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 async Task <ResultsDto> GetUserResultsCountAsync(string login)
{
if (login == null)
{
throw new ArgumentNullException();
}
var sessions = await _sessionStorage.GetFinishedSessionsAsync();
ResultsDto results = new ResultsDto
{
WinCount = GetWinsCount(sessions, login),
DrawCount = GetDrawCount(sessions, login),
LossCount = GetLossCount(sessions, login)
};
return(results);
}
public static void Write(ResultsDto results, ScoringParameterDto scores)
{
List <Alignment> alignments = results.alignments;
int simScore = results.SimilarityScore;
int count = 0;
int mismatch = 0;
int gap = 0;
int match = 0;
string sep = "";
Console.WriteLine("Local Alignment Results \n");
string baseAbsoluteUri = Directory.GetCurrentDirectory();
string relativePath = @"\Output\LocalAlignmentResults.txt";
string path = Path.GetFullPath(baseAbsoluteUri + relativePath);
if (!File.Exists(path))
{
var outFile = File.Create(path);
outFile.Close();
TextWriter tw = new StreamWriter(path);
tw.WriteLine("Alignment " + ++count);
tw.WriteLine("Match: {0}", scores.match);
tw.WriteLine("Mismatch: {0}", scores.mismatch);
tw.WriteLine("Gap: {0}", scores.gap);
tw.WriteLine("Similarity Score: " + simScore + "\n");
foreach (var align in alignments)
{
int maxlength = Math.Max(align.Sequence1.Length, align.Sequence2.Length);
for (int i = 0; i < align.Sequence1.Length; i++)
{
if (align.Sequence1[i] == align.Sequence2[i])
{
if (align.Sequence1[i].Equals('_'))
{
gap = gap + 2;
sep += " ";
}
else
{
sep += "|";
match++;
}
}
else if (align.Sequence1[i].Equals('_') || align.Sequence2[i].Equals('_'))
{
sep += " ";
gap++;
}
else
{
sep += " ";
mismatch++;
}
}
for (int line = 0; line < align.Sequence1.Length; line += 100)
{
if (line + 100 < align.Sequence1.Length)
{
tw.WriteLine(align.Sequence1.Substring(line, 100));
tw.WriteLine(sep.Substring(line, 100));
tw.WriteLine(align.Sequence2.Substring(line, 100) + "\n");
}
else
{
tw.WriteLine(align.Sequence1.Substring(line));
tw.WriteLine(sep.Substring(line));
tw.WriteLine(align.Sequence2.Substring(line) + "\n");
}
}
tw.WriteLine("Identity: {0}/{1} ({2:F1}%)", match, maxlength, (match / (double)maxlength * 100));
tw.WriteLine("Gaps: {0}/{1} ({2:F1}%) \n\n", gap, maxlength, (gap / (double)maxlength * 100));
mismatch = 0;
gap = 0;
match = 0;
tw.Close();
}
}
else if (File.Exists(path))
{
using (var tw = new StreamWriter(path, false))
{
tw.WriteLine("Alignment " + ++count);
tw.WriteLine("Match: {0}", scores.match);
tw.WriteLine("Mismatch: {0}", scores.mismatch);
tw.WriteLine("Gap: {0}", scores.gap);
tw.WriteLine("Similarity Score: " + simScore + "\n");
foreach (var align in alignments)
{
int maxlength = Math.Max(align.Sequence1.Length, align.Sequence2.Length);
for (int i = 0; i < align.Sequence1.Length; i++)
{
if (align.Sequence1[i] == align.Sequence2[i])
{
if (align.Sequence1[i].Equals('_'))
{
gap = gap + 2;
sep += " ";
}
else
{
sep += "|";
match++;
}
}
else if (align.Sequence1[i].Equals('_') || align.Sequence2[i].Equals('_'))
{
sep += " ";
gap++;
}
else
{
sep += " ";
mismatch++;
}
}
for (int line = 0; line < align.Sequence1.Length; line += 100)
{
if (line + 100 < align.Sequence1.Length)
{
tw.WriteLine(align.Sequence1.Substring(line, 100));
tw.WriteLine(sep.Substring(line, 100));
tw.WriteLine(align.Sequence2.Substring(line, 100) + "\n");
}
else
{
tw.WriteLine(align.Sequence1.Substring(line));
tw.WriteLine(sep.Substring(line));
tw.WriteLine(align.Sequence2.Substring(line) + "\n");
}
}
tw.WriteLine("Identity: {0}/{1} ({2:F1}%)", match, maxlength, (match / (double)maxlength * 100));
tw.WriteLine("Gaps: {0}/{1} ({2:F1}%) \n\n", gap, maxlength, (gap / (double)maxlength * 100));
mismatch = 0;
gap = 0;
match = 0;
}
}
}
sep = "";
foreach (var align in alignments)
{
int maxlength = Math.Max(align.Sequence1.Length, align.Sequence2.Length);
Console.WriteLine("Alignment " + ++count);
Console.WriteLine("Match: {0}", scores.match);
Console.WriteLine("Mismatch: {0}", scores.mismatch);
Console.WriteLine("Gap: {0}", scores.gap);
Console.WriteLine("Similarity Score: " + simScore + "\n");
for (int i = 0; i < align.Sequence1.Length; i++)
{
if (align.Sequence1[i] == align.Sequence2[i])
{
if (align.Sequence1[i].Equals('_'))
{
gap = gap + 2;
sep += " ";
}
else
{
sep += "|";
match++;
}
}
else if (align.Sequence1[i].Equals('_') || align.Sequence2[i].Equals('_'))
{
sep += " ";
gap++;
}
else
{
sep += " ";
mismatch++;
}
}
for (int line = 0; line < align.Sequence1.Length; line += 100)
{
if (line + 100 < align.Sequence1.Length)
{
Console.WriteLine(align.Sequence1.Substring(line, 100));
Console.WriteLine(sep.Substring(line, 100));
Console.WriteLine(align.Sequence2.Substring(line, 100) + "\n");
}
else
{
Console.WriteLine(align.Sequence1.Substring(line));
Console.WriteLine(sep.Substring(line));
Console.WriteLine(align.Sequence2.Substring(line) + "\n");
}
}
Console.WriteLine("Identity: {0}/{1} ({2:F1}%)", match, maxlength, (match / (double)maxlength * 100));
Console.WriteLine("Gaps: {0}/{1} ({2:F1}%) \n\n", gap, maxlength, (gap / (double)maxlength * 100));
mismatch = 0;
gap = 0;
match = 0;
}
Console.WriteLine("\n*** Press Any Key to Continue!");
Console.ReadKey();
}
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);
}
