public GeneNode(GeneNode prev, char x, char y, int cost)
{
this.Prev = prev;
this.X = x.ToString();
this.Y = y.ToString();
this.Cost = cost;
}
private GeneNode GetSmallest(GeneNode a, GeneNode b, GeneNode c)
{
var smallest = a;
if (b.Cost < smallest.Cost)
{
smallest = b;
}
if (c.Cost < smallest.Cost)
{
smallest = c;
}
return(smallest);
}
public GeneNode Align(GeneSequence sequenceA, GeneSequence sequenceB, ResultTable resultTableSoFar, int rowInTable, int columnInTable)
{
// Check for equal alignment
if (rowInTable == columnInTable)
{
return(new GeneNode(null, '0', '0', 0));
}
// Linear space requirement
var resultSet1 = new List <GeneNode>(); // Prev Row
var resultSet2 = new List <GeneNode>(); // Current Row
// New Sequences
string seqA = "0" + sequenceA.Sequence;
string seqB = "0" + sequenceB.Sequence;
// Clean up the length to cap at 5000
int seqALength = seqA.Length;
int seqBLength = seqB.Length;
if (seqA.Length > MaxCharactersToAlign + 1)
{
seqALength = MaxCharactersToAlign + 1;
}
if (seqB.Length > MaxCharactersToAlign + 1)
{
seqBLength = MaxCharactersToAlign + 1;
}
// Core alignment algorithm
for (int i = 0; i < seqALength; i++)
{
for (int j = 0; j < seqBLength; j++)
{
GeneNode acc = null;
// Starting position
if (i == 0 && j == 0)
{
acc = new GeneNode(null, '0', '0', 0);
}
// Edge case
else if (i == 0 && j > 0)
{
// Get the node from the left cell, and add as indel
acc = new GeneNode(resultSet2[j - 1], '-', seqB[j], (resultSet2[j - 1].Cost + indel));
}
// Edge case
else if (i > 0 && j == 0)
{
// Get the node from the top cell, and add as indel
acc = new GeneNode(resultSet1[j], seqA[i], '-', (resultSet1[j].Cost + indel));
}
// Match Case
else if ((i > 0 && j > 0) && (seqA[i] == seqB[j]))
{
// Match or indel
var top = new GeneNode(resultSet1[j], seqA[i], '-', (resultSet1[j].Cost + indel));
var left = new GeneNode(resultSet2[j - 1], '-', seqB[j], (resultSet2[j - 1].Cost + indel));
var diag = new GeneNode(resultSet1[j - 1], seqA[i], seqB[j], (resultSet1[j - 1].Cost + match));
// Get node neighbor with smallest cost in order of: left, top, diag
acc = GetSmallest(left, top, diag);
}
// Subsitution Case
else if ((i > 0 && j > 0) && (seqA[i] != seqB[j]))
{
// Sub or indel
var top = new GeneNode(resultSet1[j], seqA[i], '-', (resultSet1[j].Cost + indel));
var left = new GeneNode(resultSet2[j - 1], '-', seqB[j], (resultSet2[j - 1].Cost + indel));
var diag = new GeneNode(resultSet1[j - 1], seqA[i], seqB[j], (resultSet1[j - 1].Cost + sub));
// Get node neighbor with smallest cost in order of: left, top, diag
acc = GetSmallest(left, top, diag);
}
// Add to lower row (current row) results
resultSet2.Add(acc);
}
// Make lower row the new upper row and clear the old lower row
resultSet1 = resultSet2;
resultSet2 = new List <GeneNode>();
}
// return the node at furthest (col, row) from origin
return(resultSet1[resultSet1.Count - 1]);
}
