/usr/include/libMUSCLE-3.7/libMUSCLE/seqvect.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 | #ifndef SeqVect_h
#define SeqVect_h
#include <vector>
#include "libMUSCLE/seq.h"
namespace muscle {
typedef std::vector<Seq *> SeqVectBase;
class SeqVect : public SeqVectBase
{
public:
SeqVect() {}
virtual ~SeqVect();
private:
// Not implemented; prevent use of copy c'tor and assignment.
SeqVect(const SeqVect &);
SeqVect &operator=(const SeqVect &);
public:
void FromFile(TextFile &File)
{
FromFASTAFile(File);
}
void FromFASTAFile(TextFile &File);
void ToFASTAFile(TextFile &File) const;
void ToFile(TextFile &File) const
{
ToFASTAFile(File);
}
void PadToMSA(MSA &msa);
void Copy(const SeqVect &rhs);
void StripGaps();
void StripGapsAndWhitespace();
void ToUpper();
void Clear();
unsigned Length() const { return (unsigned) size(); }
unsigned GetSeqCount() const { return (unsigned) size(); }
void AppendSeq(const Seq &s);
bool FindName(const char *ptrName, unsigned *ptruIndex) const;
void LogMe() const;
const char *GetSeqName(unsigned uSeqIndex) const;
unsigned GetSeqId(unsigned uSeqIndex) const;
unsigned GetSeqIdFromName(const char *Name) const;
unsigned GetSeqLength(unsigned uSeqIndex) const;
void SetSeqId(unsigned uSeqIndex, unsigned uId);
Seq &GetSeq(unsigned uIndex);
Seq &GetSeqById(unsigned uId);
const Seq &GetSeq(unsigned uIndex) const;
ALPHA GuessAlpha() const;
void FixAlpha();
#ifndef _WIN32
reference at(size_type i) { return operator[](i); }
const_reference at(size_type i) const { return operator[](i); }
#endif
};
} // namespace muscle
#endif // SeqVect_h
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