public static void InitializationStep(int gapPenalty)
{
string text = System.IO.File.ReadAllText(@"C:\Users\TOSHIBA\Desktop\input2.txt");
string[] proteins = text.Trim().Split('>');
ArrayList arr = new ArrayList();
List <similarityStruct> similarity = new List <similarityStruct>();
int counter = 0;
for (int k = 0; k < proteins.Length; k++)
{
string[] proteinSeq1 = proteins[k].Trim().Split('\n');
if (proteinSeq1.Length > 1)
{
string alignSeq1 = proteinSeq1[1].Trim();
for (int l = k + 1; l < proteins.Length; l++)
{
string[] proteinSeq2 = proteins[l].Trim().Split('\n');
if (proteinSeq2.Length > 1)
{
string alignSeq2 = proteinSeq2[1].Trim();
matrixStruct[,] scoringMatrix =
new matrixStruct[alignSeq1.Length + 1, alignSeq2.Length + 1];
//Initialization Step - filled with gap penalty for the first row and the first column of matrix
for (int i = 1; i < scoringMatrix.GetLength(0); i++)
{
scoringMatrix[i, 0].val = scoringMatrix[i - 1, 0].val + gapPenalty;
scoringMatrix[i, 0].Up = "Up";
scoringMatrix[i, 0].proteinLeft = Convert.ToChar(alignSeq1.Substring(i - 1, 1));
scoringMatrix[i, 0].proteinUP = '-';
}
for (int j = 1; j < scoringMatrix.GetLength(1); j++)
{
scoringMatrix[0, j].val = scoringMatrix[0, j - 1].val + gapPenalty;
scoringMatrix[0, j].Left = "Left";
scoringMatrix[0, j].proteinUP = Convert.ToChar(alignSeq2.Substring(j - 1, 1));
scoringMatrix[0, j].proteinLeft = '-';
}
//Matrix Fill Step
for (int i = 1; i <= alignSeq1.Length; i++)
{
for (int j = 1; j <= alignSeq2.Length; j++)
{
char c1 = Convert.ToChar(alignSeq1.Substring(i - 1, 1));
char c2 = Convert.ToChar(alignSeq2.Substring(j - 1, 1));
int score = BlosumMatrix(c1, c2);
int scoreDiag = 0;
if (alignSeq1.Substring(i - 1, 1) == alignSeq2.Substring(j - 1, 1))
{
scoreDiag = scoringMatrix[i - 1, j - 1].val + score;
scoringMatrix[i, j].proteinUP = Convert.ToChar(alignSeq1.Substring(i - 1, 1));
scoringMatrix[i, j].proteinLeft = Convert.ToChar(alignSeq2.Substring(j - 1, 1));
}
else
{
scoreDiag = scoringMatrix[i - 1, j - 1].val + score;
scoringMatrix[i, j].proteinLeft = Convert.ToChar(alignSeq1.Substring(i - 1, 1));
scoringMatrix[i, j].proteinUP = Convert.ToChar(alignSeq2.Substring(j - 1, 1));
}
int scoreLeft = scoringMatrix[i, j - 1].val + gapPenalty;
int scoreUp = scoringMatrix[i - 1, j].val + gapPenalty;
int maxScore = Math.Max(Math.Max(scoreDiag, scoreLeft), scoreUp);
if (maxScore == scoreLeft)
{
scoringMatrix[i, j].val = maxScore;
scoringMatrix[i, j].Left = "Left";
}
if (maxScore == scoreUp)
{
scoringMatrix[i, j].val = maxScore;
scoringMatrix[i, j].Up = "Up";
}
if (maxScore == scoreDiag)
{
scoringMatrix[i, j].val = maxScore;
scoringMatrix[i, j].Diag = "Diag";
}
}
}
//Traceback Step
string seq1 = "";
string seq2 = "";
int smCount = 0;
// int exactMatchScore = 0;
int m = scoringMatrix.GetLength(0) - 1;
int n = scoringMatrix.GetLength(1) - 1;
while (m >= 0 && n >= 0)
{
if (scoringMatrix[m, n].Left == "Left")
{
seq2 += scoringMatrix[m, n].proteinUP;
seq1 += '-';
n--;
}
else if (scoringMatrix[m, n].Up == "Up")
{
seq1 += scoringMatrix[m, n].proteinLeft;
seq2 += '-';
m--;
}
else if (scoringMatrix[m, n].Diag == "Diag")
{
seq1 += scoringMatrix[m, n].proteinLeft;
seq2 += scoringMatrix[m, n].proteinUP;
m--;
n--;
if (scoringMatrix[m, n].proteinLeft == scoringMatrix[m, n].proteinUP)
{
smCount++;
}
}
else
{
break;
}
}
similarityStruct sm = new similarityStruct();
sm.seq1_name = proteinSeq1[0].Trim().ToString();
sm.seq2_name = proteinSeq2[0].Trim().ToString();
sm.align1_name = seq1;
sm.align2_name = seq2;
// sm.similarityValue = (double)scoringMatrix[scoringMatrix.GetLength(0)-1,scoringMatrix.GetLength(1)-1].val/(Double)seq1.Length;//burayı sequence length e bölcez
sm.similarityValue = (Double)smCount / (Double)seq1.Length;
similarity.Add(sm);
if (counter < 4)
{
if (l == 1)
{
temp2[counter] = seq1;
temp2[counter] = seq2;
}
else
{
temp2[counter] = seq1;
}
}
// seq1 += " <"+proteinSeq1[0].Trim().ToString();
// seq2 += " <"+proteinSeq2[0].Trim().ToString();
//print sequences
counter++;
PrintSeq(seq1, seq2);
Console.WriteLine();
}
}
}
}
//guide tree
GuideTree(similarity);
}
public static GuideTree GuideTree(List <similarityStruct> similarity)
{
List <String> seq = new List <String>();
