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comparison BEDTools-Version-2.14.3/src/linksBed/linksBed.cpp @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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-1:000000000000 0:dfcd8b6c1bda
1 /*****************************************************************************
2 linksBed.cpp
3
4 (c) 2009 - Aaron Quinlan
5 Hall Laboratory
6 Department of Biochemistry and Molecular Genetics
7 University of Virginia
8 aaronquinlan@gmail.com
9
10 Licenced under the GNU General Public License 2.0 license.
11 ******************************************************************************/
12 #include "lineFileUtilities.h"
13 #include "linksBed.h"
14
15 //
16 // Constructor
17 //
18 BedLinks::BedLinks(string &bedFile, string &base, string &org, string &db) {
19 _bedFile = bedFile;
20 _bed = new BedFile(bedFile);
21
22 _base = base;
23 _org = org;
24 _db = db;
25
26 CreateLinks();
27 }
28
29 //
30 // Destructor
31 //
32 BedLinks::~BedLinks(void) {
33 }
34
35
36 void BedLinks::WriteURL(BED &bed, string &base) {
37
38 string position = bed.chrom;
39 std::stringstream posStream;
40 posStream << ":" << bed.start << "-" << bed.end;
41 position.append(posStream.str());
42
43 cout << "<tr>" << endl;
44 cout << "\t<td>" << endl;
45 cout << "\t\t<a href=" << base << position << ">";
46 cout << bed.chrom << ":" << bed.start << "-" << bed.end;
47 cout << "</a>" << endl;
48 cout << "\t</td>" << endl;
49
50 if (_bed->bedType == 4) {
51 cout << "\t<td>" << endl;
52 cout << bed.name << endl;
53 cout << "\t</td>" << endl;
54 }
55 else if (_bed->bedType == 5) {
56 cout << "\t<td>" << endl;
57 cout << bed.name << endl;
58 cout << "\t</td>" << endl;
59
60 cout << "\t<td>" << endl;
61 cout << bed.score << endl;
62 cout << "\t</td>" << endl;
63 }
64 else if ((_bed->bedType == 6) || (_bed->bedType == 9) || (_bed->bedType == 12)) {
65 cout << "\t<td>" << endl;
66 cout << bed.name << endl;
67 cout << "\t</td>" << endl;
68
69 cout << "\t<td>" << endl;
70 cout << bed.score << endl;
71 cout << "\t</td>" << endl;
72
73 cout << "\t<td>" << endl;
74 cout << bed.strand << endl;
75 cout << "\t</td>" << endl;
76 }
77 cout << "</tr>" << endl;
78 }
79
80
81 void BedLinks::CreateLinks() {
82
83
84 // construct the html base.
85 string org = _org;
86 string db = _db;
87 string base = _base;
88 base.append("/cgi-bin/hgTracks?org=");
89 base.append(org);
90 base.append("&db=");
91 base.append(db);
92 base.append("&position=");
93
94 // create the HTML header
95 cout << "<html>" << endl <<"\t<body>" << endl;
96 cout << "<title>" << _bedFile << "</title>" << endl;
97
98 // start the table of entries
99 cout << "<br>Firefox users: Press and hold the \"apple\" or \"alt\" key and click link to open in new tab." << endl;
100 cout << "<p style=\"font-family:courier\">" << endl;
101 cout << "<table border=\"0\" align=\"justify\"" << endl;
102 cout << "<h3>BED Entries from: stdin </h3>" << endl;
103
104 int lineNum = 0;
105 BED bedEntry, nullBed;
106 BedLineStatus bedStatus;
107
108 _bed->Open();
109 while ((bedStatus = _bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) {
110 if (bedStatus == BED_VALID) {
111 WriteURL(bedEntry, base);
112 bedEntry = nullBed;
113 }
114 }
115 _bed->Close();
116
117 cout << "</table>" << endl;
118 cout << "</p>" << endl;
119 cout << "\t</body>" << endl <<"</html>" << endl;
120 }
121
122