static public void Test()
{
RangeCollection aRangeCollection = RangeCollection.GetInstance();
aRangeCollection.Add(0);
SpecialFunctions.CheckCondition("0-0" == aRangeCollection.ToString());
aRangeCollection.Add(1);
SpecialFunctions.CheckCondition("0-1" == aRangeCollection.ToString());
aRangeCollection.Add(4);
SpecialFunctions.CheckCondition("0-1,4-4" == aRangeCollection.ToString());
aRangeCollection.Add(5);
SpecialFunctions.CheckCondition("0-1,4-5" == aRangeCollection.ToString());
aRangeCollection.Add(7);
SpecialFunctions.CheckCondition("0-1,4-5,7-7" == aRangeCollection.ToString());
aRangeCollection.Add(2);
SpecialFunctions.CheckCondition("0-2,4-5,7-7" == aRangeCollection.ToString());
aRangeCollection.Add(3);
SpecialFunctions.CheckCondition("0-5,7-7" == aRangeCollection.ToString());
aRangeCollection.Add(6);
SpecialFunctions.CheckCondition("0-7" == aRangeCollection.ToString());
aRangeCollection.Add(-10);
SpecialFunctions.CheckCondition("-10--10,0-7" == aRangeCollection.ToString());
aRangeCollection.Add(-5);
SpecialFunctions.CheckCondition("-10--10,-5--5,0-7" == aRangeCollection.ToString());
aRangeCollection = RangeCollection.Parse("1-5,7-12,13-14");
Console.WriteLine(aRangeCollection);
Console.WriteLine(aRangeCollection.Contains(3));
Console.WriteLine(aRangeCollection.Contains(12));
Console.WriteLine(aRangeCollection.Contains(13));
Console.WriteLine(aRangeCollection.Contains(6));
aRangeCollection = RangeCollection.Parse("-10--5,-1-14");
Console.WriteLine(aRangeCollection);
Console.WriteLine(aRangeCollection.Contains(-12));
Console.WriteLine(aRangeCollection.Contains(-10));
Console.WriteLine(aRangeCollection.Contains(-7));
Console.WriteLine(aRangeCollection.Contains(-5));
Console.WriteLine(aRangeCollection.Contains(-4));
Console.WriteLine(aRangeCollection.Contains(0));
Console.WriteLine(aRangeCollection.Contains(1));
Console.WriteLine(aRangeCollection.Contains(-2));
Console.WriteLine("Count: " + aRangeCollection.Count());
Console.WriteLine("Count -5 to 2: " + aRangeCollection.Count(-5, 2));
RangeCollectionCollection rcc = RangeCollectionCollection.GetInstance(aRangeCollection);
Console.WriteLine(rcc);
Console.WriteLine(rcc.GetContainingRangeCollection(-12));
Console.WriteLine(rcc.GetContainingRangeCollection(-10));
Console.WriteLine(rcc.GetContainingRangeCollection(-5));
Console.WriteLine(rcc.GetContainingRangeCollection(3));
Console.WriteLine(rcc.GetContainingRangeCollection(15));
}
public void ScoreTree(
ModelScorer modelScorer,
PhyloTree phyloTree,
string predictorSparseFileName,
string targetSparseFileName,
string predictorVariableName,
string targetVariableName,
double[] nullModelArgs,
double[] altModelArgs)
{
//Dictionary<string, Dictionary<string, SufficientStatistics>> predictorVariableToCaseIdToRealNonMissingValue = LoadSparseFileInMemory(predictorSparseFileName);
IEnumerable <Pair <string, Dictionary <string, SufficientStatistics> > > predictorNameAndCaseIdToNonMissingValueEnumeration = LoadSparseFileEnumeration(predictorSparseFileName);
IEnumerable <Pair <string, Dictionary <string, SufficientStatistics> > > targetNameAndCaseIdToNonMissingValueEnumeration = LoadSparseFileEnumeration(targetSparseFileName);
RangeCollection nullIndexRangeCollection = RangeCollection.GetInstance(-1, -1);
NullDataCollection nullDataGenerator =
CreateNullDataGenerator("PredictorPermutation", modelScorer, phyloTree, nullIndexRangeCollection,
predictorNameAndCaseIdToNonMissingValueEnumeration, targetNameAndCaseIdToNonMissingValueEnumeration);
UniversalWorkList workList = UniversalWorkList.GetInstance(
predictorNameAndCaseIdToNonMissingValueEnumeration,
targetNameAndCaseIdToNonMissingValueEnumeration,
//targetNameAndCaseIdToNonMissingValueEnumeration,
nullDataGenerator, nullIndexRangeCollection, AlwaysKeep <Dictionary <string, string> > .GetInstance());
foreach (RowData rowAndTargetData in workList.List())
{
if (rowAndTargetData.Row[PhyloTree.PredictorVariableColumnName] == predictorVariableName &&
rowAndTargetData.Row[PhyloTree.TargetVariableColumnName] == targetVariableName)
{
Dictionary <string, SufficientStatistics> caseIdToNonNullPredictorValue = rowAndTargetData.PredictorData;//workList.GetCaseIdToNonMissingValueForNullIndexAndPredictorVariable(-1, predictorVariableName);
Dictionary <string, SufficientStatistics> caseIdToNonMissingTargetValue = rowAndTargetData.TargetData;
Converter <Leaf, SufficientStatistics> targetDistributionMap = CreateSufficientStatisticsMap(caseIdToNonMissingTargetValue);
Converter <Leaf, SufficientStatistics> predictorDistributionClassFunction = CreateSufficientStatisticsMap(caseIdToNonNullPredictorValue);
Converter <Leaf, SufficientStatistics> altDistributionMap = CreateAlternativeSufficientStatisticsMap(predictorDistributionClassFunction, targetDistributionMap);
double logLikelihood;
Score scoreIndTarget, scoreIndPredictor, scoreAlt;
MessageInitializer messageInitializer;
OptimizationParameterList nullParams = NullModelDistribution.GetParameters(nullModelArgs);
OptimizationParameterList altParams = AltModelDistribution.GetParameters(altModelArgs);
Console.WriteLine(SpecialFunctions.CreateTabString("Variable", nullParams.ToStringHeader(), "LogL"));
messageInitializer = modelScorer.CreateMessageInitializer(predictorDistributionClassFunction, targetDistributionMap, NullModelDistribution);
logLikelihood = modelScorer.ComputeLogLikelihoodModelGivenData(messageInitializer, nullParams);
scoreIndTarget = Score.GetInstance(logLikelihood, nullParams);
Console.WriteLine("Target\t" + scoreIndTarget);
messageInitializer = modelScorer.CreateMessageInitializer(targetDistributionMap, predictorDistributionClassFunction, NullModelDistribution);
logLikelihood = modelScorer.ComputeLogLikelihoodModelGivenData(messageInitializer, nullParams);
modelScorer.ComputeLogLikelihoodModelGivenData(messageInitializer, nullParams);
scoreIndPredictor = Score.GetInstance(logLikelihood, nullParams);
Console.WriteLine("Predictor\t" + scoreIndPredictor);
Console.WriteLine("\n" + SpecialFunctions.CreateTabString("Variable", altParams.ToStringHeader(), "LogL"));
messageInitializer = modelScorer.CreateMessageInitializer(null, altDistributionMap, AltModelDistribution);
logLikelihood = modelScorer.ComputeLogLikelihoodModelGivenData(messageInitializer, altParams);
scoreAlt = Score.GetInstance(logLikelihood, altParams);
Console.WriteLine(SpecialFunctions.CreateTabString(AltModelDistribution, scoreAlt));
}
}
}