Mercurial > repos > vipints > deseq_hts

annotate deseq-hts_2.0/mex/interval_overlap.cpp @ 11:cec4b4fb30be draft default tip

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DEXSeq version 1.6 added
author vipints <vipin@cbio.mskcc.org>
date Tue, 08 Oct 2013 08:22:45 -0400
parents 2fe512c7bfdf
children
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10
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1 /*
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2 * This program is free software; you can redistribute it and/or modify
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3 * it under the terms of the GNU General Public License as published by
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4 * the Free Software Foundation; either version 3 of the License, or
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5 * (at your option) any later version.
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6 *
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7 * Written (W) 2010-2011 Jonas Behr
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8 * Copyright (C) 2010-2011 Max Planck Society
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9 */
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11
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12 #include <stdio.h>
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13 #include <stdarg.h>
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14 #include <errno.h>
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15 #include <sys/types.h>
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16 #include <sys/stat.h>
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17 #include <fcntl.h>
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18 #include <ctype.h>
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19 #include <sys/stat.h>
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20 #include <stdlib.h>
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21 #include <unistd.h>
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22 #include <string.h>
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23 #include <sys/mman.h>
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24 #include <time.h>
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25 #include <math.h>
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26 #include <limits>
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27 #include <mex.h>
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28 #include <assert.h>
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29 #include <vector>
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30 using std::vector;
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31 #include <algorithm>
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32 using std::sort;
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33 using std::min;
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34 using std::max;
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35
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36 typedef struct {
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37 int start;
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38 int stop;
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39 int idx;
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40 int set_id;
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41 } interval_t;
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42
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43 bool compare (interval_t i, interval_t j)
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44 {
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45 return (i.start<j.start);
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46 }
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47
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48 bool overlaps(interval_t a, interval_t b)
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49 {
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50 int v = min(a.stop,b.stop) - max(a.start,b.start) + 1;
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51 return (v >= 1);
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52 }
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53 bool leftOf(interval_t a, interval_t b)
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54 {
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55 return (a.stop < b.start);
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56 }
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57
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58 void scan(interval_t f, vector<interval_t>* Wf, interval_t g, vector<interval_t>* Wg, vector<int>* overlap)
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59 {
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60 vector<interval_t>::iterator i;
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61 i=Wg->begin();
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62 while (i<Wg->end())
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63 {
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64 interval_t g2 = *i;
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65 if (leftOf(g2,f))
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66 {
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67 Wg->erase(i);// inefficient if Wg is large
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68 // this moves all elements, therefore i is not incremented
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69 }
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70 else if (overlaps(g2,f))
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71 {
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72 if (g2.set_id==1)
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73 {
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74 //printf("overlap: [%i | %i, %i] [%i | %i, %i]\n", g2.idx, g2.start, g2.stop, f.idx, f.start, f.stop);
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75 overlap->push_back(g2.idx);
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76 overlap->push_back(f.idx);
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77 }
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78 else if (f.set_id==1)
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79 {
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80 //printf("overlap: [%i | %i, %i] [%i | %i, %i]\n", f.idx, f.start, f.stop, g2.idx, g2.start, g2.stop);
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81 overlap->push_back(f.idx);
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82 overlap->push_back(g2.idx);
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83 }
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84 i++;
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85 }
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86 else
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87 {
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88 printf("never happens??\n");
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89 i++;
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90 }
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91 }
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92 if (!leftOf(f, g))
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93 {
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94 Wf->push_back(f);
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95 //printf("push: [%i, %i] size:%i\n", f.start, f.stop, Wf->size());
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96 }
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97 }
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98
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99 /*
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100 * prhs[0] first interval set starts
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101 * prhs[1] first interval set stops
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102 * prhs[2] second interval set starts
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103 * prhs[3] second interval set stops
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104 *
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105 * return:
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106 * plhs[0] one based index in first interval set overlapping with a interval in the second set
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107 * plhs[1] corresponding index in the second set
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108 *
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109 */
