Mercurial > repos > aaronquinlan > multi_intersect
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BEDTools-Version-2.14.3/src/linksBed/linksBed.cpp Thu Nov 03 10:25:04 2011 -0400 @@ -0,0 +1,122 @@ +/***************************************************************************** + linksBed.cpp + + (c) 2009 - Aaron Quinlan + Hall Laboratory + Department of Biochemistry and Molecular Genetics + University of Virginia + aaronquinlan@gmail.com + + Licenced under the GNU General Public License 2.0 license. +******************************************************************************/ +#include "lineFileUtilities.h" +#include "linksBed.h" + +// +// Constructor +// +BedLinks::BedLinks(string &bedFile, string &base, string &org, string &db) { + _bedFile = bedFile; + _bed = new BedFile(bedFile); + + _base = base; + _org = org; + _db = db; + + CreateLinks(); +} + +// +// Destructor +// +BedLinks::~BedLinks(void) { +} + + +void BedLinks::WriteURL(BED &bed, string &base) { + + string position = bed.chrom; + std::stringstream posStream; + posStream << ":" << bed.start << "-" << bed.end; + position.append(posStream.str()); + + cout << "<tr>" << endl; + cout << "\t<td>" << endl; + cout << "\t\t<a href=" << base << position << ">"; + cout << bed.chrom << ":" << bed.start << "-" << bed.end; + cout << "</a>" << endl; + cout << "\t</td>" << endl; + + if (_bed->bedType == 4) { + cout << "\t<td>" << endl; + cout << bed.name << endl; + cout << "\t</td>" << endl; + } + else if (_bed->bedType == 5) { + cout << "\t<td>" << endl; + cout << bed.name << endl; + cout << "\t</td>" << endl; + + cout << "\t<td>" << endl; + cout << bed.score << endl; + cout << "\t</td>" << endl; + } + else if ((_bed->bedType == 6) || (_bed->bedType == 9) || (_bed->bedType == 12)) { + cout << "\t<td>" << endl; + cout << bed.name << endl; + cout << "\t</td>" << endl; + + cout << "\t<td>" << endl; + cout << bed.score << endl; + cout << "\t</td>" << endl; + + cout << "\t<td>" << endl; + cout << bed.strand << endl; + cout << "\t</td>" << endl; + } + cout << "</tr>" << endl; +} + + +void BedLinks::CreateLinks() { + + + // construct the html base. + string org = _org; + string db = _db; + string base = _base; + base.append("/cgi-bin/hgTracks?org="); + base.append(org); + base.append("&db="); + base.append(db); + base.append("&position="); + + // create the HTML header + cout << "<html>" << endl <<"\t<body>" << endl; + cout << "<title>" << _bedFile << "</title>" << endl; + + // start the table of entries + cout << "<br>Firefox users: Press and hold the \"apple\" or \"alt\" key and click link to open in new tab." << endl; + cout << "<p style=\"font-family:courier\">" << endl; + cout << "<table border=\"0\" align=\"justify\"" << endl; + cout << "<h3>BED Entries from: stdin </h3>" << endl; + + int lineNum = 0; + BED bedEntry, nullBed; + BedLineStatus bedStatus; + + _bed->Open(); + while ((bedStatus = _bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) { + if (bedStatus == BED_VALID) { + WriteURL(bedEntry, base); + bedEntry = nullBed; + } + } + _bed->Close(); + + cout << "</table>" << endl; + cout << "</p>" << endl; + cout << "\t</body>" << endl <<"</html>" << endl; +} + +