alignment_base.h

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/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *    * Redistributions of source code must retain the above copyright
 *      notice, this list of conditions and the following disclaimer.
 *    * Redistributions in binary form must reproduce the above copyright
 *      notice, this list of conditions and the following disclaimer in the
 *      documentation and/or other materials provided with the distribution.
 *    * Neither the name of the NVIDIA CORPORATION nor the
 *      names of its contributors may be used to endorse or promote products
 *      derived from this software without specific prior written permission.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#pragma once

#include <nvbio/basic/types.h>

namespace nvbio {

namespace aln {



enum AlignmentType { GLOBAL, LOCAL, SEMI_GLOBAL };



struct PatternBlockingTag {};  

struct TextBlockingTag {};     

template <uint32 ALPHABET_SIZE_T> struct MyersTag { static const uint32 ALPHABET_SIZE = ALPHABET_SIZE_T; }; 

template <typename T> struct transpose_tag {};
template <>           struct transpose_tag<PatternBlockingTag> { typedef TextBlockingTag type; };
template <>           struct transpose_tag<TextBlockingTag>    { typedef PatternBlockingTag type; };

template <typename T> struct transpose_aligner {};



struct SmithWatermanTag {}; 
struct GotohTag {};         
struct EditDistanceTag {};  
struct HammingDistanceTag {};  

template <typename aligner_type>
struct aligner_tag {
    typedef typename aligner_type::aligner_tag type; 
};


template <typename ScoreType>
struct Alignment
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    Alignment() {}

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    Alignment(const ScoreType _score, const uint2 _source, const uint2 _sink) : score( _score ), source( _source ), sink(_sink) {}

    ScoreType score;    
    uint2     source;   
    uint2     sink;     
};

enum DirectionVector {
    SUBSTITUTION   = 0u,
    INSERTION      = 1u,
    DELETION       = 2u,
    SINK           = 3u,
    INSERTION_EXT  = 4u,
    DELETION_EXT   = 8u,
    // MASKS
    HMASK          = 3u,
    EMASK          = 4u,
    FMASK          = 8u,
};

enum State
{
    HSTATE = 0,
    ESTATE = 1,
    FSTATE = 2
};


template <AlignmentType T_TYPE, typename AlgorithmType = PatternBlockingTag>
struct EditDistanceAligner
{
    static const AlignmentType TYPE =   T_TYPE;         

    typedef EditDistanceTag             aligner_tag;    
    typedef AlgorithmType               algorithm_tag;  
};

template <AlignmentType T_TYPE, typename AlgorithmTag>
struct transpose_aligner< EditDistanceAligner<T_TYPE,AlgorithmTag> >
{
    typedef EditDistanceAligner<T_TYPE, typename transpose_tag<AlgorithmTag>::type> type;
};

template <AlignmentType TYPE>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
EditDistanceAligner<TYPE> make_edit_distance_aligner()
{
    return EditDistanceAligner<TYPE>();
}

template <AlignmentType TYPE, typename algorithm_tag>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
EditDistanceAligner<TYPE,algorithm_tag> make_edit_distance_aligner()
{
    return EditDistanceAligner<TYPE,algorithm_tag>();
}

template <AlignmentType TYPE>
EditDistanceAligner<TYPE,TextBlockingTag> transpose(const EditDistanceAligner<TYPE,PatternBlockingTag>& aligner)
{
    return EditDistanceAligner<TYPE,TextBlockingTag>();
}
template <AlignmentType TYPE, typename scoring_scheme_type>
EditDistanceAligner<TYPE,PatternBlockingTag> transpose(const EditDistanceAligner<TYPE,TextBlockingTag>& aligner)
{
    return EditDistanceAligner<TYPE,PatternBlockingTag>();
}

template <AlignmentType T_TYPE, typename scoring_scheme_type, typename AlgorithmType = PatternBlockingTag>
struct GotohAligner
{
    static const AlignmentType TYPE =   T_TYPE;         

    typedef GotohTag                    aligner_tag;    
    typedef AlgorithmType               algorithm_tag;  
 
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    GotohAligner(const scoring_scheme_type _scheme) : scheme(_scheme) {}

    scoring_scheme_type scheme;
};

template <AlignmentType T_TYPE, typename scoring_scheme_type, typename AlgorithmTag>
struct transpose_aligner< GotohAligner<T_TYPE, scoring_scheme_type, AlgorithmTag> >
{
    typedef GotohAligner<T_TYPE, scoring_scheme_type, typename transpose_tag<AlgorithmTag>::type> type;
};

template <AlignmentType TYPE, typename scoring_scheme_type>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
GotohAligner<TYPE,scoring_scheme_type> make_gotoh_aligner(const scoring_scheme_type& scheme)
{
    return GotohAligner<TYPE,scoring_scheme_type>( scheme );
}

template <AlignmentType TYPE, typename algorithm_tag, typename scoring_scheme_type>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
GotohAligner<TYPE,scoring_scheme_type,algorithm_tag> make_gotoh_aligner(const scoring_scheme_type& scheme)
{
    return GotohAligner<TYPE,scoring_scheme_type,algorithm_tag>( scheme );
}

