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54 lines
1.6 KiB
C++
54 lines
1.6 KiB
C++
// $Id: mulAlphabet.h 6420 2009-06-25 11:17:08Z adist $
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// version 1.01
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// last modified 1 Jan 2004
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#ifndef ___MUL_ALPHABET_H
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#define ___MUL_ALPHABET_H
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#include "definitions.h"
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#include "alphabet.h"
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#include "someUtil.h"
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class mulAlphabet : public alphabet {
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public:
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mulAlphabet(const alphabet* baseAlphabet, int mulFactor);
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mulAlphabet(const mulAlphabet& other);
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virtual ~mulAlphabet();
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virtual alphabet* clone() const { return new mulAlphabet(*this); }
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mulAlphabet& operator=(const mulAlphabet &other);
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int unknown() const ;
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int gap() const;
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int size() const {return _size;}
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int stringSize() const ;
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bool isSpecific(const int id) const ;
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int fromChar(const string& str, const int pos) const;
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vector<int> fromString(const string& str) const;
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string fromInt(const int id) const;
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int relations(const int charInSeq, const int charToCheck) const;
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int compareCategories(int charA, int charB) const;
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enum rateShiftType {noRateShift=0, acceleration, deceleration};
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static rateShiftType compareCategories(int charA, int charB, int baseAlphabetSize, int multiplicationFactor) ;
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const alphabet* getBaseAlphabet() const {return _baseAlphabet;}
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public:
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int convertFromBasedAlphaInt(int id) const;
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int convertToBasedAlphaInt(int id) const;
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private:
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alphabet* _baseAlphabet; // This alphabet must use single characters, i.e. - not codon. (or we will have to add to every alphabet a member which holds its character's size)
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int _mulFactor ; // number of times that the alphabet is multiplied by = Number of categories (g in Galtier paper)
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int _size ; // this is simply the _baseAlphabet->size() * _mulFactor
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};
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#endif
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