List <similarityStruct> new_sm = new List <similarityStruct>();
foreach (var item in similarity)
{
if (!seq.Contains(item.seq1_name))
{
seq.Add(item.seq1_name);
seq.Add(item.align1_name);
}
else if (!seq.Contains(item.seq2_name))
{
seq.Add(item.seq2_name);
seq.Add(item.align2_name);
}
}
int length = seq.Count();
similarityStruct sm = new similarityStruct();
double val = 0;
foreach (var item in similarity)
{
if (item.similarityValue > val)
{
val = item.similarityValue;
sm = item;
}
}
new_sm.Add(sm);
GuideTree gd;
gd = new GuideTree();
gd.seq1 = sm.seq1_name;
gd.seq2 = sm.seq2_name;
gd.align1_name = sm.align1_name;
gd.align2_name = sm.align2_name;
gd.val = sm.similarityValue;
guideTree.Add(gd);
List <similarityStruct> new_similarity = new List <similarityStruct>();
foreach (var item in similarity)
{
if (!sm.Equals(item))
{
new_similarity.Add(item);
}
}
bool flag1 = false;
bool flag2 = false;
bool flag3 = false;
int count = 0;
string s1 = "";
string s2 = "";
List <similarityStruct> temp = new List <similarityStruct>();
for (int i = 0; i < guideTree.Count; i++)
{
double x = 0;
for (int j = 0; j < new_similarity.Count; j++)
{
if (new_similarity.ElementAt(j).seq2_name != guideTree.ElementAt(i).seq1&& new_similarity
.ElementAt(j)
.seq2_name !=
guideTree.ElementAt(i).seq2 &&
new_similarity
.ElementAt(j)
.seq1_name !=
guideTree.ElementAt(i)
.seq2&& new_similarity
.ElementAt(j)
.seq1_name !=
guideTree.ElementAt(i).seq1 &&
!new_similarity
.ElementAt(j).isMerged)
{
similarityStruct a = new similarityStruct();
a = new_similarity.ElementAt(j);
a.isMerged = true;
new_similarity.RemoveAt(j);
new_similarity.Add(a);
s1 = "";
s2 = "";
x = 0;
count = 0;
temp = new List <similarityStruct>();
}
if (j < new_similarity.Count && s1 == "")
{
if (guideTree.ElementAt(i).seq1 == new_similarity.ElementAt(j).seq1_name)
{
x += new_similarity.ElementAt(j).similarityValue;
flag1 = true;
s1 = new_similarity.ElementAt(j).seq2_name;
}
}
if (j < new_similarity.Count && s1 == "")
{
if (guideTree.ElementAt(i).seq1 == new_similarity.ElementAt(j).seq2_name)
{
x += new_similarity.ElementAt(j).similarityValue;
flag2 = true;
s1 = new_similarity.ElementAt(j).seq1_name;
}
}
if ((flag1 == false && flag2 == true) || (flag2 == false && flag1 == true))
{
temp.Add(new_similarity.ElementAt(j));
new_similarity.RemoveAt(j);
flag3 = true;
j = -1;
count++;
}
flag1 = false;
flag2 = false;
if (j < new_similarity.Count && flag3 != true && s2 == "")
{
if (guideTree.ElementAt(i).seq2 == new_similarity.ElementAt(j).seq1_name)
{
x += new_similarity.ElementAt(j).similarityValue;
flag1 = true;
s2 = new_similarity.ElementAt(j).seq2_name;
}
}
if (j < new_similarity.Count && flag3 != true && s2 == "")
{
if (guideTree.ElementAt(i).seq2 == new_similarity.ElementAt(j).seq2_name)
{
x += new_similarity.ElementAt(j).similarityValue;
flag2 = true;
s2 = new_similarity.ElementAt(j).seq1_name;
}
}
if ((flag1 == false && flag2 == true) || (flag2 == false && flag1 == true))
{
count++;
temp.Add(new_similarity.ElementAt(j));
new_similarity.RemoveAt(j);
j = -1;
}
if (count == 2 && s1 == s2)
{
x = x / 2;
similarityStruct s = new similarityStruct();
s.seq1_name = s1;
s.seq2_name = guideTree.ElementAt(i).seq1 + "/" + guideTree.ElementAt(i).seq2;
s.similarityValue = x;
s.isMerged = true;
new_similarity.Add(s);
s1 = "";
s2 = "";
x = 0;
count = 0;
temp = new List <similarityStruct>();
}
else if (count == 2)
{
foreach (var item in temp)
{
new_similarity.Add(item);
}
temp = new List <similarityStruct>();
count = 0;
x = 0;
}
flag3 = false;
flag1 = false;
flag2 = false;
}
}
if (new_similarity.Count != 0)
{
return(GuideTree(new_similarity));
}
else
{
gd = new GuideTree();
if (s1 != "")
{
gd.seq1 = s1;
}
else if (s2 != "")
{
gd.seq2 = s2;
}
guideTree.Add(gd);
string str = "";
foreach (var item in guideTree)
{
if (item.seq1 != null && item.seq2 != null)
{
str += "[";
Console.WriteLine("---------------------");
}
if (item.seq1 != null)
{
str += item.seq1 + "/";
Console.WriteLine(item.seq1);
}
if (item.seq2 != null)
{
str += item.seq2 + "/";
Console.WriteLine(item.seq2);
}
if (item.seq1 != null && item.seq2 != null)
{
str += "]";
Console.WriteLine("---------------------");
}
}
Console.WriteLine();
Console.WriteLine(str.ToString());
return(gd);
}
}
