alignment/configuration/detail.hpp

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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause

 
#pragma once
 
#include <seqan3/core/configuration/detail/concept.hpp>
 
namespace seqan3::detail
{

enum struct align_config_id : uint8_t
{
    band,                  
    debug,                 
    gap,                   
    global,                
    local,                 
    min_score,             
    on_result,             
    output_alignment,      
    output_begin_position, 
    output_end_position,   
    output_sequence1_id,   
    output_sequence2_id,   
    output_score,          
    parallel,              
    result_type,           
    score_type,            
    scoring,               
    vectorised,            
    SIZE                   
};
 
// ----------------------------------------------------------------------------
// compatibility_table
// ----------------------------------------------------------------------------

template <>
inline constexpr std::array<std::array<bool, static_cast<uint8_t>(align_config_id::SIZE)>,
                            static_cast<uint8_t>(align_config_id::SIZE)>
    compatibility_table<align_config_id>{{
        //band
        //|  debug
        //|  |  gap
        //|  |  |  global
        //|  |  |  |  local
        //|  |  |  |  |  min_score
        //|  |  |  |  |  |  on_result
        //|  |  |  |  |  |  |  output_alignment
        //|  |  |  |  |  |  |  |  output_begin_position
        //|  |  |  |  |  |  |  |  |  output_end_position
        //|  |  |  |  |  |  |  |  |  |  output_sequence1_id
        //|  |  |  |  |  |  |  |  |  |  |  output_sequence2_id
        //|  |  |  |  |  |  |  |  |  |  |  |  output_score
        //|  |  |  |  |  |  |  |  |  |  |  |  |  parallel
        //|  |  |  |  |  |  |  |  |  |  |  |  |  |  result_type
        //|  |  |  |  |  |  |  |  |  |  |  |  |  |  | score_type
        //|  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  scoring
        //|  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  vectorised
        {0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, //  0: band
        {1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, //  1: debug
        {1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, //  2: gap
        {1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, //  3: global
        {1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, //  4: local
        {1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, //  5: max_error
        {1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, //  6: on_result
        {1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, //  7: output_alignment
        {1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1}, //  8: output_begin_position
        {1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1}, // 9: output_end_position
        {1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1}, // 10: output_sequence1_id
        {1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1}, // 11: output_sequence2_id
        {1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1}, // 12: output_score
        {1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1}, // 13: parallel
        {1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1}, // 14: result_type
        {1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1}, // 15: score_type
        {1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1}, // 16: scoring
        {1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0}  // 17: vectorised
    }};
 
} // namespace seqan3::detail