Mercurial > repos > aaronquinlan > multi_intersect

diff BEDTools-Version-2.14.3/src/linksBed/linksBed.cpp @ 1:bec36315bd12 default tip

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author aaronquinlan
date Sat, 19 Nov 2011 14:17:03 -0500
parents dfcd8b6c1bda
children
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--- a/BEDTools-Version-2.14.3/src/linksBed/linksBed.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,122 +0,0 @@
-/*****************************************************************************
-  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;
-}
-
-