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 (1511 downloads)

Source

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291

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;
 
        }
    }
}

Leave a message

Your email address will not be published. Required fields are marked *

*