/usr/include/bamtools/api/SamSequenceDictionary.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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// SamSequenceDictionary.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 16 October 2011
// ---------------------------------------------------------------------------
// Provides methods for operating on a collection of SamSequence entries.
// ***************************************************************************
#ifndef SAM_SEQUENCE_DICTIONARY_H
#define SAM_SEQUENCE_DICTIONARY_H
#include "api/api_global.h"
#include "api/SamSequence.h"
#include <map>
#include <string>
#include <vector>
namespace BamTools {
typedef std::vector<SamSequence> SamSequenceContainer;
typedef SamSequenceContainer::iterator SamSequenceIterator;
typedef SamSequenceContainer::const_iterator SamSequenceConstIterator;
class API_EXPORT SamSequenceDictionary {
// ctor & dtor
public:
SamSequenceDictionary(void);
SamSequenceDictionary(const SamSequenceDictionary& other);
~SamSequenceDictionary(void);
// query/modify sequence data
public:
// adds a sequence
void Add(const SamSequence& sequence);
void Add(const std::string& name, const int& length);
// adds multiple sequences
void Add(const SamSequenceDictionary& sequences);
void Add(const std::vector<SamSequence>& sequences);
void Add(const std::map<std::string, int>& sequenceMap);
// clears all sequence entries
void Clear(void);
// returns true if dictionary contains this sequence
bool Contains(const SamSequence& sequence) const;
bool Contains(const std::string& sequenceName) const;
// returns true if dictionary is empty
bool IsEmpty(void) const;
// removes sequence, if found
void Remove(const SamSequence& sequence);
void Remove(const std::string& sequenceName);
// removes multiple sequences
void Remove(const std::vector<SamSequence>& sequences);
void Remove(const std::vector<std::string>& sequenceNames);
// returns number of sequences in dictionary
int Size(void) const;
// retrieves a modifiable reference to the SamSequence object associated with this name
SamSequence& operator[](const std::string& sequenceName);
// retrieve STL-compatible iterators
public:
SamSequenceIterator Begin(void); // returns iterator to begin()
SamSequenceConstIterator Begin(void) const; // returns const_iterator to begin()
SamSequenceConstIterator ConstBegin(void) const; // returns const_iterator to begin()
SamSequenceIterator End(void); // returns iterator to end()
SamSequenceConstIterator End(void) const; // returns const_iterator to end()
SamSequenceConstIterator ConstEnd(void) const; // returns const_iterator to end()
// data members
private:
SamSequenceContainer m_data;
std::map<std::string, size_t> m_lookupData;
};
} // namespace BamTools
#endif // SAM_SEQUENCE_DICTIONARY_H
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