private AlignmentResult GetAlignmentByAncestorsMatrix(string S1, string S2, int[,] ancestorsMatrix, double[,] scoringMatrix, int maxScoreI, int maxScoreJ)
{
int k = maxScoreI;
int l = maxScoreJ;
AlignmentResult result = new AlignmentResult();
while (scoringMatrix[k, l] > 0)
{
if (ancestorsMatrix[k, l] == 0)
{
result.S1 = S1[k] + result.S1;
result.S2 = S2[l] + result.S2;
k = k - 1;
l = l - 1;
}
else if (ancestorsMatrix[k, l] == 1)
{
result.S1 = S1[k] + result.S1;
result.S2 = "-" + result.S2;
k = k - 1;
}
else
{
result.S1 = "-" + result.S1;
result.S2 = S2[l] + result.S2;
l = l - 1;
}
}
if (k < l)
{
result.S1 = new string('-', l - k) + S1.Substring(0, k) + "***" + result.S1 + "***";
result.S2 = S2.Substring(0, l) + "***" + result.S2 + "***";
}
else
{
result.S1 = S1.Substring(0, k) + "***" + result.S1 + "***";
result.S2 = new string('-', k - l) + S2.Substring(0, l) + "***" + result.S2 + "***";
}
result.S1 = result.S1 + S1.Substring(maxScoreI, S1.Length - maxScoreI);
result.S2 = result.S2 + S2.Substring(maxScoreJ, S2.Length - maxScoreJ);
if (result.S1.Length < result.S2.Length)
{
result.S1 = result.S1 += new string('-', result.S2.Length - result.S1.Length);
}
else
{
result.S2 = result.S2 += new string('-', result.S1.Length - result.S2.Length);
}
return(result);
}
private AlignmentResult GetAlignmentByAncestorsMatrix(string S1, string S2, int[,] ancestors)
{
int k = S1.Length - 1;
int l = S2.Length - 1;
AlignmentResult result = new AlignmentResult();
while (k > 0 && l > 0)
{
if (ancestors[k, l] == 0)
{
result.S1 = S1[k] + result.S1;
result.S2 = S2[l] + result.S2;
k = k - 1;
l = l - 1;
}
else if (ancestors[k, l] == 1)
{
result.S1 = S1[k] + result.S1;
result.S2 = "-" + result.S2;
k = k - 1;
}
else
{
result.S1 = "-" + result.S1;
result.S2 = S2[l] + result.S2;
l = l - 1;
}
}
if (k >= 0)
{
result.S1 = S1.Substring(0, k + 1) + result.S1;
result.S2 = new string('-', k + 1) + result.S2;
}
if (l >= 0)
{
result.S1 = new string('-', l + 1) + result.S1;
result.S2 = S2.Substring(0, l + 1) + result.S2;
}
return(result);
}
private AlignmentResult GetAlignmentByAncestorsMatrix(string S1, string S2, StepType[,] pointersM, StepType[,] pointersGaps1,
StepType[,] pointersGaps2, StepType startStep)
{
int k = S1.Length;
int l = S2.Length;
AlignmentResult result = new AlignmentResult();
StepType curStep = startStep;
while (k > 0 || l > 0)
{
if (curStep == StepType.M && k >= 0 && l >= 0)
{
result.S1 = S1[k - 1] + result.S1;
result.S2 = S2[l - 1] + result.S2;
curStep = pointersM[k, l];
k--;
l--;
}
else
if ((k > 0 && curStep == StepType.Gaps2) || (k > 0 && l <= 0))
{
result.S1 = S1[k - 1] + result.S1;
result.S2 = "-" + result.S2;
curStep = pointersGaps2[k, Math.Max(0, l)];
k--;
}
else if ((l > 0 && curStep == StepType.Gaps1) || (l > 0 && k <= 0))
{
result.S1 = "-" + result.S1;
result.S2 = S2[l - 1] + result.S2;
curStep = pointersGaps1[Math.Max(k, 0), l];
l--;
}
}
return(result);
}
