/// <summary>
/// The dynamic table generation.
/// </summary>
/// <param name="first">The first sequence.</param>
/// <param name="second">The second sequence.</param>
/// <returns>The dynamic table.</returns>
private ProfileTableItem GenerateDynamicTable(Profile first, Profile second)
{
var length1 = first.Count + 1;
var length2 = second.Count + 1;
var dynamicTable = new ProfileTableItem(first, second)
{
{ new Index(0, 0), new DynamicTableItem(0, new List<Index>()) }
};
// first row set
for (var i = 1; i < length2; i++)
{
var ii = i - 1; // in sequence
dynamicTable.Add(new Index(0, i), new DynamicTableItem(i * this.Estimator.ProfileItemNucleotideDistance(second[ii], Nucleotide._), new List<Index> { new Index(0, i - 1) }));
}
// first column set
for (var i = 1; i < length1; i++)
{
var ii = i - 1; // in sequence
dynamicTable.Add(new Index(i, 0), new DynamicTableItem(i * this.Estimator.ProfileItemNucleotideDistance(first[ii], Nucleotide._), new List<Index> { new Index(i - 1, 0) }));
}
for (var i = 1; i < length1; i++)
{
for (var j = 1; j < length2; j++)
{
var pj = new Index(i - 1, j); // same column
var pi = new Index(i, j - 1); // same row
var pij = new Index(i - 1, j - 1);
var ii = i - 1; // in sequence
var jj = j - 1; // in sequence
var estimates = new Dictionary<Index, double>
{
{ pj, dynamicTable[pj].Distance + this.Estimator.ProfileItemNucleotideDistance(first[ii], Nucleotide._) },
{ pi, dynamicTable[pi].Distance + this.Estimator.ProfileItemNucleotideDistance(Nucleotide._, second[jj]) },
{
pij,
dynamicTable[pij].Distance + this.Estimator.ProfileItemsDistance(first[ii], second[jj])
}
};
var d = estimates.Values.Min();
var dynamicTableItem = new DynamicTableItem(d, estimates.Where(e => e.Value.IsEqualTo(d)).Select(e => e.Key).ToList());
dynamicTable.Add(new Index(i, j), dynamicTableItem);
}
}
return dynamicTable;
}
/// <summary>
/// The generate aligned.
/// </summary>
/// <param name="alignment">The alignment.</param>
/// <param name="table">The dynamic table.</param>
/// <param name="way">The way in dynamic table</param>
/// <returns>The aligned sequence variants.</returns>
public MultipleSequence GenerateAlignedSequence(MultipleAlignment alignment, ProfileTableItem table, List<Index> way)
{
var sequence = new MultipleSequence();
for (var i = 1; i < way.Count; i++)
{
var pred = way[i - 1];
var cur = way[i];
var ii = cur.Item1 - 1; // in sequence
var jj = cur.Item2 - 1; // in sequence
if (pred.Item1.Equals(cur.Item1))
{
var secondSequence = alignment.Second.AlignedSequences[table.Second.Id];
sequence.Add(new Column(Column.GetClearColumn(alignment.First.Count), secondSequence[jj]));
}
else if (pred.Item2.Equals(cur.Item2))
{
var firstSequence = alignment.First.AlignedSequences[table.First.Id];
sequence.Add(new Column(firstSequence[ii], Column.GetClearColumn(alignment.Second.Count)));
}
else
{
var firstSequence = alignment.First.AlignedSequences[table.First.Id];
var secondSequence = alignment.Second.AlignedSequences[table.Second.Id];
sequence.Add(new Column(firstSequence[ii], secondSequence[jj]));
}
}
return sequence;
}
/// <summary>
/// The generate aligned.
/// </summary>
/// <param name="dynamicTable">The dynamic table.</param>
/// <returns>The aligned sequence variants.</returns>
public List<List<Index>> GenerateGraphWays(ProfileTableItem dynamicTable)
{
// fill variants
var ways = new List<List<Index>>();
ways.Add(new List<Index> { new Index(dynamicTable.First.Count, dynamicTable.Second.Count) });
while (ways.Any(l => !(l.First().Item1 == 0 && l.First().Item2 == 0)))
{
var waysCopy = new List<List<Index>>();
foreach (var way in ways.Where(l => !(l.First().Item1 == 0 && l.First().Item2 == 0)))
{
var pair = way.First();
var predecessors = dynamicTable[pair].Predecessors;
var newWays = new List<List<Index>> { way };
for (var i = 1; i < predecessors.Count; i++)
{
newWays.Add(new List<Index>(way));
}
for (var i = 0; i < predecessors.Count; i++)
{
newWays[i].Insert(0, predecessors[i]);
}
waysCopy.AddRange(newWays);
}
ways = waysCopy;
}
return ways;
}