints")
{
hlaFactory = new NoConstraints();
}
else if (name == "MixedWithB15AndA68")
{
hlaFactory = new MixedWithB15AndA68();
}
else if (name == "FourDigit")
{
hlaFactory = new FourDigit();
}
else if (name == "JustSlash")
{
hlaFactory = new JustSlash();
}
else
{
SpecialFunctions.CheckCondition(false, "Don't know how to create HlaFactory " + name);
hlaFactory = null;
}
hlaFactory.Name = name;
return(hlaFactory);
}
void stopButton_Click(object sender, RoutedEventArgs e)
{
SpecialFunctions.CheckCondition(stopButton.IsEnabled, "expect stopButton to be enabled");
switch ((string)stopButton.Content)
{
case "Pause": //!!!Const
{
CompositionTarget.Rendering -= CurrentRenderingDelegate;
stopButton.Content = "Continue";
showLastCheckBox.IsEnabled = true;
break;
}
case "Continue": //!!!Const
{
stopButton.Content = "Pause";
CompositionTarget.Rendering += CurrentRenderingDelegate;
showLastCheckBox.IsEnabled = false;
break;
}
default:
{
SpecialFunctions.CheckCondition(false, "Don't know state " + stopButton.Content);
break;
}
}
}
//private bool AllVarianceZero(Dictionary<string, GaussianStatistics> caseNameToTarget)
private static bool AllVarianceZero(IEnumerable <Leaf> LeafCollection, Converter <Leaf, SufficientStatistics> caseNameToTarget)
{
bool varianceIsZero = false; //If empty input, then return false
bool firstTime = true;
foreach (Leaf leaf in LeafCollection)
{
SufficientStatistics stats = caseNameToTarget(leaf);
if (stats.IsMissing())
{
continue;
}
GaussianStatistics gaussianStatistics = (GaussianStatistics)stats;
SpecialFunctions.CheckCondition((gaussianStatistics.Variance == 0) == (gaussianStatistics.SampleSize == 1), "Variance must be zero exactly when the sample size is 1");
if (firstTime)
{
firstTime = false;
varianceIsZero = (gaussianStatistics.Variance == 0);
}
else
{
SpecialFunctions.CheckCondition(varianceIsZero == (gaussianStatistics.Variance == 0), "If any variances are zero, then all must be zero");
}
}
return(varianceIsZero);
}
public static OneDOptimization GetInstance(string optimizerName)
{
//Console.WriteLine("Using {0} for 1D optimization.", optimizerName);
if (optimizerName.Equals("default", StringComparison.CurrentCultureIgnoreCase))
{
optimizerName = "brentthengrid";
}
optimizerName = optimizerName.ToLower();
if (optimizerName == "grid")
{
return(new OneDGrid());
}
string brentwithnogrid = "brentwithnogrid";
if (optimizerName.StartsWith(brentwithnogrid))
{
double tol = GetTolOrDefault(optimizerName, brentwithnogrid);
return(new Brent(tol));
}
string brentthengrid = "brentthengrid";
if (optimizerName.StartsWith(brentthengrid))
{
double tol = GetTolOrDefault(optimizerName, brentthengrid);
return(new BrentThenGrid(tol));
}
SpecialFunctions.CheckCondition(false, string.Format("The optimizer named {0} is no known", optimizerName));
return(null);
}
internal static PatchTable GetInstanceWithUniformWeights(VaccineMaker vaccineMaker)
{
SpecialFunctions.CheckCondition(vaccineMaker is Greedy);
Greedy greedy = (Greedy)vaccineMaker;
return(GetInstanceWithUniformWeightByLength(PatchPatternCollection(greedy)));
}
static public HlaToLength GetInstanceABMixed(string hlaPattern)
{
HlaToLength aHlaToLength = new HlaToLength();
aHlaToLength.HlaResolution = HlaResolution.ABMixed;
