/// <summary>
/// Best Alignments
/// </summary>
/// <param name="swapPossibilities"> Value swap in DB </param>
/// <param name="DB"> Data Base if sequence </param>
/// <returns>Key Value Pair contains maxvalue (i.e. best alignment), DBIndex, SwapIndex, SeqPosIndex </returns>
public KeyValuePair <int, List <List <int> > > ProvideBestSwapBulkAlignments(List <List <int[]> > swapPossibilities, List <FastaItem> DB)
{
int maxValue = int.MinValue;
List <int> DBIndex = new List <int>();
List <int> SwapIndex = new List <int>();
List <int> SeqPosIndex = new List <int>();
int counter = 0;
for (int i = 0; i < swapPossibilities.Count; i++) //
{
counter++;
Console.WriteLine("Verifying swap " + counter + " of " + swapPossibilities.Count);
List <int[]> swapOptions = swapPossibilities[i];
for (int j = 0; j < swapOptions.Count; j++) //SwappedOptions
{
for (int k = 0; k < swapOptions[j].Length; k++)
{
if (swapOptions[j][k] > maxValue)
{
maxValue = swapOptions[j][k];
DBIndex = new List <int>()
{
i
};
SwapIndex = new List <int>()
{
j
};
SeqPosIndex = new List <int>()
{
k
};
}
else if (swapOptions[j][k] == maxValue)
{
DBIndex.Add(i);
SwapIndex.Add(j);
SeqPosIndex.Add(k);
}
}
}
}
Console.WriteLine();
return(new KeyValuePair <int, List <List <int> > >(maxValue, new List <List <int> >()
{
DBIndex, SwapIndex, SeqPosIndex
}));
}