public MAlignment(int size1)
{
result1=new List<char>(size1*size1);
result2=new List<char>(size1*size1);
size1++;
scoreTab = new cell[size1, size1];
scoreTab1 = new cell[size1, size1];
scoreTab2 = new cell[size1, size1];
for (int i = 0; i < size1; i++)
for (int j = 0; j < size1; j++)
{
scoreTab[i, j] = new cell();
scoreTab1[i, j] = new cell();
scoreTab2[i, j] = new cell();
}
}
public MAlignment(int size1)
{
result1 = new List <char>(size1 * size1);
result2 = new List <char>(size1 * size1);
size1++;
scoreTab = new cell[size1, size1];
scoreTab1 = new cell[size1, size1];
scoreTab2 = new cell[size1, size1];
for (int i = 0; i < size1; i++)
{
for (int j = 0; j < size1; j++)
{
scoreTab[i, j] = new cell();
scoreTab1[i, j] = new cell();
scoreTab2[i, j] = new cell();
}
}
}
alignSeq TraceBack(string str1, string str2)
{
result1.Clear();
result2.Clear();
//string result1="";
//string result2="";
alignSeq alignRes;
int val1, val2, val3;
val1 = scoreTab[size1 - 1, size2 - 1].value;
val2 = scoreTab1[size1 - 1, size2 - 1].value;
val3 = scoreTab2[size1 - 1, size2 - 1].value;
cell aux = scoreTab[size1 - 1, size2 - 1];
if (val1 > val2 && val1 > val3)
{
aux = scoreTab[size1 - 1, size2 - 1];
}
else
if (val2 >= val1 && val2 >= val3)
{
aux = scoreTab1[size1 - 1, size2 - 1];
}
else
{
aux = scoreTab2[size1 - 1, size2 - 1];
}
do
{
if (aux.direction == 2)
{
result1.Add(str1[aux.ai - 1]);
result2.Add(str2[aux.aj - 1]);
}
else
if (aux.direction == 0)
{
result2.Add('-');
result1.Add(str1[aux.ai - 1]);
}
else
{
result1.Add('-');
result2.Add(str2[aux.aj - 1]);
}
aux = aux.tab[aux.i, aux.j];
}while (aux.ai != 0 && aux.aj != 0);
while (aux.ai > 0)
{
result1.Add(str1[--aux.ai]);
result2.Add('-');
}
while (aux.aj > 0)
{
result2.Add(str1[--aux.aj]);
result1.Add('-');
}
alignRes.seq1 = ReverseString(result1);
alignRes.seq2 = ReverseString(result2);
return(alignRes);
}