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#ifndef seqdb_h
#define seqdb_h
#include <vector>
#include <map>
struct SeqData;
using namespace std;
struct SeqDB
{
private:
SeqDB(const SeqDB &rhs);
SeqDB &operator=(const SeqDB &rhs);
public:
string m_FileName;
char **m_Labels;
byte **m_Seqs;
unsigned *m_SeqLengths;
unsigned m_SeqCount;
unsigned m_Size;
bool m_Aligned;
bool m_IsNucleo;
bool m_IsNucleoSet;
public:
SeqDB();
~SeqDB();
void Clear(bool ctor = false);
void InitEmpty(bool Nucleo);
unsigned AddSeq(const char *Label, const byte *Seq, unsigned L);
byte *GetSeq(unsigned SeqIndex) const
{
asserta(SeqIndex < m_SeqCount);
return m_Seqs[SeqIndex];
}
const char *GetLabel(unsigned SeqIndex) const
{
asserta(SeqIndex < m_SeqCount);
return m_Labels[SeqIndex];
}
unsigned GetSeqLength(unsigned SeqIndex) const
{
asserta(SeqIndex < m_SeqCount);
return m_SeqLengths[SeqIndex];
}
unsigned GetSeqCount() const
{
return m_SeqCount;
}
unsigned GetPairCount() const
{
unsigned SeqCount = GetSeqCount();
return (SeqCount*(SeqCount - 1))/2;
}
unsigned GetPairIndex(unsigned SeqIndex1, unsigned SeqIndex2) const
{
if (SeqIndex1 > SeqIndex2)
return (SeqIndex1*(SeqIndex1 - 1))/2 + SeqIndex2;
return (SeqIndex2*(SeqIndex2 - 1))/2 + SeqIndex1;
}
unsigned GetColCount() const
{
if (!m_Aligned)
Die("SeqDB::GetColCount, not aligned");
if (m_SeqCount == 0)
Die("SeqDB::GetColCount, empty");
return m_SeqLengths[0];
}
bool IsNucleo() const
{
asserta(m_IsNucleoSet);
return m_IsNucleo;
}
void GetSeqData(unsigned Id, SeqData &Buffer) const;
unsigned GetMaxLabelLength() const;
unsigned GetMaxSeqLength() const;
void SetIsNucleo();
unsigned GetIndex(const char *Label) const;
void MakeLabelToIndex(map<string, unsigned> &LabelToIndex);
void LogMe() const;
void FromFasta(const string &FileName, bool AllowGaps = false);
void ToFasta(const string &FileName) const;
void ToFasta(FILE *f, unsigned SeqIndex) const;
void SeqToFasta(FILE *f, unsigned SeqIndex, bool WithLabel = false) const;
unsigned GetTotalLength() const;
};
bool isgap(byte c);
#endif
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