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110 void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
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111 {
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112 if (nrhs!=4)
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113 mexErrMsgTxt("Expected 4 arguments: starts1, stops1, starts2, stops2 \n");
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114 if (nlhs!=2)
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115 mexErrMsgTxt("Expected 2 output arguments \n");
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116
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117 int num_intervals1 = mxGetNumberOfElements(prhs[0]);
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118 assert(num_intervals1 == mxGetNumberOfElements(prhs[1]));
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119 int num_intervals2 = mxGetNumberOfElements(prhs[2]);
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120 assert(num_intervals2 == mxGetNumberOfElements(prhs[3]));
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121
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122 //printf("num_intervals1: %i\n", num_intervals1);
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123 //printf("num_intervals2: %i\n", num_intervals2);
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124
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125 double* starts1 = mxGetPr(prhs[0]);
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126 double* stops1 = mxGetPr(prhs[1]);
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127 double* starts2 = mxGetPr(prhs[2]);
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128 double* stops2 = mxGetPr(prhs[3]);
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129
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130 vector<interval_t> intervals1;
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131 for (int i=0; i<num_intervals1; i++)
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132 {
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133 interval_t interval;
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134 interval.start = starts1[i];
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135 interval.stop = stops1[i];
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136 interval.set_id = 1;
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137 interval.idx = i+1;
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138 intervals1.push_back(interval);
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139 //printf("int1: [%i, %i] \n",intervals1[i].start, intervals1[i].stop);
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140 }
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141 interval_t i;
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142 i.start = std::numeric_limits<int>::max();
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143 i.stop = std::numeric_limits<int>::max();
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144 i.set_id = std::numeric_limits<int>::max();
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145 i.idx = std::numeric_limits<int>::max();
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146 intervals1.push_back(i);
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147
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148 //printf("num_intervals1: %i\n", intervals1.size());
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149 vector<interval_t> intervals2;
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150 for (int i=0; i<num_intervals2; i++)
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151 {
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152 interval_t interval;
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153 interval.start = starts2[i];
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154 interval.stop = stops2[i];
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155 interval.set_id = 2;
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156 interval.idx = i+1;
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157 intervals2.push_back(interval);
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158 //printf("int2: [%i, %i] \n",intervals2[i].start, intervals2[i].stop);
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159 }
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160 intervals2.push_back(i);
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161 //printf("num_intervals2: %i\n", intervals2.size());
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162
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163 sort(intervals1.begin(), intervals1.end(), compare);
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164 sort(intervals2.begin(), intervals2.end(), compare);
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165
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166
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167 vector<int> overlap;
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168 vector<interval_t> Wx;
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169 vector<interval_t> Wy;
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170 vector<interval_t>::iterator x = intervals1.begin();
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171 vector<interval_t>::iterator y = intervals2.begin();
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172 while (x<intervals1.end() && y<intervals2.end())
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173 {
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174 //vector<interval_t>::iterator x;
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175 //vector<interval_t>::iterator y;
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176 //if (it1>intervals1.end())
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177 // x = inf_interval();
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178 //else
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179 // x = it1;
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180 //if (it2>intervals2.end())
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181 // y = inf_interval();
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182 //else
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183 // y=it2;
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184
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185 if (x->start <= y->start)
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186 {
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187 scan(*x, &Wx, *y, &Wy, &overlap);
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188 x++;
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189 }
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190 else
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191 {
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192 if (y<=intervals2.end())
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193 {
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194 scan(*y, &Wy, *x, &Wx, &overlap);
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195 y++;
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196 }
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197 }
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198 }
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199
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200 plhs[0] = mxCreateDoubleMatrix(1, overlap.size()/2, mxREAL);
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201 double* idx1 = mxGetPr(plhs[0]);
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202
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203 plhs[1] = mxCreateDoubleMatrix(1, overlap.size()/2, mxREAL);
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204 double* idx2 = mxGetPr(plhs[1]);
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205
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206 for (int i=0; i<overlap.size(); i+=2)
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207 {
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208 //printf("ov: %i [%i, %i] \n", i, overlap[i], overlap[i+1]);
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209 idx1[i/2] = (double) overlap[i];
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210 idx2[i/2] = (double) overlap[i+1];
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211 }
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212 }
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213
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214
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215
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216
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217