private void ComputeScoreMatrix()
{
// Will be initalized to all zeros since that is the default int value in c#
this.scoreMatrix = new int[Protein1.Encoding.Length + 1, Protein2.Encoding.Length + 1];
for (int i = 0; i < Protein1.Encoding.Length; i++)
{
for (int j = 0; j < Protein2.Encoding.Length; j++)
{
int v1 = scoreMatrix[i, j] + Blosum62.Sigma(Protein1.Encoding[i].ToString(), Protein2.Encoding[j].ToString());
int v2 = scoreMatrix[i, j + 1] + SW.GapPenalty;
int v3 = scoreMatrix[i + 1, j] + SW.GapPenalty;
int v4 = 0;
int max = Math.Max(Math.Max(v1, v2), Math.Max(v3, v4));
this.scoreMatrix[i + 1, j + 1] = max;
// Update with the new score
if (max > this.Score)
{
this.Score = max;
this.scorePosition = new Tuple <int, int>(i + 1, j + 1);
}
}
}
}
private void ComputeTraceback()
{
this.P1Trace = new List <int>();
this.P2Trace = new List <int>();
if (this.scoreMatrix == null)
{
return;
}
// Start at the location of the max score and work backwards
int i = this.scorePosition.Item1;
int j = this.scorePosition.Item2;
while (true)
{
if (this.scoreMatrix[i, j] == 0)
{
break;
}
int current = this.scoreMatrix[i, j];
// Check which adjacent location caused us to get here
// Check above
int x = this.scoreMatrix[i - 1, j];
if (this.scoreMatrix[i - 1, j] + SW.GapPenalty == current)
{
P1Trace.Add(i);
P2Trace.Add(-1); // gap
// We could have landed here from the element to the above
i = i - 1;
continue;
}
// Check left
x = this.scoreMatrix[i, j - 1];
if (this.scoreMatrix[i, j - 1] + SW.GapPenalty == current)
{
P1Trace.Add(-1); // gap
P2Trace.Add(j);
// We could have landed here from the element to the left
j = j - 1;
continue;
}
// Check diagonal
int a = this.scoreMatrix[i - 1, j - 1];
int b = Blosum62.Sigma(Protein1.Encoding[i - 1].ToString(), Protein2.Encoding[j - 1].ToString());
x = a + b;
if (this.scoreMatrix[i - 1, j - 1] + Blosum62.Sigma(Protein1.Encoding[i - 1].ToString(), Protein2.Encoding[j - 1].ToString()) == current)
{
P1Trace.Add(i);
P2Trace.Add(j);
// We could have landed here from the diagonal adjacent element
i = i - 1;
j = j - 1;
continue;
}
break;
}
this.P1Trace.Reverse();
this.P2Trace.Reverse();
}