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1 import java.io.*;
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2 import java.lang.*;
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3
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4 public class HmmGlocal
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5 {
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6 private double[] qual2prob;
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7 private double cd, ce; // gap open probility [1e-3], gap extension probability [0.1]
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8 private int cb; // band width [7]
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9
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10 public HmmGlocal(final double d, final double e, final int b) {
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11 cd = d; ce = e; cb = b;
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12 qual2prob = new double[256];
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13 for (int i = 0; i < 256; ++i)
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14 qual2prob[i] = Math.pow(10, -i/10.);
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15 }
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16 private static int set_u(final int b, final int i, final int k) {
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17 int x = i - b;
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18 x = x > 0? x : 0;
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19 return (k + 1 - x) * 3;
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20 }
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21 public int hmm_glocal(final byte[] _ref, final byte[] _query, final byte[] _iqual, int[] state, byte[] q) {
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22 int i, k;
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23 /*** initialization ***/
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24 // change coordinates
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25 int l_ref = _ref.length;
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26 byte[] ref = new byte[l_ref+1];
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27 for (i = 0; i < l_ref; ++i) ref[i+1] = _ref[i]; // FIXME: this is silly...
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28 int l_query = _query.length;
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29 byte[] query = new byte[l_query+1];
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30 double[] qual = new double[l_query+1];
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31 for (i = 0; i < l_query; ++i) {
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32 query[i+1] = _query[i];
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33 qual[i+1] = qual2prob[_iqual[i]];
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34 }
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35 // set band width
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36 int bw2, bw = l_ref > l_query? l_ref : l_query;
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37 if (bw > cb) bw = cb;
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38 if (bw < Math.abs(l_ref - l_query)) bw = Math.abs(l_ref - l_query);
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39 bw2 = bw * 2 + 1;
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40 // allocate the forward and backward matrices f[][] and b[][] and the scaling array s[]
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41 double[][] f = new double[l_query+1][bw2*3 + 6];
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42 double[][] b = new double[l_query+1][bw2*3 + 6];
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43 double[] s = new double[l_query+2];
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44 // initialize transition probabilities
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45 double sM, sI, bM, bI;
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46 sM = sI = 1. / (2 * l_query + 2);
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47 bM = (1 - cd) / l_query; bI = cd / l_query; // (bM+bI)*l_query==1
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48 double[] m = new double[9];
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49 m[0*3+0] = (1 - cd - cd) * (1 - sM); m[0*3+1] = m[0*3+2] = cd * (1 - sM);
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50 m[1*3+0] = (1 - ce) * (1 - sI); m[1*3+1] = ce * (1 - sI); m[1*3+2] = 0.;
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51 m[2*3+0] = 1 - ce; m[2*3+1] = 0.; m[2*3+2] = ce;
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52 /*** forward ***/
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53 // f[0]
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54 f[0][set_u(bw, 0, 0)] = s[0] = 1.;
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55 { // f[1]
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56 double[] fi = f[1];
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57 double sum;
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58 int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1, _beg, _end;
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59 for (k = beg, sum = 0.; k <= end; ++k) {
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60 int u;
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61 double e = (ref[k] > 3 || query[1] > 3)? 1. : ref[k] == query[1]? 1. - qual[1] : qual[1] / 3.;
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62 u = set_u(bw, 1, k);
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63 fi[u+0] = e * bM; fi[u+1] = .25 * bI;
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64 sum += fi[u] + fi[u+1];
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65 }
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66 // rescale
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67 s[1] = sum;
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68 _beg = set_u(bw, 1, beg); _end = set_u(bw, 1, end); _end += 2;
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69 for (k = _beg; k <= _end; ++k) fi[k] /= sum;
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70 }
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71 // f[2..l_query]
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72 for (i = 2; i <= l_query; ++i) {
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73 double[] fi = f[i], fi1 = f[i-1];
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74 double sum, qli = qual[i];
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75 int beg = 1, end = l_ref, x, _beg, _end;
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76 byte qyi = query[i];
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77 x = i - bw; beg = beg > x? beg : x; // band start
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78 x = i + bw; end = end < x? end : x; // band end
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79 for (k = beg, sum = 0.; k <= end; ++k) {
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80 int u, v11, v01, v10;
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81 double e;
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82 e = (ref[k] > 3 || qyi > 3)? 1. : ref[k] == qyi? 1. - qli : qli / 3.;
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83 u = set_u(bw, i, k); v11 = set_u(bw, i-1, k-1); v10 = set_u(bw, i-1, k); v01 = set_u(bw, i, k-1);
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84 fi[u+0] = e * (m[0] * fi1[v11+0] + m[3] * fi1[v11+1] + m[6] * fi1[v11+2]);
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85 fi[u+1] = .25 * (m[1] * fi1[v10+0] + m[4] * fi1[v10+1]);
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86 fi[u+2] = m[2] * fi[v01+0] + m[8] * fi[v01+2];
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87 sum += fi[u] + fi[u+1] + fi[u+2];
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88 //System.out.println("("+i+","+k+";"+u+"): "+fi[u]+","+fi[u+1]+","+fi[u+2]);
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89 }
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90 // rescale