template <AlignmentType TYPE, typename scoring_scheme_type>
GotohAligner<TYPE,scoring_scheme_type,TextBlockingTag> transpose(const GotohAligner<TYPE,scoring_scheme_type,PatternBlockingTag>& aligner)
{
    return GotohAligner<TYPE,scoring_scheme_type,TextBlockingTag>( aligner.scheme );
}
template <AlignmentType TYPE, typename scoring_scheme_type>
GotohAligner<TYPE,scoring_scheme_type,PatternBlockingTag> transpose(const GotohAligner<TYPE,scoring_scheme_type,TextBlockingTag>& aligner)
{
    return GotohAligner<TYPE,scoring_scheme_type,PatternBlockingTag>( aligner.scheme );
}

template <AlignmentType T_TYPE, typename scoring_scheme_type, typename AlgorithmType = PatternBlockingTag>
struct SmithWatermanAligner
{
    static const AlignmentType TYPE =   T_TYPE;         

    typedef SmithWatermanTag            aligner_tag;    
    typedef AlgorithmType               algorithm_tag;  

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    SmithWatermanAligner(const scoring_scheme_type _scheme) : scheme(_scheme) {}

    scoring_scheme_type scheme;
};

template <AlignmentType T_TYPE, typename scoring_scheme_type, typename AlgorithmTag>
struct transpose_aligner< SmithWatermanAligner<T_TYPE, scoring_scheme_type, AlgorithmTag> >
{
    typedef SmithWatermanAligner<T_TYPE, scoring_scheme_type, typename transpose_tag<AlgorithmTag>::type> type;
};

template <AlignmentType TYPE, typename scoring_scheme_type>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
SmithWatermanAligner<TYPE,scoring_scheme_type> make_smith_waterman_aligner(const scoring_scheme_type& scheme)
{
    return SmithWatermanAligner<TYPE,scoring_scheme_type>( scheme );
}

template <AlignmentType TYPE, typename scoring_scheme_type>
SmithWatermanAligner<TYPE,scoring_scheme_type,TextBlockingTag> transpose(const SmithWatermanAligner<TYPE,scoring_scheme_type,PatternBlockingTag>& aligner)
{
    return SmithWatermanAligner<TYPE,scoring_scheme_type,TextBlockingTag>( aligner.scheme );
}
template <AlignmentType TYPE, typename scoring_scheme_type>
SmithWatermanAligner<TYPE,scoring_scheme_type,PatternBlockingTag> transpose(const SmithWatermanAligner<TYPE,scoring_scheme_type,TextBlockingTag>& aligner)
{
    return SmithWatermanAligner<TYPE,scoring_scheme_type,PatternBlockingTag>( aligner.scheme );
}

template <AlignmentType T_TYPE, typename scoring_scheme_type, typename AlgorithmType = PatternBlockingTag>
struct HammingDistanceAligner
{
    static const AlignmentType TYPE =   T_TYPE;         

    typedef HammingDistanceTag            aligner_tag;  
    typedef AlgorithmType               algorithm_tag;  

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    HammingDistanceAligner(const scoring_scheme_type _scheme) : scheme(_scheme) {}

    scoring_scheme_type scheme;
};

template <AlignmentType T_TYPE, typename scoring_scheme_type, typename AlgorithmTag>
struct transpose_aligner< HammingDistanceAligner<T_TYPE,scoring_scheme_type,AlgorithmTag> >
{
    typedef HammingDistanceAligner<T_TYPE,scoring_scheme_type,typename transpose_tag<AlgorithmTag>::type> type;
};

template <AlignmentType TYPE, typename scoring_scheme_type>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
HammingDistanceAligner<TYPE,scoring_scheme_type> make_hamming_distance_aligner(const scoring_scheme_type& scheme)
{
    return HammingDistanceAligner<TYPE,scoring_scheme_type>( scheme );
}

template <AlignmentType TYPE, typename scoring_scheme_type, typename algorithm_tag>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
HammingDistanceAligner<TYPE,scoring_scheme_type,algorithm_tag> make_hamming_distance_aligner(const scoring_scheme_type& scheme)
{
    return HammingDistanceAligner<TYPE,scoring_scheme_type,algorithm_tag>( scheme );
}

template <AlignmentType TYPE, typename scoring_scheme_type>
HammingDistanceAligner<TYPE,scoring_scheme_type,TextBlockingTag> transpose(const HammingDistanceAligner<TYPE,scoring_scheme_type,PatternBlockingTag>& aligner)
{
    return HammingDistanceAligner<TYPE,scoring_scheme_type,TextBlockingTag>( aligner.scheme );
}
template <AlignmentType TYPE, typename scoring_scheme_type>
HammingDistanceAligner<TYPE,scoring_scheme_type,PatternBlockingTag> transpose(const HammingDistanceAligner<TYPE,scoring_scheme_type,TextBlockingTag>& aligner)
{
    return HammingDistanceAligner<TYPE,scoring_scheme_type,PatternBlockingTag>( aligner.scheme );
}



} // namespace aln
} // namespace nvbio

#include <nvbio/alignment/utils.h>