bmvmin.h

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: bmvmin.h,v $
 * PRODUCTION Revision 1000.0  2004/04/21 16:01:02  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [CATCHUP_003] Dev-tree R1.1
 * PRODUCTION
 * ===========================================================================
 */

/*
Copyright (c) 2002 Anatoliy Kuznetsov.

Permission is hereby granted, free of charge, to any person 
obtaining a copy of this software and associated documentation 
files (the "Software"), to deal in the Software without restriction, 
including without limitation the rights to use, copy, modify, merge, 
publish, distribute, sublicense, and/or sell copies of the Software, 
and to permit persons to whom the Software is furnished to do so, 
subject to the following conditions:

The above copyright notice and this permission notice shall be included 
in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES 
OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 
IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, 
DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, 
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 
OTHER DEALINGS IN THE SOFTWARE.
*/

#ifndef BMVMIN__H__INCLUDED__
#define BMVMIN__H__INCLUDED__

namespace bm
{


#define BM_MINISET_GAPLEN (bm::gap_len_table<true>::_len[0])
#define BM_MINISET_ARRSIZE(x) ((x / 32) + ( (x % 32) && 1 ))

/*! @defgroup mset Small sets functionality
 *  Templates in this group are used to keep block types in BM library.
 *  Classes of this group can tune bvector template (MS parameter)
 *  for best performance or minimal memory usage.
 *  @{
 */


/*!
    @brief Template class implements memory saving set functionality
    
    Template can be used as template parameter for bvector if we 
    want to tune bvector for minimal memory consumption.

    @sa bvmini
*/
template <class A, size_t N> class miniset
{
public:

    miniset() 
        : m_buf(0),
          m_type(1)
    {}

    miniset(const miniset& mset)
    {
        if (mset.m_buf)
        {
            if (mset.m_type)
                init_gapbuf(mset.m_buf);
            else
                init_bitbuf(mset.m_buf);
        }
        else
        {
            m_type = mset.m_type;
            m_buf = 0;
        }
    }

    ~miniset()
    {
        if (m_buf)
        {
            A::deallocate(m_buf, m_type ? 
                (BM_MINISET_GAPLEN / (sizeof(bm::word_t) / sizeof(bm::gap_word_t)))
                : 
                (BM_MINISET_ARRSIZE(N)));
        }
    }

    /// Checks if bit pos 1 or 0. Returns 0 if 0 and non zero otherwise.
    unsigned test(bm::id_t n) const 
    { 
        return
            !m_buf ? 0 
            :
            m_type ? 
              gap_test((gap_word_t*)m_buf, n)
              : 
              m_buf[n>>bm::set_word_shift] & (1<<(n & bm::set_word_mask));
    }

    void set(bm::id_t n, bool val=true)
    {
        if (m_type == 0)
        {
            if (!m_buf)
            {
                if (!val) return;
                init_bitbuf(0);
            }

            unsigned nword  = n >> bm::set_word_shift; 
            unsigned mask = unsigned(1) << (n & bm::set_word_mask);

            val ? (m_buf[nword] |= mask) : (m_buf[nword] &= ~mask);
        }
        else
        {
            if (!m_buf)
            {
                if (!val) return;
                init_gapbuf(0);
            }
            
            unsigned is_set;
            unsigned new_block_len = 
                gap_set_value(val, (gap_word_t*)m_buf, n, &is_set);

            if (new_block_len > unsigned(BM_MINISET_GAPLEN-4))
            {
                convert_buf();
            }
        }
    }

    unsigned mem_used() const
    {
        return sizeof(*this) +
               m_buf ? 
                 (m_type ? (BM_MINISET_GAPLEN * sizeof(gap_word_t))
                        : (BM_MINISET_ARRSIZE(N) * sizeof(bm::word_t)))
                : 0; 
    }

    void swap(miniset& mset)
    {
        bm::word_t* buftmp = m_buf;
        m_buf = mset.m_buf;
        mset.m_buf = buftmp;
        unsigned typetmp = m_type;
        m_type = mset.m_type;
        mset.m_type = typetmp;
    }


private:

    void init_bitbuf(bm::word_t* buf)
    {
        unsigned arr_size = BM_MINISET_ARRSIZE(N);
        m_buf = A::allocate(arr_size, 0);
        if (buf)
        {
            ::memcpy(m_buf, buf, arr_size * sizeof(bm::word_t));
        }
        else
        {
            ::memset(m_buf, 0, arr_size * sizeof(bm::word_t));
        }
        m_type = 0;
    }

