/// <summary>
/// The trace back procedure of Smith Wunsch algorithm is similar to needlemen
/// but:
/// 1. start from the high score cells
/// 2. end at zero-score cell or 0,0 point
/// </summary>
public AlignResult traceBack(char[,] traceBackMatrix, string seq1, string seq2, int x, int y)
{
// start from the highest cells
//Seed site
int ti = x;
int tj = y;
char[] seq_1 = seq1.ToCharArray();
char[] seq_2 = seq2.ToCharArray();
StringBuilder seq1Builder = new StringBuilder();
StringBuilder seq2Builder = new StringBuilder();
while (ti > 0 || tj > 0) // stop at (0,0) point
{
if (traceBackMatrix[ti, tj] == '.')
{
break; //stop at zero cell
}
switch (traceBackMatrix[ti, tj])
{
case '|':
seq1Builder.Insert(0, '-');
seq2Builder.Insert(0, seq_2[ti - 1]);
ti--;
break;
case '\\':
seq1Builder.Insert(0, seq_1[tj - 1]);
seq2Builder.Insert(0, seq_2[ti - 1]);
ti--;
tj--;
break;
case '-':
seq1Builder.Insert(0, seq_1[tj - 1]);
seq2Builder.Insert(0, '-');
tj--;
break;
default:
break;
}
}
AlignResult AR = new AlignResult(seq1Builder.ToString(), seq2Builder.ToString());
AR.seq2_end = x; //ti;
AR.seq1_end = y; // tj;
return(AR);
}
public void AlignMatchTypeTest()
{
MatchResult <int, string> mr1 = new MatchResult <int, string>(5, "A");
MatchResult <int, string> mr2 = new MatchResult <int, string>(5, "A");
Assert.IsTrue(mr1.Equals(mr2));
mr2 = new MatchResult <int, string>(5, "A1");
Assert.IsTrue(!mr1.Equals(mr2));
//-----------------//
MatchResult <string, string> mr3 = new MatchResult <string, string>("5", "A");
MatchResult <string, string> mr4 = new MatchResult <string, string>("5", "A");
Assert.IsTrue(mr3.Equals(mr4));
mr4 = new MatchResult <string, string>("A", "5");
Assert.IsTrue(!mr3.Equals(mr4));
Assert.IsTrue(!mr3.Equals(null));
Assert.IsTrue(mr3.GetHashCode() == mr4.GetHashCode());
//-----------------//
AlignResult <int, string> ar1 = new AlignResult <int, string>(5, "A");
AlignResult <int, string> ar2 = new AlignResult <int, string>(5, "A");
Assert.IsTrue(ar1.Equals(ar2));
ar2 = new AlignResult <int, string>(5, "A1");
Assert.IsTrue(!ar1.Equals(ar2));
//-----------------//
AlignResult <string, string> ar3 = new AlignResult <string, string>("5", "A");
AlignResult <string, string> ar4 = new AlignResult <string, string>("5", "A");
Assert.IsTrue(ar3.Equals(ar4));
ar4 = new AlignResult <string, string>("A", "5");
Assert.IsTrue(!ar3.Equals(ar4));
Assert.IsTrue(!ar3.Equals(null));
Assert.IsTrue(ar3.GetHashCode() == ar4.GetHashCode());
}
