diff BEDTools-Version-2.14.3/src/nucBed/nucBed.h @ 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/nucBed/nucBed.h	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,55 @@
+/*****************************************************************************
+  nucBed.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 NUCBED_H
+#define NUCBED_H
+
+#include "bedFile.h"
+#include "sequenceUtils.h"
+#include "Fasta.h"
+#include <vector>
+#include <iostream>
+#include <fstream>
+
+using namespace std;
+
+//************************************************
+// Class methods and elements
+//************************************************
+class NucBed {
+
+public:
+
+    // constructor
+    NucBed(string &dbFile, string &bedFile, bool printSeq, 
+           bool hasPattern, const string &pattern,
+           bool forceStrand);
+    // destructor
+    ~NucBed(void);
+
+    void ProfileDNA();
+
+
+private:
+    string _dbFile;
+    string _bedFile;
+    bool   _printSeq;
+    bool   _hasPattern;
+    string _pattern;
+    bool _forceStrand;
+
+    // instance of a bed file class.
+    BedFile  *_bed;
+    void PrintHeader(void);
+    void ReportDnaProfile(const BED& bed, const string &sequence, int seqLength);
+};
+
+#endif