public void ValidateBooleanStatisticsAsDiscreteStatistics()
{
BooleanStatistics boolStat1 = BooleanStatistics.GetInstance(true);
DiscreteStatistics dStat = boolStat1.AsDiscreteStatistics();
Assert.AreEqual(boolStat1, dStat.AsBooleanStatistics());
}
public void ValidateGaussianStatisticsAsBooleanStatistics()
{
GaussianStatistics boolStat1 = GaussianStatistics.GetInstance(0, 2, 2);
BooleanStatistics gStat = boolStat1.AsBooleanStatistics();
Assert.AreEqual(0, gStat.AsGaussianStatistics().Mean);
}
public void ValidateBooleanStatisticsAsContinuousStatistics()
{
BooleanStatistics boolStat1 = BooleanStatistics.GetInstance(true);
ContinuousStatistics cStat = boolStat1.AsContinuousStatistics();
Assert.AreEqual(1, cStat.Value);
}
public void ValidateBooleanStatisticsExplicitInt()
{
DiscreteStatistics discreteStat2 = DiscreteStatistics.GetInstance(5);
BooleanStatistics boolStat2 = (BooleanStatistics)discreteStat2;
Assert.AreEqual(5, (int)boolStat2);
Assert.IsFalse((bool)boolStat2);
try
{
DiscreteStatistics discreteStat = DiscreteStatistics.GetMissingInstance;
BooleanStatistics boolStat1 = (BooleanStatistics)discreteStat;
Assert.IsFalse((bool)boolStat1);
int temp = (int)boolStat1;
}
catch (InvalidCastException)
{
Console.WriteLine("BooleanStatistics : Successfully validated the int(0)");
}
DiscreteStatistics discreteStat3 = null;
try
{
BooleanStatistics boolStat3 = (BooleanStatistics)discreteStat3;
Assert.Fail();
}
catch (ArgumentException)
{
Console.WriteLine("BooleanStatistics : Successfully validated the int(booleanstatistics)");
}
}
public void ValidateBooleanStatisticsAsStatisticsList()
{
BooleanStatistics boolStat1 = BooleanStatistics.GetInstance(true);
StatisticsList sList = boolStat1.AsStatisticsList();
Assert.AreEqual(1, sList.Count);
}
public void ValidateBooleanStatisticsAsGaussianStatistics()
{
BooleanStatistics boolStat1 = BooleanStatistics.GetInstance(true);
GaussianStatistics gStat = boolStat1.AsGaussianStatistics();
Assert.AreEqual(boolStat1, gStat.AsBooleanStatistics());
}
public void ValidateBooleanStatisticsTryParse()
{
SufficientStatistics result = null;
BooleanStatistics boolStat = BooleanStatistics.GetInstance(true);
Assert.IsTrue(BooleanStatistics.TryParse("true", out result));
Assert.IsTrue(boolStat.Equals(result));
}
public void ValidateBooleanStatisticsToString()
{
BooleanStatistics boolStat1 = BooleanStatistics.GetInstance(true);
BooleanStatistics boolStat2 = BooleanStatistics.GetMissingInstance;
Assert.AreEqual("1", boolStat1.ToString());
Assert.AreEqual("-1", boolStat2.ToString());
}
public void ValidateBooleanStatisticsGetHashCode()
{
// This is a stupid test. It likely changes on each release of the .NET framework since
// we are using an integer as our value here. So it broke for .NET 4.5, I am simply removing
// it because it doesn't test anything anyway.
BooleanStatistics boolStat1 = BooleanStatistics.GetInstance(true);
Assert.AreEqual(372029325, boolStat1.GetHashCode());
}
public void ValidateCharToSufficientStatisticsConverter()
{
CharToSufficientStatisticsConverter ctssConverter = new CharToSufficientStatisticsConverter();
DiscreteStatistics discreteStat = DiscreteStatistics.GetInstance(1);
char convertedChar = ctssConverter.ConvertBackward(discreteStat);
Assert.AreEqual('1', convertedChar);
BooleanStatistics convertedBooleanStat = ctssConverter.ConvertForward('1') as BooleanStatistics;
Assert.AreEqual("1", convertedBooleanStat.ToString());
}
public void ValidateBooleanStatisticsExplicitMissingStatistics()
{
MissingStatistics missStat = MissingStatistics.GetInstance;
BooleanStatistics boolStat2 = (BooleanStatistics)missStat;
Assert.IsTrue(boolStat2.IsMissing());