if (HlaResolution.TwoDigitHlaPatternIsOK(hlaPattern))
{
aHlaToLength._hlaClass = hlaPattern.Substring(0, 1);
aHlaToLength._hlaNumberToLength = int.Parse(hlaPattern.Substring(1));
SpecialFunctions.CheckCondition(aHlaToLength._hlaClass != "B" || aHlaToLength._hlaNumberToLength != 15); //!!!raise error
SpecialFunctions.CheckCondition(aHlaToLength._hlaClass != "A" || aHlaToLength._hlaNumberToLength != 68); //!!!raise error
}
else
{
HlaToLength hlaToLengthFour = GetInstanceFour(hlaPattern);
int twoDigits = hlaToLengthFour.TwoDigits();
if ((twoDigits == 15 && hlaToLengthFour.HlaClass == "B") || (twoDigits == 68 && hlaToLengthFour.HlaClass == "A"))
{
aHlaToLength._hlaClass = hlaToLengthFour.HlaClass;
aHlaToLength._hlaNumberToLength = hlaToLengthFour._hlaNumberToLength;
}
else
{
aHlaToLength._hlaClass = hlaToLengthFour.HlaClass;
aHlaToLength._hlaNumberToLength = twoDigits;
}
}
return(aHlaToLength);
}
// public bool IsLessGeneralThan(Disjunct other)
// {
// SpecialFunctions.CheckCondition(this != other); //!!! raise error
// SpecialFunctions.CheckCondition(FullAsString != other.FullAsString); //!!! raise error
//
// bool b = CoreIsLessGeneralThan(other) && BeforeOrAfterIsLessGeneralThan(Before, other.Before) && BeforeOrAfterIsLessGeneralThan(After, other.After);
// return b;
// }
// private bool CoreIsLessGeneralThan(Disjunct other)
// {
// SpecialFunctions.CheckCondition(Core.Count == other.Core.Count); //!!! raise error
// bool bAtLeastOneCharOfOtherIsMoreGeneral = false;
// for(int i = 0; i < Core.Count; ++i)
// {
// AASet cMe = Core[i];
// AASet cOther = other.Core[i];
// if (CoreIsMoreGeneralThan(cMe, cOther))
// {
// return false;
// }
// else if (CoreIsMoreGeneralThan(cOther, cMe))
// {
// bAtLeastOneCharOfOtherIsMoreGeneral = true;
// }
// }
// return bAtLeastOneCharOfOtherIsMoreGeneral;
// }
// static private bool BeforeOrAfterIsLessGeneralThan(AASetSequence flanking1, AASetSequence flanking2)
// {
// if (flanking1.Count > flanking2.Count)
// {
// return false;
// }
//
// bool bAtLeastOneCharOfOtherIsMoreGeneral = (flanking2.Count > flanking1.Count);
// for(int i = 0; i < flanking1.Count; ++i)
// {
// AASet c1 = flanking1[i];
// AASet c2 = flanking2[i];
// if (BeforeOrAfterIsMoreGeneralThan(c1, c2))
// {
// return false;
// }
// else if (BeforeOrAfterIsMoreGeneralThan(c2, c1))
// {
// bAtLeastOneCharOfOtherIsMoreGeneral = true;
// }
// }
// return bAtLeastOneCharOfOtherIsMoreGeneral;
// }
static private bool BeforeOrAfterIsMoreGeneralThan(AASet c1, AASet c2)
{
SpecialFunctions.CheckCondition(!IsCore(c1) && !IsCore(c2)); //!!!raise error
bool b = (c1 == AASet.OptionalAny && c2 != AASet.OptionalAny);
return(b);
}
public string ToZero6SupertypeNoBlanksString()
{
SpecialFunctions.CheckCondition(HlaResolution == HlaResolution.ABMixed, "Currently, supertype is only defined for ABMixed");
string asString = ToString();
return(ToZero6SupertypeNoBlanksString(asString));
}
public bool IsLessGeneralThan(Disjunct other)
{
SpecialFunctions.CheckCondition(this != other); //!!! raise error
SpecialFunctions.CheckCondition(FullAsString != other.FullAsString); //!!! raise error
bool falseForSure;
bool bAtLeastOneCharOfOtherIsMoreGeneral = false;
