/usr/include/bamtools/api/SamProgramChain.h is in libbamtools-dev 2.4.1+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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// SamProgramChain.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides methods for operating on a SamProgram record "chain"
// ***************************************************************************
#ifndef SAM_PROGRAMCHAIN_H
#define SAM_PROGRAMCHAIN_H
#include "api/api_global.h"
#include "api/SamProgram.h"
#include <string>
#include <vector>
namespace BamTools {
// chain is *NOT* sorted in any order
// use First()/Last() to retrieve oldest/newest programs, respectively
typedef std::vector<SamProgram> SamProgramContainer;
typedef SamProgramContainer::iterator SamProgramIterator;
typedef SamProgramContainer::const_iterator SamProgramConstIterator;
class API_EXPORT SamProgramChain {
// ctor & dtor
public:
SamProgramChain(void);
SamProgramChain(const SamProgramChain& other);
~SamProgramChain(void);
// query/modify program data
public:
// appends a program record to the chain
void Add(SamProgram& program);
void Add(std::vector<SamProgram>& programs);
// clears all read group entries
void Clear(void);
// returns true if chain contains this program record (matches on ID)
bool Contains(const SamProgram& program) const;
bool Contains(const std::string& programId) const;
// returns the first (oldest) program in the chain
SamProgram& First(void);
const SamProgram& First(void) const;
// returns true if chain is empty
bool IsEmpty(void) const;
// returns last (most recent) program in the chain
SamProgram& Last(void);
const SamProgram& Last(void) const;
// returns number of program records in the chain
int Size(void) const;
// retrieves a modifiable reference to the SamProgram object associated with this ID
SamProgram& operator[](const std::string& programId);
// retrieve STL-compatible iterators
public:
SamProgramIterator Begin(void); // returns iterator to begin()
SamProgramConstIterator Begin(void) const; // returns const_iterator to begin()
SamProgramConstIterator ConstBegin(void) const; // returns const_iterator to begin()
SamProgramIterator End(void); // returns iterator to end()
SamProgramConstIterator End(void) const; // returns const_iterator to end()
SamProgramConstIterator ConstEnd(void) const; // returns const_iterator to end()
// internal methods
private:
int IndexOf(const std::string& programId) const;
const std::string NextIdFor(const std::string& programId) const;
// data members
private:
SamProgramContainer m_data;
};
} // namespace BamTools
#endif // SAM_PROGRAMCHAIN_H
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