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 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 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();
}