CoreIsLessGeneralThan(other, out falseForSure, ref bAtLeastOneCharOfOtherIsMoreGeneral);
if (falseForSure)
{
return(false);
}
BeforeOrAfterIsLessGeneralThan(Before, other.Before, out falseForSure, ref bAtLeastOneCharOfOtherIsMoreGeneral);
if (falseForSure)
{
return(false);
}
BeforeOrAfterIsLessGeneralThan(After, other.After, out falseForSure, ref bAtLeastOneCharOfOtherIsMoreGeneral);
if (falseForSure)
{
return(false);
}
;
return(bAtLeastOneCharOfOtherIsMoreGeneral);
}
static public HlaToLength GetInstance(string hlaPattern, HlaResolution hlaResolution)
{
HlaToLength aHlaToLength = hlaResolution.GetHlaLengthInstance(hlaPattern);
SpecialFunctions.CheckCondition(aHlaToLength != null);
return(aHlaToLength);
}
private static bool ExtractFlankSize(out int flankSize, out string given, string featurerizerName, params string[] mainNameCollection)
{
//!!!should use regex
int posGiven = featurerizerName.IndexOf('@');
if (posGiven < 0)
{
given = null;
flankSize = int.MinValue;
return(false);
}
string prefix = featurerizerName.Substring(0, posGiven + 1);
int posDot = featurerizerName.IndexOf('.');
SpecialFunctions.CheckCondition(posDot >= 0 && posDot > posGiven, "'Given' features must have an explicit '.FlankSize'");
given = featurerizerName.Substring(posGiven + 1, posDot - posGiven - 1);
string flankSizeAsString = featurerizerName.Substring(posDot + 1);
flankSize = int.Parse(flankSizeAsString);
foreach (string mainName in mainNameCollection)
{
if (prefix.Equals(mainName))
{
return(true);
}
}
return(false);
}
/// <summary>
/// Read table from http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html
/// </summary>
private void ReadTheGeneticCode()
{
Debug.Assert(CodonToAminoAcid == null); // real assert
CodonToAminoAcid = new Dictionary <string, GeneticCodeMapping>();
AminoAcidCollection = new Dictionary <string, bool>();
//!!!could load these into memory instead of reading them over and over again
string sTheGenenicCodeFile = @"GeneticCodeDna.txt"; //!!!const
using (StreamReader streamreaderTheGenenicCodeFile = OpenResource(sTheGenenicCodeFile))
{
string sLine = null;
while (null != (sLine = streamreaderTheGenenicCodeFile.ReadLine()))
{
string[] rgFields = sLine.Split('\t');
SpecialFunctions.CheckCondition(rgFields.Length == 3); //!!!raise error
string sCodon = rgFields[0];
SpecialFunctions.CheckCondition(sCodon.Length == 3); //!!!raise error
string sAminoAcid = rgFields[1];
bool bNormal = bool.Parse(rgFields[2]); //!!!could raise error
GeneticCodeMapping aGeneticCodeMapping = new GeneticCodeMapping(sCodon, sAminoAcid, bNormal);
CodonToAminoAcid.Add(sCodon, aGeneticCodeMapping);
if (!AminoAcidCollection.ContainsKey(sAminoAcid))
{
AminoAcidCollection.Add(sAminoAcid, true);
}
}
}
}
// !! Add support for ModelTesterGaussian
public static NullDataGenerator GetInstance(string generatorName, ModelScorer modelScorer, IDistribution distribution)
{
switch (generatorName.ToLower())
{
case "predictorpermutation":
return(new NullDataGeneratorPredictorPermutation());
case "targetpermutation":
return(new NullDataGeneratorTargetPermutation());
case "predictorparametric":
//!!HACK!! We can currently only evolve binary data. But even if modelTester is gaussian, the predictor is still binary.
