Smith-Waterman Algorithm Program And Source Code

June 25, 2012

smithwaterman[1]

Calculates the optimal alignment, distance matrices and the traceback for two given strings. Costs can be adjusted in the source, right now using a Blosum62 matrix.

SmithWaterman (1555 downloads)

Source

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using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using System.Drawing;
 
namespace SmithWaterman
{
    class SmithWaterman
    {
            private static int[,] matrix = {
	{ 4, -1, -2, -2,  0, -1, -1,  0, -2, -1, -1, -1, -1, -2, -1,  1,  0, -3, -2,  0},
	{-1,  5,  0, -2, -3,  1,  0, -2,  0, -3, -2,  2, -1, -3, -2, -1, -1, -3, -2, -3},
	{-2,  0,  6,  1, -3,  0,  0,  0,  1, -3, -3,  0, -2, -3, -2,  1,  0, -4, -2, -3},
	{-2, -2,  1,  6, -3,  0,  2, -1, -1, -3, -4, -1, -3, -3, -1,  0, -1, -4, -3, -3},
	{ 0, -3, -3, -3,  9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1},
	{-1,  1,  0,  0, -3,  5,  2, -2,  0, -3, -2,  1,  0, -3, -1,  0, -1, -2, -1, -2},
	{-1,  0,  0,  2, -4,  2,  5, -2,  0, -3, -3,  1, -2, -3, -1,  0, -1, -3, -2, -2},
	{ 0, -2,  0, -1, -3, -2, -2,  6, -2, -4, -4, -2, -3, -3, -2,  0, -2, -2, -3, -3},
	{-2,  0,  1, -1, -3,  0,  0, -2,  8, -3, -3, -1, -2, -1, -2, -1, -2, -2,  2, -3},
	{-1, -3, -3, -3, -1, -3, -3, -4, -3,  4,  2, -3,  1,  0, -3, -2, -1, -3, -1,  3},
	{-1, -2, -3, -4, -1, -2, -3, -4, -3,  2,  4, -2,  2,  0, -3, -2, -1, -2, -1,  1},
	{-1,  2,  0, -1, -3,  1,  1, -2, -1, -3, -2,  5, -1, -3, -1,  0, -1, -3, -2, -2},
	{-1, -1, -2, -3, -1,  0, -2, -3, -2,  1,  2, -1,  5,  0, -2, -1, -1, -1, -1,  1},
	{-2, -3, -3, -3, -2, -3, -3, -3, -1,  0,  0, -3,  0,  6, -4, -2, -2,  1,  3, -1},
	{-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4,  7, -1, -1, -4, -3, -2},
	{ 1, -1,  1,  0, -1,  0,  0,  0, -1, -2, -2,  0, -1, -2, -1,  4,  1, -3, -2, -2},
	{ 0, -1,  0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1,  1,  5, -2, -2,  0},
	{-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1,  1, -4, -3, -2, 11,  2, -3},
	{-2, -2, -2, -3, -2, -1, -2, -3,  2, -1, -1, -2, -1,  3, -3, -2, -2,  2,  7, -1},
	{ 0, -3, -3, -3, -1, -2, -2, -3, -3,  3,  1, -2,  1, -1, -2, -2,  0, -3, -1,  4}};
 
	// quick and dirty equivalent of typesafe enum pattern, can also use HashMap
    // or even better, EnumMap in Java 5. 
    // This code is for Java 1.4.2, so we will stick to the simple implementation
    private static int getIndex(char a) {
    	// check for upper and lowercase characters
    	switch (char.ToUpper(a)) {
            case 'A': return 0;
            case 'R': return 1;
            case 'N': return 2;
            case 'D': return 3;
            case 'C': return 4;
            case 'Q': return 5;
            case 'E': return 6;
            case 'G': return 7;
            case 'H': return 8;
            case 'I': return 9;
            case 'L': return 10;
            case 'K': return 11;
            case 'M': return 12;
            case 'F': return 13;
            case 'P': return 14;
            case 'S': return 15;
            case 'T': return 16;
            case 'W': return 17;
            case 'Y': return 18;
            case 'V': return 19;
            default: System.Windows.Forms.MessageBox.Show("Test"); return 0;
    	}
    }
 