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91 s[i] = sum;
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92 _beg = set_u(bw, i, beg); _end = set_u(bw, i, end); _end += 2;
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93 for (k = _beg, sum = 1./sum; k <= _end; ++k) fi[k] *= sum;
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94 }
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95 { // f[l_query+1]
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96 double sum;
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97 for (k = 1, sum = 0.; k <= l_ref; ++k) {
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98 int u = set_u(bw, l_query, k);
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99 if (u < 3 || u >= bw2*3+3) continue;
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100 sum += f[l_query][u+0] * sM + f[l_query][u+1] * sI;
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101 }
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102 s[l_query+1] = sum; // the last scaling factor
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103 }
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104 /*** backward ***/
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105 // b[l_query] (b[l_query+1][0]=1 and thus \tilde{b}[][]=1/s[l_query+1]; this is where s[l_query+1] comes from)
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106 for (k = 1; k <= l_ref; ++k) {
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107 int u = set_u(bw, l_query, k);
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108 double[] bi = b[l_query];
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109 if (u < 3 || u >= bw2*3+3) continue;
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110 bi[u+0] = sM / s[l_query] / s[l_query+1]; bi[u+1] = sI / s[l_query] / s[l_query+1];
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111 }
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112 // b[l_query-1..1]
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113 for (i = l_query - 1; i >= 1; --i) {
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114 int beg = 1, end = l_ref, x, _beg, _end;
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115 double[] bi = b[i], bi1 = b[i+1];
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116 double y = (i > 1)? 1. : 0., qli1 = qual[i+1];
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117 byte qyi1 = query[i+1];
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118 x = i - bw; beg = beg > x? beg : x;
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119 x = i + bw; end = end < x? end : x;
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120 for (k = end; k >= beg; --k) {
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121 int u, v11, v01, v10;
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122 double e;
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123 u = set_u(bw, i, k); v11 = set_u(bw, i+1, k+1); v10 = set_u(bw, i+1, k); v01 = set_u(bw, i, k+1);
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124 e = (k >= l_ref? 0 : (ref[k+1] > 3 || qyi1 > 3)? 1. : ref[k+1] == qyi1? 1. - qli1 : qli1 / 3.) * bi1[v11];
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125 bi[u+0] = e * m[0] + .25 * m[1] * bi1[v10+1] + m[2] * bi[v01+2]; // bi1[v11] has been foled into e.
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126 bi[u+1] = e * m[3] + .25 * m[4] * bi1[v10+1];
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127 bi[u+2] = (e * m[6] + m[8] * bi[v01+2]) * y;
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128 }
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129 // rescale
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130 _beg = set_u(bw, i, beg); _end = set_u(bw, i, end); _end += 2;
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131 for (k = _beg, y = 1./s[i]; k <= _end; ++k) bi[k] *= y;
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132 }
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133 double pb;
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134 { // b[0]
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135 int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1;
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136 double sum = 0.;
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137 for (k = end; k >= beg; --k) {
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138 int u = set_u(bw, 1, k);
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139 double e = (ref[k] > 3 || query[1] > 3)? 1. : ref[k] == query[1]? 1. - qual[1] : qual[1] / 3.;
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140 if (u < 3 || u >= bw2*3+3) continue;
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141 sum += e * b[1][u+0] * bM + .25 * b[1][u+1] * bI;
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142 }
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143 pb = b[0][set_u(bw, 0, 0)] = sum / s[0]; // if everything works as is expected, pb == 1.0
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144 }
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145 int is_diff = Math.abs(pb - 1.) > 1e-7? 1 : 0;
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146 /*** MAP ***/
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147 for (i = 1; i <= l_query; ++i) {
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148 double sum = 0., max = 0.;
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149 double[] fi = f[i], bi = b[i];
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150 int beg = 1, end = l_ref, x, max_k = -1;
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151 x = i - bw; beg = beg > x? beg : x;
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152 x = i + bw; end = end < x? end : x;
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153 for (k = beg; k <= end; ++k) {
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154 int u = set_u(bw, i, k);
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155 double z;
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156 sum += (z = fi[u+0] * bi[u+0]); if (z > max) { max = z; max_k = (k-1)<<2 | 0; }
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157 sum += (z = fi[u+1] * bi[u+1]); if (z > max) { max = z; max_k = (k-1)<<2 | 1; }
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158 }
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159 max /= sum; sum *= s[i]; // if everything works as is expected, sum == 1.0
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160 if (state != null) state[i-1] = max_k;
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161 if (q != null) {
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162 k = (int)(-4.343 * Math.log(1. - max) + .499);
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163 q[i-1] = (byte)(k > 100? 99 : k);
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164 }
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165 //System.out.println("("+pb+","+sum+")"+" ("+(i-1)+","+(max_k>>2)+","+(max_k&3)+","+max+")");
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166 }
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167 return 0;
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168 }
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169
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170 public static void main(String[] args) {
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171 byte[] ref = {'\0', '\1', '\3', '\3', '\1'};
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172 byte[] query = {'\0', '\3', '\3', '\1'};
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173 byte[] qual = new byte[4];
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174 qual[0] = qual[1] = qual[2] = qual[3] = (byte)20;
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175 HmmGlocal hg = new HmmGlocal(1e-3, 0.1, 7);
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176 hg.hmm_glocal(ref, query, qual, null, null);
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177 }
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178 } |
