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