        private const char NON_ALPHABETIC_CHARACTER1 = '§';
        private const char NON_ALPHABETIC_CHARACTER2 = '$';
 
        private enum Herkunft
        {
            KeineInformation,
            Oben,
            ObenLinks,
            Links
        }
        private struct Alignment
        {
            public string Seq1 { get; set; }
            public string Seq2 { get; set; }
        }
 
        private string SeqU = string.Empty, SeqV = string.Empty;
        private int[,] Matrix;
        private Herkunft[,] Herkunftsmatrix;
        private List OptimaleAlignments;
 
        public SmithWaterman(string sequenceU, string sequenceV)
        {
            SeqU = NON_ALPHABETIC_CHARACTER1 + sequenceU;
            SeqV = NON_ALPHABETIC_CHARACTER2 + sequenceV;
 
            this.Initialisieren();
            this.MatrixBerechnen();
            this.Backtrace();
        }
 
        private void Initialisieren()
        {
            Matrix = new int[SeqU.Length, SeqV.Length]; //Setzt praktischerweise gleichzeitig alles auf 0
            Herkunftsmatrix = new Herkunft[SeqU.Length, SeqV.Length];
            OptimaleAlignments = new List();
        }
 
        private void MatrixBerechnen()
        {
            int a, b, c;
 
            for (int SeqUCounter = 1; SeqUCounter < SeqU.Length; SeqUCounter++)
            {
                for (int SeqVCounter = 1; SeqVCounter < SeqV.Length; SeqVCounter++)
                {
                    a = 0; b = 0; c = 0;
 
                    a = Matrix[SeqUCounter - 1, SeqVCounter - 1] + Score(SeqU[SeqUCounter], SeqV[SeqVCounter]);
                    b = Matrix[SeqUCounter - 1, SeqVCounter] + Score(SeqU[SeqUCounter], '-');
                    c = Matrix[SeqUCounter, SeqVCounter - 1] + Score('-', SeqV[SeqVCounter]);
                    int max = this.Max(a, b, c);
 
                    if (max < 0)
                    {
                        max = 0;
                    }
 
                    if (max != 0)
                    {
                        if (max == a)
                        { Herkunftsmatrix[SeqUCounter, SeqVCounter] = Herkunft.ObenLinks; }
                        if (max == b)
                        { Herkunftsmatrix[SeqUCounter, SeqVCounter] = Herkunft.Links; }
                        if (max == c)
                        { Herkunftsmatrix[SeqUCounter, SeqVCounter] = Herkunft.Oben; }
                    }
 
                    Matrix[SeqUCounter, SeqVCounter] = max;
 
                }
            }
 
        }
 
        private int Score(char uj, char vj)
        {
            if (uj != '-' && vj != '-')
            {
                //if (uj == vj)
                //{ 
                //    return 1; 
                //}
 
                //if (uj != vj)
                //{
                    return matrix[getIndex(uj), getIndex(vj)];
 
                //}
            }
            else
            {
                return -5;
            }
 
            throw new Exception("Unreachable code reached...what?");
        }
 
        private void Backtrace()
        {
            List HöchsteZahl = new List();
 
            int tempHöchsteZahl = 0;
 
            //Höchste Zahl ermitteln
            for (int SeqUCounter = 1; SeqUCounter < SeqU.Length; SeqUCounter++)
            {
                for (int SeqVCounter = 1; SeqVCounter < SeqV.Length; SeqVCounter++)                 {                     if (Matrix[SeqUCounter, SeqVCounter] > tempHöchsteZahl)
                    { tempHöchsteZahl = Matrix[SeqUCounter, SeqVCounter]; }
                }
            }
 