    void init_gapbuf(bm::word_t* buf)
    {
        unsigned arr_size = 
            BM_MINISET_GAPLEN / (sizeof(bm::word_t) / sizeof(bm::gap_word_t));
        m_buf = A::allocate(arr_size, 0);
        if (buf)
        {
            ::memcpy(m_buf, buf, arr_size * sizeof(bm::word_t));
        }
        else
        {
            *m_buf = 0;
            gap_set_all((gap_word_t*)m_buf, bm::gap_max_bits, 0);
        }
        m_type = 1;
    }

    void convert_buf()
    {
        unsigned arr_size = BM_MINISET_ARRSIZE(N);
        bm::word_t* buf = A::allocate(arr_size, 0);

        gap_convert_to_bitset(buf, (gap_word_t*) m_buf, arr_size);
        arr_size = 
            BM_MINISET_GAPLEN / (sizeof(bm::word_t) / sizeof(bm::gap_word_t));
        A::deallocate(m_buf, arr_size);
        m_buf = buf;
        m_type = 0;
    }

private:
    bm::word_t*   m_buf;      //!< Buffer pointer
    unsigned      m_type;     //!< buffer type (0-bit, 1-gap)
};


/*!
    @brief Mini bitvector used in bvector template to keep block type flags
    
    Template is used as a default template parameter MS for bvector  
    Offers maximum performance comparing to miniset.

    @sa miniset
*/
template<size_t N> class bvmini
{
public:

    bvmini(int start_strategy = 0) 
    {
        ::memset(m_buf, 0, sizeof(m_buf));
    }

    bvmini(const bvmini& mset)
    {
        ::memcpy(m_buf, mset.m_buf, sizeof(m_buf));
    }


    /// Checks if bit pos 1 or 0. Returns 0 if 0 and non zero otherwise.
    unsigned test(bm::id_t n) const 
    { 
        return m_buf[n>>bm::set_word_shift] & (1<<(n & bm::set_word_mask));
    }

    void set(bm::id_t n, bool val=true)
    {
        unsigned nword  = n >> bm::set_word_shift; 
        unsigned mask = unsigned(1) << (n & bm::set_word_mask);

        val ? (m_buf[nword] |= mask) : (m_buf[nword] &= ~mask);
    }

    unsigned mem_used() const
    {
        return sizeof(*this);
    }

    void swap(bvmini& mset)
    {
        for (unsigned i = 0; i < BM_MINISET_ARRSIZE(N); ++i)
        {
            bm::word_t tmp = m_buf[i];
            m_buf[i] = mset.m_buf[i];
            mset.m_buf[i] = tmp;
        }
    }

private:
    bm::word_t   m_buf[BM_MINISET_ARRSIZE(N)];
};


/*!@} */

/*!
    @brief Bitvector class with very limited functionality.

    Class implements simple bitset and used for internal 
    and testing purposes. 
*/
template<class A> class bvector_mini
{
public:
    bvector_mini(unsigned size) 
      : m_buf(0),
        m_size(size)
    {
        unsigned arr_size = (size / 32) + 1; 
        m_buf = A::allocate(arr_size, 0);
        ::memset(m_buf, 0, arr_size * sizeof(unsigned));
    }
    bvector_mini(const bvector_mini& bvect)
       : m_size(bvect.m_size)
    {
        unsigned arr_size = (m_size / 32) + 1;
        m_buf = A::allocate(arr_size, 0);
        ::memcpy(m_buf, bvect.m_buf, arr_size * sizeof(unsigned));        
    }

    ~bvector_mini()
    {
        A::deallocate(m_buf, (m_size / 32) + 1); 
    }

    /// Checks if bit pos 1 or 0. Returns 0 if 0 and non zero otherwise.
    int is_bit_true(unsigned pos) const
    {
        unsigned char  mask = (unsigned char)((char)0x1 << (pos & 7));
        unsigned char* offs = (unsigned char*)m_buf + (pos >> 3); // m_buf + (pos/8)

        return (*offs) & mask;
    }

    /// Sets bit number pos to 1
    void set_bit(unsigned pos)
    {
        unsigned char  mask = (unsigned char)(0x1 << (pos & 7));
        unsigned char* offs = (unsigned char*)m_buf + (pos >> 3); 
        *offs |= mask;
    }


