public void ValidateMatrixFactoryParse()
{
_denseMatObj = GetDenseMatrix();
MatrixFactory <String, String, Double> mfObj =
MatrixFactory <String, String, Double> .GetInstance();
ParallelOptions poObj = new ParallelOptions();
TryParseMatrixDelegate <string, string, double> a =
new TryParseMatrixDelegate <string, string, double>(this.TryParseMatrix);
mfObj.RegisterMatrixParser(a);
// Writes the text file
_denseMatObj.WritePaddedDouble(Constants.FastQTempTxtFileName, poObj);
Matrix <string, string, double> newMatObj =
mfObj.Parse(Constants.FastQTempTxtFileName, double.NaN, poObj);
Assert.AreEqual(_denseMatObj.RowCount, newMatObj.RowCount);
Assert.AreEqual(_denseMatObj.RowKeys.Count, newMatObj.RowKeys.Count);
Assert.AreEqual(_denseMatObj.ColCount, newMatObj.ColCount);
Assert.AreEqual(_denseMatObj.ColKeys.Count, newMatObj.ColKeys.Count);
Assert.AreEqual(_denseMatObj.Values.Count(), newMatObj.Values.Count());
Console.WriteLine(
"MatrixFactory BVT : Successfully validated Parse() method");
ApplicationLog.WriteLine(
"MatrixFactory BVT : Successfully validated Parse() method");
}
//public void ParseArgs(ArgumentCollection argumentCollection)
//{
// KeepOneValueVariables = argumentCollection.ExtractOptionalFlag("keepOneValueVariables");
// //MissingChar = argumentCollection.ExtractOptional<char>("missingChar", '?');
// //int? merLengthOrNull = argumentCollection.ExtractOptional<int?>("Mer", null); // we don't seem to actually use this...
// CurrentMixtureSemantics = argumentCollection.ExtractOptional<MixtureSemantics>("MixtureSemantics", MixtureSemantics.Uncertainty);
// //Helper.CheckCondition(null == merLengthOrNull || mixtureSemantics == MixtureSemantics.Uncertainty, "The 'Mer' option cannot be used with '-MixtureSemantics pure' or '-MixtureSemantics any'");
//}
//public override void ParseReadArgs(ArgumentCollection argumentCollection)
//{
// base.ParseReadArgs(argumentCollection);
// ParseArgs(argumentCollection);
//}
//public override void ParseWriteArgs(ArgumentCollection argumentCollection)
//{
// base.ParseWriteArgs(argumentCollection);
// ParseArgs(argumentCollection);
// Format = argumentCollection.ExtractNext<SequenceMatrix.WriteFormat>("WriteFormat");
// Type = argumentCollection.ExtractNext<SequenceMatrix.WriteType>("WriteFormat");
//}
public override List <NamedSequence> Parse(TextReader reader)
{
MatrixFactory <string, string, SufficientStatistics> mf = MatrixFactory <string, string, SufficientStatistics> .GetInstance();
string filename = MBT.Escience.FileUtils.WriteTextReaderToTempFile(reader);
var matrix = mf.Parse(filename, MissingStatistics.GetInstance(), new ParallelOptions());
return(ConvertToSequences(matrix));
}
public void ValidateMatrixFactoryRegisterMatrixParser()
{
MatrixFactory <String, String, Double> mfactObj =
MatrixFactory <String, String, Double> .GetInstance();
TryParseMatrixDelegate <string, string, double> tryParseDelObj =
new TryParseMatrixDelegate <string, string, double>(TryParseMatrix);
mfactObj.RegisterMatrixParser(tryParseDelObj);
Assert.IsTrue(true,
"No exceptions were thrown on running RegisterMatrixParser() method");
}
public void ValidateMatrixFactoryAllMethods()
{
denseMatObj = GetDenseMatrix();
MatrixFactory <String, String, Double> mfObj =
MatrixFactory <String, String, Double> .GetInstance();
Assert.IsTrue(string.IsNullOrEmpty(mfObj.ErrorMessages));
ApplicationLog.WriteLine(
"MatrixFactory BVT : Successfully validated All methods");
}
/// <summary>
/// Loads a single mergeView matrix from the list of files.
/// </summary>
/// <typeparam name="TRowKey"></typeparam>
/// <typeparam name="TColKey"></typeparam>
/// <typeparam name="TVal"></typeparam>
/// <param name="files"></param>
/// <param name="missingVal"></param>
/// <param name="colsMustMatch"></param>
/// <returns></returns>
public static Matrix <TRowKey, TColKey, TVal> LoadAsSingleMatrix <TRowKey, TColKey, TVal>(this IEnumerable <FileInfo> files, TVal missingVal, bool colsMustMatch = false)
{
MatrixFactory <TRowKey, TColKey, TVal> mf = MatrixFactory <TRowKey, TColKey, TVal> .GetInstance();
//var matrices = files.Select(dataFile => mf.Parse(dataFile.FullName, missingVal, ParallelOptionsScope.Current)).ToArray();
var matrices = (from f in files
let name = f.Name == "-" ? MBT.Escience.FileUtils.WriteStdInToTempFile() : f.FullName
select mf.Parse(name, missingVal, ParallelOptionsScope.Current)).ToArray();
var result = new MergeRowsView <TRowKey, TColKey, TVal>(colsMustMatch, matrices);
return(result);
}
public static IEnumerable <TwoByTwo> GetCollectionFromMatrices(bool unsorted, string inputMatrixFileName1, string inputMatrixFileName2, ParallelOptions parallelOptions)
{
MatrixFactory <string, string, SufficientStatistics> mf = MatrixFactory <string, string, SufficientStatistics> .GetInstance();
var m1 = mf.Parse(inputMatrixFileName1, MissingStatistics.GetInstance(), parallelOptions);
var m2 = mf.Parse(inputMatrixFileName2, MissingStatistics.GetInstance(), parallelOptions);
List <TwoByTwo> tableList = new List <TwoByTwo>();
foreach (string key in m1.RowKeys)
{
if (m2.ContainsRowKey(key))
{
TwoByTwo table = TwoByTwo.GetInstance(inputMatrixFileName1, key, false);
var m1NonMissing = m1.RowView(key).Select(kvp => kvp);
var m2NonMissing = m2.RowView(key).Select(kvp => kvp);
// m1 is T for first col, m2 is F for first Col.
table.TT = m1NonMissing.Select(kvp => (int)kvp.Value.AsDiscreteStatistics()).Sum();
table.TF = m1NonMissing.Count() - table.TT;
table.FT = m2NonMissing.Select(kvp => (int)kvp.Value.AsDiscreteStatistics()).Sum();
table.FF = m2NonMissing.Count() - table.FT;
if (unsorted)
{
yield return(table);
}
else
{
tableList.Add(table);
}
}
}
if (!unsorted)
{
tableList.Sort((t1, t2) => t1.FisherExactTest.CompareTo(t2.FisherExactTest));
foreach (var table in tableList)
{
yield return(table);
}
}
}