bbq Implementation Documentation

---

bitsets.h

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// bbq - Copyright (C) 2005, Axel Mosig, University of Leipzig. See
// main.cpp for details.

#ifndef BITSET_H
#define BITSET_H

#include <iostream>

namespace bbq {

class uint_bitset 
{
private:
        
        unsigned int bits;

public:

        // k corresponds to the number of bits and hence the number of
        // sequence fragments in footprint_detector.  In uint64_bitset,
        // this variable only exists for formal reasons and does not have
        // an influence on the number of bits, which is fixed to
        // 8*sizeof(unsigned int), which is usually 32.
        static int k;
        
        uint_bitset()
                {
                        bits = 0;
                }

        bool subseteq(const uint_bitset&);
        
        bool operator<(const uint_bitset&);

        bool operator==(const uint_bitset&);

        // this version of subseteq checks only up to the J-th bit whether
        // *this is a subset of the set passed as an argument.
        bool subseteq(const uint_bitset&, const unsigned int& J);
        
        int cardinality();

        friend std::ostream& operator<<(std::ostream& o,const uint_bitset&);
        
        void intersect(const uint_bitset& b);

        void set(const int& j);

        void remove(const int& j);
        
};

class uint64_bitset 
{
private:
        
        unsigned long long bits;

public:

        // k corresponds to the number of bits and hence the number of
        // sequence fragments in footprint_detector.  In uint64_bitset,
        // this variable only exists for formal reasons and does not have
        // an influence on the number of bits, which is fixed to
        // 8*sizeof(unsigned long long), which is usually 64.
        static int k;
        
        uint64_bitset()
                {
                        bits = 0;
                }
        
        bool subseteq(const uint64_bitset&);
        
        bool operator<(const uint64_bitset&) const;

        bool operator==(const uint64_bitset&) const;

        int cardinality();

        friend std::ostream& operator<<(std::ostream& o,const uint64_bitset&);
        
        void intersect(const uint64_bitset& b);

        void set(const int& j);

        void remove(const int& j);
        
};

class variable_bitset 
{
private:
        
        unsigned int* bits;

public:

        // k corresponds to the number of bits and hence the number of
        // sequence fragments in footprint_detector
        static int k;

        variable_bitset(const variable_bitset&);

        variable_bitset& operator=(const variable_bitset& vb);
        
        variable_bitset();

        ~variable_bitset()
                {
                        delete[] bits;
                }

        bool subseteq(const variable_bitset&) const;
        
        int cardinality();

        friend std::ostream& operator<<(std::ostream& o,const variable_bitset&);
        
        void intersect(const variable_bitset& b);

        void set(const int& j);

        void remove(const int& j);
        
        bool operator<(const variable_bitset&);

        bool operator==(const variable_bitset&);
        
};


} // end namespace bbq

#endif

bbq Implementation Documentation
Axel Mosig, Bioinformatics, University of Leipzig