    /// Sets bit number pos to 0
    void clear_bit(unsigned pos)
    {
        unsigned char  mask = (unsigned char)(0x1 << (pos & 7));
        unsigned char* offs = (unsigned char*)m_buf + (pos >> 3); 

        *offs &= ~mask;
    }

    /// Counts number of bits ON 
    unsigned bit_count() const
    {
        register unsigned count = 0;
        const unsigned* end = m_buf + (m_size / 32)+1;    

        for (unsigned* start = m_buf; start < end; ++start)
        {
            register unsigned value = *start;
            for (count += (value!=0); value &= value - 1; ++count);
        }
        return count;
    }

    /// Comparison.
    int compare(const bvector_mini& bvect)
    {
        unsigned cnt1 = bit_count();
        unsigned cnt2 = bvect.bit_count();

        if (!cnt1 && !cnt2) return 0;

        unsigned cnt_min = cnt1 < cnt2 ? cnt1 : cnt2;

        if (!cnt_min) return cnt1 ? 1 : -1;

        unsigned idx1 = get_first();
        unsigned idx2 = bvect.get_first();

        for (unsigned i = 0; i < cnt_min; ++i)
        {
            if (idx1 != idx2)
            {
                return idx1 < idx2 ? 1 : -1;
            }
            idx1 = get_next(idx1);
            idx2 = bvect.get_next(idx2);
        }

        BM_ASSERT(idx1==0 || idx2==0);

        if (idx1 != idx2)
        {
            if (!idx1) return -1;
            if (!idx2) return  1;
            return idx1 < idx2 ? 1 : -1;
        }

        return 0;
    }


    /// Returns index of the first ON bit
    unsigned get_first() const
    {
        unsigned pos = 0;
        const unsigned char* ptr = (unsigned char*) m_buf;

        for (unsigned i = 0; i < (m_size/8)+1; ++i)
        {
            register unsigned char w = ptr[i];


            if (w != 0)
            {
                while ((w & 1) == 0)
                {
                    w >>= 1;
                    ++pos;
                }
                return pos;
            }
            pos += sizeof(unsigned char) * 8;
        }
        return 0;
    }


    /// Returns index of next bit, which is ON
    unsigned get_next(unsigned idx) const
    {
        register unsigned i;

        for (i = idx+1; i < m_size; ++i)
        {
            unsigned char* offs = (unsigned char*)m_buf + (i >> 3); 
            if (*offs)
            {
                unsigned char mask = (unsigned char)((char)0x1 << (i & 7));

                if (*offs & mask)
                {
                    return i;
                }
            }
            else
            {
                i += 7;
            }
        }
        return 0;
    }


    void combine_and(const bvector_mini& bvect)
    {
        const unsigned* end = m_buf + (m_size / 32)+1;
    
        const unsigned* src = bvect.get_buf();

        for (unsigned* start = m_buf; start < end; ++start)
        {
            *start &= *src++;
        }
    }

    void combine_xor(const bvector_mini& bvect)
    {
        const unsigned* end = m_buf + (m_size / 32)+1;
    
        const unsigned* src = bvect.get_buf();

        for (unsigned* start = m_buf; start < end; ++start)
        {
            *start ^= *src++;
        }
    }


    void combine_or(const bvector_mini& bvect)
    {
        const unsigned* end = m_buf + (m_size / 32)+1;
    
        const unsigned* src = bvect.get_buf();

        for (unsigned* start = m_buf; start < end; ++start)
        {
            *start |= *src++;
        }
    }

    void combine_sub(const bvector_mini& bvect)
    {
        const unsigned* end = m_buf + (m_size / 32)+1;
    
        const unsigned* src = bvect.get_buf();

        for (unsigned* start = m_buf; start < end; ++start)
        {
            *start &= ~(*src++);
        }
    }

    const unsigned* get_buf() const { return m_buf; }
    unsigned mem_used() const
    {
        return sizeof(bvector_mini) + (m_size / 32) + 1;
    }

    void swap(bvector_mini& bvm)
    {
        BM_ASSERT(m_size == bvm.m_size);
        bm::word_t* buftmp = m_buf;
        m_buf = bvm.m_buf;
        bvm.m_buf = buftmp;
    }

private:
    bm::word_t*   m_buf;
    unsigned      m_size;
};



} // namespace bm

#endif