public static void RunTheCode(string seq1File, string seq2File, int matchWeight, int misMatchWeight, int indlWeight)
{
ScoringParameterDto scoringParameter = new ScoringParameterDto(matchWeight, misMatchWeight, indlWeight);
var seq1 = LoadProteinDatabase.GetProteins(seq1File);
var seq2 = LoadProteinDatabase.GetProteins(seq2File);
SequencesDto sequences = new SequencesDto(seq1[0].Seq, seq2[0].Seq);
EvaluateDto evaluation = GridEvaluateFunction.Evaluate(scoringParameter, sequences);
ResultsDto results = Traceback.Trace(evaluation, sequences);
WriteAlignment.Write(results, scoringParameter);
}
public static ResultsDto Trace(EvaluateDto eval, SequencesDto seqs)
{
string seq1 = seqs.Sequence1;
string seq2 = seqs.Sequence2;
string remstrA = seq1;
string remstrB = seq2;
int i = seq1.Length;
int j = seq2.Length;
string A = "";
string B = "";
while (remstrA.Length > 0 && remstrB.Length > 0)
{
if (eval.directs[i, j][0] == eval.matrix[i, j])
{
B = seq2[j - 1].ToString() + B;
A = '_'.ToString() + A;
j--;
}
else if (eval.directs[i, j][1] == eval.matrix[i, j])
{
A = seq1[i - 1].ToString() + A;
B = '_'.ToString() + B;
i--;
}
else if (eval.directs[i, j][2] == eval.matrix[i, j])
{
A = seq1[i - 1].ToString() + A;
B = seq2[j - 1].ToString() + B;
i--;
j--;
remstrA = remstrA.Substring(0, i);
remstrB = remstrB.Substring(0, j);
}
}
int simScore = eval.matrix[seq1.Length, seq2.Length];
Alignment align = new Alignment(A, B);
List <Alignment> aligns = new List <Alignment>();
aligns.Add(align);
ResultsDto results = new ResultsDto(aligns, simScore);
return(results);
}
public static EvaluateDto Evaluate(ScoringParameterDto scoringParameters, SequencesDto sequences)
{
int[,] matrx = new int[sequences.Sequence1.Length + 1, sequences.Sequence2.Length + 1];
List <int>[,] direx = new List <int> [sequences.Sequence1.Length + 1, sequences.Sequence2.Length + 1];
for (int j = 0; j < sequences.Sequence2.Length + 1; j++)
{
for (int i = 0; i < sequences.Sequence1.Length + 1; i++)
{
direx[i, j] = new List <int>();
if (i == 0 || j == 0)
{
direx[i, j].Add(0);
direx[i, j].Add(0);
direx[i, j].Add(0);
}
}
}
for (int j = 1; j < sequences.Sequence2.Length + 1; j++)
{
for (int i = 1; i < sequences.Sequence1.Length + 1; i++)
{
if (sequences.Sequence1[i - 1] == sequences.Sequence2[j - 1])
{
direx[i, j].Add(matrx[i, j - 1] + scoringParameters.gap);
direx[i, j].Add(matrx[i - 1, j] + scoringParameters.gap);
direx[i, j].Add(matrx[i - 1, j - 1] + scoringParameters.match);
direx[i, j].Add(0);
}
else
{
direx[i, j].Add(matrx[i, j - 1] + scoringParameters.gap);
direx[i, j].Add(matrx[i - 1, j] + scoringParameters.gap);
direx[i, j].Add(matrx[i - 1, j - 1] + scoringParameters.mismatch);
direx[i, j].Add(0);
}
matrx[i, j] = direx[i, j].Max();
}
}
EvaluateDto evaluation = new EvaluateDto(matrx, direx);
return(evaluation);
}
public static ResultsDto Trace(EvaluateDto eval, SequencesDto seqs)
{
string seq1 = seqs.Sequence1;
string seq2 = seqs.Sequence2;
int largest = eval.matrix.Cast <int>().Max();
List <Alignment> aligns = new List <Alignment>();
int c = 0;
List <int> rowmax = new List <int>();
List <int> colmax = new List <int>();
for (int row = 0; row < eval.matrix.GetLength(0); row++)
{
for (int col = 0; col < eval.matrix.GetLength(1); col++)
{
if (eval.matrix[row, col] == largest)
{
rowmax.Add(row);
colmax.Add(col);
c++;
}
}
}
List <string> A = new List <string>();
List <string> B = new List <string>();
for (int count = 0; count < c; count++)
{
string remstrA = seq1.Substring(0, rowmax[count] - 1);
string remstrB = seq2.Substring(0, colmax[count] - 1);
int i = rowmax[count];
int j = colmax[count];
A.Add("");
B.Add("");
while (remstrA.Length > 0 && remstrB.Length > 0)
{
if (eval.directs[i, j][0] == eval.matrix[i, j])
{
B[count] = seq2[j - 1].ToString() + B[count];
A[count] = '_'.ToString() + A[count];
j--;
}
else if (eval.directs[i, j][1] == eval.matrix[i, j])
{
A[count] = seq1[i - 1].ToString() + A[count];
B[count] = '_'.ToString() + B[count];
i--;
}
else if (eval.directs[i, j][2] == eval.matrix[i, j])
{
A[count] = seq1[i - 1].ToString() + A[count];
B[count] = seq2[j - 1].ToString() + B[count];
i--;
j--;
remstrA = remstrA.Substring(0, i);
remstrB = remstrB.Substring(0, j);
}
else
{
break;
}
}
Alignment align = new Alignment(A[count], B[count]);
aligns.Add(align);
}
int simScore = largest;
ResultsDto results = new ResultsDto(aligns, simScore);
return(results);
}
