/// <summary>
/// This method takes as input a permutation (and possibly a cutoff) and returns the mmHG score and the mmHG p-value.
/// </summary>
/// <param name="perm">
/// A permutation over the numbers 1,...,totalElements
/// </param>
/// <param name="nstar">
/// Indicates whether the list should be cut at a specific position.
/// </param>
/// <returns>
/// The mmHG score which is the minimal hyper-geometric tail found. The p-value field contains the Bonferroni correction.
/// <see cref="HGScore"/>
/// .
/// </returns>
public static MMHGScore CalcScore(int[] perm)
{
int totalElements = perm.Length;
var indMapper = new Dictionary <int, int>();
int totalElementsBeforeThreshold = Math.Min(totalElements, c_maxThreshold);
Score min = new HGScore(totalElements, 0, 0, 0, 1);
if (perm == null || perm.Length == 0)
{
return(new MMHGScore(min, -1, -1, -1));
}
for (int k = 0; k < totalElements; k++)
{
indMapper.Add(perm[k], k);
}
int finalIndex1 = perm.Length - 1;
int finalIndex2 = perm.Length - 1;
int commonElements = perm.Length;
int maxVal = perm[0];
for (int n2 = 1; n2 < totalElementsBeforeThreshold; n2++)
{
// n2 represents the position in the permutation
if (perm[n2] > maxVal)
{
maxVal = perm[n2];
}
int b = 0;
for (int n1 = 1; n1 <= maxVal && n1 <= totalElementsBeforeThreshold; n1++)
{
// n1 represents the range 0...n1-1
if (indMapper[n1 - 1] < n2)
{
b++;
Score s = MHG.CalculateHGT(totalElements, n1, n2, b);
if (s.ScoreValue < min.ScoreValue)
{
min = s;
finalIndex1 = n1;
finalIndex2 = n2;
commonElements = b;
}
}
}
}
return(new MMHGScore(min, finalIndex1, finalIndex2, commonElements));
}
/// <summary>
/// The calculate hgt.
/// </summary>
/// <param name="totalElements">
/// The total elements.
/// </param>
/// <param name="indices">
/// The indices.
/// </param>
/// <param name="elementsOnTop">
/// The elements on top.
/// </param>
/// <returns>
/// The <see cref="HGScore"/>.
/// </returns>
public static HGScore CalculateHGT(int totalElements, SortedSet <int> indices, int elementsOnTop)
{
int totalMatches = indices.Count;
int matchesOnTop = 0;
foreach (int index in indices)
{
if (index <= elementsOnTop)
{
matchesOnTop++;
}
else
{
break;
}
}
HGScore s = CalculateHGT(totalElements, elementsOnTop, totalMatches, matchesOnTop);
return(s);
}