// so all we need is a discrete model tester with any distribution (they all have the same null distribution, which is all
// that's used.
SpecialFunctions.CheckCondition(distribution is DistributionDiscrete, "Parametric data generation is currently only supported for discrete variables");
return(new NullDataGeneratorPredictorParametric(modelScorer, (DistributionDiscrete)distribution));
case "targetparametric":
SpecialFunctions.CheckCondition(distribution is DistributionDiscrete, "Parametric data generation is currently only supported for discrete variables");
return(new NullDataGeneratorTargetParametric(modelScorer, (DistributionDiscrete)distribution));
default:
throw new ArgumentException("Cannot parse " + generatorName + " into a NullDataGenerator");
}
}
//public AAMatch Match(SimpleAminoAcidSet aminoAcidCollection2)
//{
// Debug.Fail("Be sure this has Match defined the desired way");
// Debug.Assert(false); //!!!where is this called?
// if (this == null || aminoAcidCollection2 == null) //!!!const
// {
// return AAMatch.NA;
// }
// if (PositiveCount != 1 || aminoAcidCollection2.PositiveCount() != 1)
// {
// return AAMatch.FALSE;
// }
// // There is only one item
// foreach (string s in Positives)
// {
// if (aminoAcidCollection2.Contains(s))
// {
// return AAMatch.TRUE;
// }
// else
// {
// return AAMatch.FALSE;
// }
// }
// Debug.Assert(false);
// return AAMatch.NA;
//}
static public AAMatch Match(string sAminoAcid, string sAminoAcidPatientHiv)
{
SpecialFunctions.CheckCondition(sAminoAcid != "<none>"); //!!!const //!!! raise error
SpecialFunctions.CheckCondition(!sAminoAcid.StartsWith("Not an amino acid:")); //!!!const //!!!raise error
//Debug.Assert(sAminoAcid.Length == 3 || sAminoAcid == "STOP"); //!!!const
if (sAminoAcidPatientHiv == "<none>") //!!!const
{
return(AAMatch.NA);
}
if (sAminoAcidPatientHiv == sAminoAcid)
{
// Being equal is a match only if they are not ambiguous
if (sAminoAcid == "Ambiguous Amino Acid") //!!!const
{
return(AAMatch.FALSE);
}
else
{
return(AAMatch.TRUE);
}
}
else
{
Debug.Assert(sAminoAcidPatientHiv != null); //real assert
return(AAMatch.FALSE);
}
}
private static string LanlFileNormalizedOutput(string fileSuffix, HlaResolution hlaResolution)
{
SpecialFunctions.CheckCondition(fileSuffix == "Lanl"); //!!!raise error
string sInputFileName = string.Format(@"lanl-{0}digit.Normalized.new.txt", hlaResolution.ShortName); //!!!const
return(sInputFileName);
}
public override HlaToLength GetHlaLengthInstanceWithFixup(string name)
{
Match aMatch = HlaParseRegex.Match(name);
SpecialFunctions.CheckCondition(aMatch.Success);
string theClass = aMatch.Groups["class"].Value;
string num = aMatch.Groups["number"].Value;
string s = null;
if (num.Length == 4)
{
s = string.Format("{0}{1}", theClass[0], num);
}
else
{
SpecialFunctions.CheckCondition(false);
}
return(GetHlaLengthInstance(s));
/*
* HLA-A*0201
* HLA-A*1101
* HLA-B*0801
* HLA-B*2705
* HLA-B*2709
* HLA-B*3501
* HLA-B*4402
* HLA-B*4403
* HLA-B*5101
* HLA-B*5301
* HLA-CW*3
* HLA-CW*4
*/
}