MissingStatistics missStat2 = null;
Assert.IsNull((BooleanStatistics)missStat2);
}
public void ValidateBooleanStatisticsConvertToBooleanStatistics()
{
BooleanStatistics boolStat1 = BooleanStatistics.GetInstance(true);
SufficientStatistics suffStats = (SufficientStatistics)boolStat1;
Dictionary <string, SufficientStatistics> testSuffStats = new Dictionary <string, SufficientStatistics>();
testSuffStats.Add("Test", suffStats);
Dictionary <string, BooleanStatistics> boolStats = BooleanStatistics.ConvertToBooleanStatistics(testSuffStats);
Assert.AreEqual(boolStat1, boolStats["Test"]);
}
/// <summary>
/// Converts positional variations in sequences to statistics
/// </summary>
/// <param name="positionalAminoAcidDistribution">Positional distribution of alphabets.</param>
/// <param name="sequences">List of List of positional sequence variation.</param>
/// <param name="keepOneValueVariables">Keeps variables with single value only.</param>
/// <param name="rowValues">Values in rows</param>
/// <returns>Positional sequence statistics</returns>
private static IList <List <SufficientStatistics> > CreateSequenceStatistics(
HashSet <byte>[] positionalAminoAcidDistribution,
IList <IList <IList <byte> > > sequences,
bool keepOneValueVariables,
out IList <string> rowValues)
{
IList <List <SufficientStatistics> > statistics = new List <List <SufficientStatistics> >();
rowValues = new List <string>();
for (int pos = 0; pos < positionalAminoAcidDistribution.Length; pos++)
{
foreach (byte aa in positionalAminoAcidDistribution[pos])
{
string merAndPos = (pos + 1) + "@" + (char)aa;
int?[] values = new int?[sequences.Count];
HashSet <int> nonMissingValues = new HashSet <int>();
for (int pidIdx = 0; pidIdx < sequences.Count; pidIdx++)
{
int? value;
IList <byte> observedAAs = sequences[pidIdx][pos];
if (observedAAs.Contains(Alphabets.Protein.Gap) || observedAAs.Contains(Alphabets.AmbiguousProtein.X) || observedAAs.Count == 0 ||
(observedAAs.Count > 1 && MixtureSemanticsValue == MixtureSemantics.none && observedAAs.Contains(aa)))
{
value = null;
}
else if (observedAAs.Contains(aa) && (MixtureSemanticsValue != MixtureSemantics.pure || observedAAs.Count == 1))
{
value = 1;
}
else
{
value = 0;
}
values[pidIdx] = value;
if (value != null)
{
nonMissingValues.Add((int)value);
}
}
if (nonMissingValues.Count > 1 || (keepOneValueVariables && nonMissingValues.Count == 1 && nonMissingValues.First() == 1))
{
rowValues.Add(merAndPos);
statistics.Add(
values.Select(value => value.HasValue ?
(value.Value > 0 ? BooleanStatistics.GetInstance(true) : BooleanStatistics.GetInstance(false))
: MissingStatistics.GetInstance).ToList <SufficientStatistics>());
}
}
}
return(statistics);
}
protected override void WriteDistilled(IEnumerable <KeyValuePair <string, List <HlaIGenotype> > > patientsAndGenotypes, bool multipleGenotypesPerPatient)
{
var patientsAndGenotypesAsList = patientsAndGenotypes.ToList();
Dictionary <string, MultinomialStatistics> pidToMultinomial = new Dictionary <string, MultinomialStatistics>();
Dictionary <string, HlaIGenotype> pidGenoNameToGeno = new Dictionary <string, HlaIGenotype>(patientsAndGenotypesAsList.Count);
foreach (var pidAndGenos in patientsAndGenotypes)
{
if (pidAndGenos.Value.Count == 1)
{
pidGenoNameToGeno.Add(pidAndGenos.Key, pidAndGenos.Value.Single());
}
else
{
pidToMultinomial.Add(pidAndGenos.Key, MultinomialStatistics.GetInstance(pidAndGenos.Value.Select(g => g.Probability))); // keep track of the probabilities in this dictionary
HlaIGenotype unionGenotype = HlaIGenotype.Union(pidAndGenos.Value.ToArray());
pidGenoNameToGeno.Add(pidAndGenos.Key, unionGenotype); //Add the union genotype to the matrix.
