/usr/include/libMUSCLE-3.7/libMUSCLE/seq.h is in libmuscle-3.7-dev 3.7+4565-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 | #ifndef Seq_h
#define Seq_h
#include <vector>
namespace muscle {
class TextFile;
class MSA;
typedef std::vector<char> CharVect;
class Seq : public CharVect
{
public:
Seq()
{
m_ptrName = 0;
// Start with moderate size to avoid
// thrashing the heap.
reserve(200);
}
virtual ~Seq()
{
delete[] m_ptrName;
}
private:
// Not implemented; prevent use of copy c'tor and assignment.
Seq(const Seq &);
Seq &operator=(const Seq &);
public:
void Clear()
{
clear();
delete[] m_ptrName;
m_ptrName = 0;
m_uId = uInsane;
}
const char *GetName() const
{
return m_ptrName;
}
unsigned GetId() const
{
if (uInsane == m_uId)
Quit("Seq::GetId, id not set");
return m_uId;
}
void SetId(unsigned uId) { m_uId = uId; }
bool FromFASTAFile(TextFile &File);
void ToFASTAFile(TextFile &File) const;
void ExtractUngapped(MSA &msa) const;
void FromString(const char *pstrSeq, const char *pstrName);
void Copy(const Seq &rhs);
void CopyReversed(const Seq &rhs);
void StripGaps();
void StripGapsAndWhitespace();
void ToUpper();
void SetName(const char *ptrName);
unsigned GetLetter(unsigned uIndex) const;
unsigned Length() const { return (unsigned) size(); }
bool Eq(const Seq &s) const;
bool EqIgnoreCase(const Seq &s) const;
bool EqIgnoreCaseAndGaps(const Seq &s) const;
bool HasGap() const;
unsigned GetUngappedLength() const;
void LogMe() const;
char GetChar(unsigned uIndex) const { return operator[](uIndex); }
void SetChar(unsigned uIndex, char c) { operator[](uIndex) = c; }
void AppendChar(char c) { push_back(c); }
void FixAlpha();
#ifndef _WIN32
reference at(size_type i) { return operator[](i); }
const_reference at(size_type i) const { return operator[](i); }
#endif
private:
char *m_ptrName;
unsigned m_uId;
};
} // namespace muscle
#endif // Seq.h
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