--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/annotateBed/annotateBed.h	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,71 @@
+/*****************************************************************************
+  annotateBed.h
+
+  (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.
+******************************************************************************/
+#ifndef ANNOTATEBED_H
+#define ANNOTATEBED_H
+
+#include "bedFile.h"
+#include <vector>
+#include <algorithm>
+#include <iostream>
+#include <iomanip>
+#include <fstream>
+#include <stdlib.h>
+
+using namespace std;
+
+//************************************************
+// Class methods and elements
+//************************************************
+class BedAnnotate {
+
+public:
+
+    // constructor
+    BedAnnotate(const string &mainFile, const vector<string> &annoFileNames,
+                const vector<string> &annoTitles, bool sameStrand, bool diffStrand, bool reportCounts, bool reportBoth);
+
+    // destructor
+    ~BedAnnotate(void);
+
+    // annotate the master file with all of the annotation files.
+    void AnnotateBed();
+
+private:
+
+    // input files.
+    string _mainFile;
+    vector<string> _annoFileNames;
+    vector<string> _annoTitles;
+
+    // instance of a bed file class.
+    BedFile *_bed;
+    vector<BedFile*> _annoFiles;
+
+    // do we care about strandedness when counting coverage?
+    bool _sameStrand;
+    bool _diffStrand;
+    
+    bool _reportCounts;
+    bool _reportBoth;
+
+    // private function for reporting coverage information
+    void ReportAnnotations();
+
+    void OpenAnnoFiles();
+
+    void CloseAnnoFiles();
+
+    void PrintHeader();
+
+    void InitializeMainFile();
+};
+#endif /* ANNOTATEBED_H */