for (int i = 0; i < pidAndGenos.Value.Count; i++)
{
string pidGenoId = pidAndGenos.Key + "_" + i;
pidGenoNameToGeno.Add(pidGenoId, pidAndGenos.Value[i]);
}
}
}
Matrix <string, string, SufficientStatistics> m = DenseMatrix <string, string, SufficientStatistics> .CreateDefaultInstance(
HlaEnumerator.GenerateHlas(patientsAndGenotypes.SelectMany(pidAndGenos => pidAndGenos.Value)),
pidGenoNameToGeno.Keys,
MissingStatistics.GetInstance());
foreach (string hlastr in m.RowKeys)
{
HlaI hla = HlaI.Parse(hlastr);
foreach (string pid in m.ColKeys)
{
bool?match = pidGenoNameToGeno[pid].Matches(hla, MixtureSemantics);
m.SetValueOrMissing(hlastr, pid, BooleanStatistics.GetInstance(match));
//m.SetValueOrMissing(hlastr, pid, !match.HasValue ? "?" : match.Value ? "1" : "0");
}
}
m.WriteDense(this.Out.CreateTextOrUseConsole());
string baseName = Path.GetFileNameWithoutExtension(this.Out.ToString());
string probabilityFile = this.Out.ToString() == "-" ? "HaplotypeCompletionProbs.txt" : this.Out.ToString().Replace(baseName, baseName + "_haplotypeProbs");
pidToMultinomial.WriteDelimitedFile(probabilityFile);
}
public void ValidateStatisticsListAsBooleanStatistics()
{
StatisticsList statList = new StatisticsList();
GaussianStatistics gaussStat = GaussianStatistics.GetInstance(2.33, 1.256, 7);
DiscreteStatistics discreteStat = DiscreteStatistics.GetInstance(1);
MissingStatistics missingStat = MissingStatistics.GetInstance;
statList.Add(gaussStat);
statList.Add(discreteStat);
statList.Add(missingStat);
BooleanStatistics dStat = statList.AsBooleanStatistics();
Assert.AreEqual(statList, dStat.AsStatisticsList());
}
public void ValidateStatisticsListRemoveRangeAndRemove()
{
StatisticsList statList = new StatisticsList();
GaussianStatistics gaussStat = GaussianStatistics.GetInstance(2.33, 1.256, 7);
DiscreteStatistics discreteStat = DiscreteStatistics.GetInstance(1);
ContinuousStatistics contStat = ContinuousStatistics.GetInstance(2.333);
MissingStatistics missingStat = MissingStatistics.GetInstance;
BooleanStatistics boolStat = BooleanStatistics.GetInstance(true);
statList.Add(gaussStat);
statList.Add(discreteStat);
statList.Add(contStat);
statList.Add(missingStat);
statList.Add(boolStat);
Assert.AreEqual(5, statList.Count);
statList.RemoveRange(3, 2);
Assert.AreEqual(3, statList.Count);
statList.Remove(2);
Assert.AreEqual(2, statList.Count);
}
public void ValidateStatisticsListTryParse()
{
StatisticsList statList = new StatisticsList();
GaussianStatistics gaussStat = GaussianStatistics.GetInstance(2.33, 1.256, 7);
DiscreteStatistics discreteStat = DiscreteStatistics.GetInstance(1);
ContinuousStatistics contStat = ContinuousStatistics.GetInstance(2.333);
MissingStatistics missingStat = MissingStatistics.GetInstance;
BooleanStatistics boolStat = BooleanStatistics.GetInstance(true);
statList.Add(gaussStat);
statList.Add(discreteStat);
statList.Add(contStat);
statList.Add(missingStat);
statList.Add(boolStat);
Assert.AreEqual(5, statList.Count);
SufficientStatistics result = null;
StatisticsList statListSubSequence = (StatisticsList)statList.SubSequence(0, 2);
Assert.IsTrue(StatisticsList.TryParse(statList.ToString(), out result));
Assert.IsTrue(StatisticsList.TryParse(statListSubSequence.ToString(), out result));
}
public void ValidateBooleanStatisticsEquals()
{
SufficientStatistics suffStat = BooleanStatistics.GetInstance(false);
BooleanStatistics boolStat = BooleanStatistics.GetMissingInstance;
Assert.IsFalse(boolStat.Equals(suffStat));
suffStat = (SufficientStatistics)boolStat;
Assert.IsTrue(boolStat.Equals(suffStat));
boolStat = BooleanStatistics.GetInstance(true);
suffStat = (SufficientStatistics)boolStat;
Assert.IsTrue(boolStat.Equals(suffStat));
boolStat = BooleanStatistics.GetInstance(false);
suffStat = (SufficientStatistics)boolStat;
Assert.IsTrue(boolStat.Equals(suffStat));
object suffStatObj = (object)boolStat;
Assert.IsTrue(boolStat.Equals(suffStat));
}
public void ValidateBooleanStatisticsExplicitDiscrete()
{
DiscreteStatistics discreteStat2 = DiscreteStatistics.GetInstance(5);
BooleanStatistics boolStat2 = (BooleanStatistics)discreteStat2;
Assert.AreEqual(5, (int)(DiscreteStatistics)boolStat2);
DiscreteStatistics discreteStat = DiscreteStatistics.GetMissingInstance;
BooleanStatistics boolStat1 = (BooleanStatistics)discreteStat;
Assert.AreEqual(discreteStat, (DiscreteStatistics)boolStat1);
DiscreteStatistics discreteStat3 = null;
try
{
BooleanStatistics boolStat3 = (BooleanStatistics)discreteStat3;
Assert.Fail();
}
catch (ArgumentException)
{
Console.WriteLine("BooleanStatistics : Successfully validated the BooleanStatistics(Discrete)");
}
}
public void ValidateBooleanStatisticsGetHashCode()
{
BooleanStatistics boolStat1 = BooleanStatistics.GetInstance(true);
Assert.AreEqual(372029325, boolStat1.GetHashCode());
}
public void ValidateBooleanStatisticsGetMissingInstance()
{
BooleanStatistics boolStat = BooleanStatistics.GetMissingInstance;
Assert.IsTrue(boolStat.IsMissing());
}
