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#ifndef Seq_h
#define Seq_h
#include <vector>
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);
}
~Seq()
{
delete[] m_ptrName;
}
Seq &operator=(const Seq &rhs)
{
Copy(rhs);
return *this;
}
private:
// Not implemented; prevent use of copy c'tor and assignment.
Seq(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
{
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;
void LogMeSeqOnly() 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();
void ToString(char String[], unsigned Bytes) const;
void RevComp();
#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;
};
#endif // Seq.h
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