            //Alle raussuchen
            for (int SeqUCounter = 1; SeqUCounter < SeqU.Length; SeqUCounter++)
            {
                for (int SeqVCounter = 1; SeqVCounter < SeqV.Length; SeqVCounter++)
                {
                    if (Matrix[SeqUCounter, SeqVCounter] == tempHöchsteZahl)
                    { HöchsteZahl.Add(new Point(SeqUCounter, SeqVCounter)); }
                }
            }
 
            for (int i = 0; i < HöchsteZahl.Count; i++)
            {
                Alignment tempAlignment = new Alignment();
                int u = HöchsteZahl[i].X, v = HöchsteZahl[i].Y;
 
                while (Matrix[u, v] != 0)
                {
 
                    switch (Herkunftsmatrix[u,v])
                    {
                        case Herkunft.KeineInformation:
                            System.Windows.Forms.MessageBox.Show("Hummm");
                            break;
                        case Herkunft.Oben:
                            tempAlignment.Seq1 = '-' + tempAlignment.Seq1;
                            tempAlignment.Seq2 = SeqU[v] + tempAlignment.Seq2;
                            v--;
                            break;
                        case Herkunft.ObenLinks:
                            tempAlignment.Seq1 = SeqU[u] + tempAlignment.Seq1;
                            tempAlignment.Seq2 = SeqV[v] + tempAlignment.Seq2;
                            u--;v--;
                            break;
                        case Herkunft.Links:
                            tempAlignment.Seq1 = SeqU[u] + tempAlignment.Seq1;
                            tempAlignment.Seq2 = '-' + tempAlignment.Seq2;
                            u--;
                            break;
                        default:
                            break;
                    }
 
                }
 
                OptimaleAlignments.Add(tempAlignment);
            }
        }
        private int Max(int a, int b, int c)
        {
            return Math.Max(a, Math.Max(b, c));
 
        }
 
        public string Print()
        { 
            string tempString = string.Empty;
            SeqU = SeqU.Replace(NON_ALPHABETIC_CHARACTER1, '§');
            SeqV = SeqV.Replace(NON_ALPHABETIC_CHARACTER2, '§');
 
            //Matrix
            tempString += "Smith-Waterman Matrix\r\n";
            tempString += "§\t";
            for (int SeqUCounter = 0; SeqUCounter < SeqU.Length; SeqUCounter++)
            {
                tempString += SeqU[SeqUCounter] + "\t";
            }
            tempString += "\r\n";
 
            for (int SeqVCounter = 0; SeqVCounter < SeqV.Length; SeqVCounter++)
            {
                tempString += SeqV[SeqVCounter] + "\t";
                for (int SeqUCounter = 0; SeqUCounter < SeqU.Length; SeqUCounter++)
                {
 
                    tempString += Matrix[SeqUCounter, SeqVCounter] + "\t";
 
                }
                tempString += "\r\n";
            }
 
            tempString += "\r\n";
 
            //Optimale Alignments
            tempString += "Optimale Alignments\r\n";
            foreach (Alignment a in OptimaleAlignments)
            {
                foreach (char c in a.Seq1)
                { tempString += c + "\t"; }
 
                tempString += "\r\n";
 
                foreach (char c in a.Seq2)
                { tempString += c + "\t"; }
 
                tempString += "\r\n";
                tempString += "\r\n";
            }
 
            //Herkunftsmatrix
            tempString += "Herkunftsmatrix\r\n";
            for (int SeqUCounter = 0; SeqUCounter < SeqU.Length; SeqUCounter++)
            {
                for (int SeqVCounter = 0; SeqVCounter < SeqV.Length; SeqVCounter++)
                {
                    if (Herkunftsmatrix[SeqUCounter, SeqVCounter] != Herkunft.KeineInformation)
                    {
                        tempString += string.Format("[{0}][{1}] = [{2}]\r\n", SeqUCounter, SeqVCounter, Herkunftsmatrix[SeqUCounter, SeqVCounter]);
                    }
                }
                tempString += "\r\n";
            }
 
            return tempString;
 
        }
    }
}

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