static void Main(string[] args)
{
char[] seq1 = null;
char[] seq2 = null;
try
{
using (StreamReader sr = new StreamReader("sequence1.txt"))
{
String line = sr.ReadToEnd();
seq1 = line.ToCharArray();
}
using (StreamReader sr = new StreamReader("sequence2.txt"))
{
String line = sr.ReadToEnd();
seq2 = line.ToCharArray();
}
}
catch (Exception e)
{
Console.WriteLine("The file could not be read:");
Console.WriteLine(e.Message);
}
//sample sequences
//char[] s11 = { 'G', 'C', 'A', 'T', 'G','C','U' };
//char[] s22 = { 'G', 'A', 'T', 'T', 'A','C','A' };
char[] s1 = new char[seq1.Length + 1];
char[] s2 = new char[seq2.Length + 1];
s1[0] = ' ';
s2[0] = ' ';
seq1.CopyTo(s1, 1);
seq2.CopyTo(s2, 1);
Console.WriteLine("Needleman-Wunsch algorithm with gap penalty");
AlignmentWithPenalty withPenalty = new AlignmentWithPenalty();
int[,] arr = withPenalty.GetSimilarityMatrix(s1, s2);
withPenalty.GetBacktrace(arr, s1, s2);
Console.WriteLine("\nHirschberg algorithm without gap penalty");
Hirschberg hirschberg = new Hirschberg();
hirschberg.GetAlignment(seq1, seq2);
}
public void GetAlignment(char[] s1, char[] s2)
{
StringBuilder Z = new StringBuilder();
StringBuilder W = new StringBuilder();
if (s1.Length == 0)
{
for (int i = 1; i < s2.Length - 1; i++)
{
Z.Append("-");
W.Append(s2[i]);
}
}
else if (s2.Length == 0)
{
for (int i = 1; i < s2.Length - 1; i++)
{
Z.Append(s1[i]);
W.Append("-");
}
}
else if (s1.Length == 1 || s2.Length == 1)
{
AlignmentWithPenalty withPenalty = new AlignmentWithPenalty();
int[,] arr = withPenalty.GetSimilarityMatrix(s1, s2);
withPenalty.GetBacktrace(arr, s1, s2);
}
else
{
int xlen = s1.Length;
int ylen = s2.Length;
int xmid = xlen / 2;
int[] prefScore = GetNWScore(s1, s2, xmid, "pref");
int[] suffScore = GetNWScore(s1, s2, xmid, "suff");
int[] score = new int[prefScore.Length];
for (int i = 0; i < s2.Length; i++)
{
score[i] = prefScore[i] + suffScore[i];
}
int max = score.Max();
int ymid = Array.IndexOf(score, max);
char[] pref_s1 = new char[xmid];
char[] suff_s1 = new char[s1.Length - xmid];
char[] pref_s2 = new char[ymid];
char[] suff_s2 = new char[s2.Length - ymid];
Array.Copy(s1, 0, pref_s1, 0, xmid);
Array.Copy(s2, 0, pref_s2, 0, ymid);
Array.Copy(s1, xmid, suff_s1, 0, s1.Length - xmid);
Array.Copy(s1, ymid, suff_s2, 0, s2.Length - ymid);
GetAlignment(pref_s1, pref_s2);
if (ymid != 0)
{
GetAlignment(suff_s1, suff_s2);
}
}
}