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1 /*****************************************************************************
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2 linksBed.cpp
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3
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4 (c) 2009 - Aaron Quinlan
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5 Hall Laboratory
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6 Department of Biochemistry and Molecular Genetics
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7 University of Virginia
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8 aaronquinlan@gmail.com
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9
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10 Licenced under the GNU General Public License 2.0 license.
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11 ******************************************************************************/
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12 #include "lineFileUtilities.h"
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13 #include "linksBed.h"
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14
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15 //
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16 // Constructor
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17 //
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18 BedLinks::BedLinks(string &bedFile, string &base, string &org, string &db) {
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19 _bedFile = bedFile;
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20 _bed = new BedFile(bedFile);
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21
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22 _base = base;
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23 _org = org;
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24 _db = db;
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25
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26 CreateLinks();
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27 }
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28
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29 //
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30 // Destructor
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31 //
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32 BedLinks::~BedLinks(void) {
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33 }
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34
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35
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36 void BedLinks::WriteURL(BED &bed, string &base) {
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37
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38 string position = bed.chrom;
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39 std::stringstream posStream;
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40 posStream << ":" << bed.start << "-" << bed.end;
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41 position.append(posStream.str());
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42
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43 cout << "<tr>" << endl;
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44 cout << "\t<td>" << endl;
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45 cout << "\t\t<a href=" << base << position << ">";
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46 cout << bed.chrom << ":" << bed.start << "-" << bed.end;
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47 cout << "</a>" << endl;
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48 cout << "\t</td>" << endl;
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49
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50 if (_bed->bedType == 4) {
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51 cout << "\t<td>" << endl;
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52 cout << bed.name << endl;
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53 cout << "\t</td>" << endl;
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54 }
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55 else if (_bed->bedType == 5) {
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56 cout << "\t<td>" << endl;
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57 cout << bed.name << endl;
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58 cout << "\t</td>" << endl;
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59
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60 cout << "\t<td>" << endl;
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61 cout << bed.score << endl;
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62 cout << "\t</td>" << endl;
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63 }
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64 else if ((_bed->bedType == 6) || (_bed->bedType == 9) || (_bed->bedType == 12)) {
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65 cout << "\t<td>" << endl;
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66 cout << bed.name << endl;
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67 cout << "\t</td>" << endl;
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68
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69 cout << "\t<td>" << endl;
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70 cout << bed.score << endl;
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71 cout << "\t</td>" << endl;
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72
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73 cout << "\t<td>" << endl;
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74 cout << bed.strand << endl;
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75 cout << "\t</td>" << endl;
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76 }
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77 cout << "</tr>" << endl;
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78 }
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79
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80
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81 void BedLinks::CreateLinks() {
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82
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83
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84 // construct the html base.
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85 string org = _org;
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86 string db = _db;
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87 string base = _base;
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88 base.append("/cgi-bin/hgTracks?org=");
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89 base.append(org);
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90 base.append("&db=");
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91 base.append(db);
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92 base.append("&position=");
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93
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94 // create the HTML header
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95 cout << "<html>" << endl <<"\t<body>" << endl;
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96 cout << "<title>" << _bedFile << "</title>" << endl;
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97
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98 // start the table of entries
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99 cout << "<br>Firefox users: Press and hold the \"apple\" or \"alt\" key and click link to open in new tab." << endl;
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100 cout << "<p style=\"font-family:courier\">" << endl;
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101 cout << "<table border=\"0\" align=\"justify\"" << endl;
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102 cout << "<h3>BED Entries from: stdin </h3>" << endl;
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103
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104 int lineNum = 0;
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105 BED bedEntry, nullBed;
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106 BedLineStatus bedStatus;
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107
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108 _bed->Open();
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109 while ((bedStatus = _bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) {
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110 if (bedStatus == BED_VALID) {
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111 WriteURL(bedEntry, base);
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112 bedEntry = nullBed;
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113 }
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114 }
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115 _bed->Close();
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116
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117 cout << "</table>" << endl;
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118 cout << "</p>" << endl;
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119 cout << "\t</body>" << endl <<"</html>" << endl;
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120 }
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121
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122
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