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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 | // $Id: alphabet.h 1901 2007-03-15 13:21:06Z nimrodru $
// version 1.01
// last modified 1 Jan 2004
#ifndef ___ALPHABET_H
#define ___ALPHABET_H
#include <string>
#include <vector>
using namespace std;
class alphabet {
public:
virtual int relations(const int charInSeq, const int charToCheck) const =0;
virtual int fromChar(const string& seq,const int pos) const =0;
virtual string fromInt(const int in_id) const =0;
virtual int size() const =0;
virtual ~alphabet()=0;
virtual int unknown() const =0;
virtual int gap() const =0;
virtual alphabet* clone() const = 0;
virtual int stringSize() const =0;
virtual vector<int> fromString(const string& str) const =0;
// "specific" here is not unknown, nor ambiguity, nor gap (for example, for nucleotides it will true for A,C,G, or T).
virtual bool isSpecific(const int in_id) const =0;
};
#endif
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