SeqAn3  3.0.3
The Modern C++ library for sequence analysis.
detail.hpp
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1 // -----------------------------------------------------------------------------------------------------
2 // Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
3 // Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
4 // This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
5 // shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
6 // -----------------------------------------------------------------------------------------------------
7 
13 #pragma once
14 
15 #include <seqan3/core/configuration/detail/configuration_utility.hpp>
16 
17 namespace seqan3::detail
18 {
19 
23 enum struct align_config_id : uint8_t
24 {
25  band,
26  debug,
27  gap,
28  global,
29  local,
30  min_score,
31  on_result,
32  output_alignment,
33  output_begin_position,
34  output_end_position,
35  output_sequence1_id,
36  output_sequence2_id,
37  output_score,
38  parallel,
39  result_type,
40  score_type,
41  scoring,
42  vectorised,
43  SIZE
44 };
45 
46 // ----------------------------------------------------------------------------
47 // compatibility_table
48 // ----------------------------------------------------------------------------
49 
55 template <>
56 inline constexpr std::array<std::array<bool, static_cast<uint8_t>(align_config_id::SIZE)>,
57  static_cast<uint8_t>(align_config_id::SIZE)> compatibility_table<align_config_id>
58 {
59  { //band
60  //| debug
61  //| | gap
62  //| | | global
63  //| | | | local
64  //| | | | | min_score
65  //| | | | | | on_result
66  //| | | | | | | output_alignment
67  //| | | | | | | | output_begin_position
68  //| | | | | | | | | output_end_position
69  //| | | | | | | | | | output_sequence1_id
70  //| | | | | | | | | | | output_sequence2_id
71  //| | | | | | | | | | | | output_score
72  //| | | | | | | | | | | | | parallel
73  //| | | | | | | | | | | | | | result_type
74  //| | | | | | | | | | | | | | | score_type
75  //| | | | | | | | | | | | | | | | scoring
76  //| | | | | | | | | | | | | | | | | vectorised
77  { 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, // 0: band
78  { 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, // 1: debug
79  { 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, // 2: gap
80  { 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, // 3: global
81  { 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, // 4: local
82  { 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, // 5: max_error
83  { 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, // 6: on_result
84  { 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, // 7: output_alignment
85  { 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1}, // 8: output_begin_position
86  { 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1}, // 9: output_end_position
87  { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1}, // 10: output_sequence1_id
88  { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1}, // 11: output_sequence2_id
89  { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1}, // 12: output_score
90  { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1}, // 13: parallel
91  { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1}, // 14: result_type
92  { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1}, // 15: score_type
93  { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1}, // 16: scoring
94  { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0} // 17: vectorised
95  }
96 };
97 
98 } // namespace seqan3::detail
configuration_utility.hpp
Provides various auxiliary functions with which parts of the configurations can be checked.
seqan3::detail::compatibility_table< align_config_id >
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 >
Declaration of algorithm specific compatibility table.
Definition: detail.hpp:58
seqan3::detail::align_config_id
align_config_id
An internal enum to check for a consistent configuration object.
Definition: detail.hpp:24
seqan3::detail::align_config_id::output_score
@ output_score
ID for the score output option.
seqan3::detail::align_config_id::output_sequence2_id
@ output_sequence2_id
ID for the sequence2 id output option.
seqan3::detail::align_config_id::output_alignment
@ output_alignment
ID for the alignment output option.
seqan3::detail::align_config_id::on_result
@ on_result
ID for the on_result option.
seqan3::detail::align_config_id::parallel
@ parallel
ID for the parallel option.
seqan3::detail::align_config_id::band
@ band
ID for the band option.
seqan3::detail::align_config_id::output_end_position
@ output_end_position
ID for the end position output option.
seqan3::detail::align_config_id::SIZE
@ SIZE
Represents the number of configuration elements.
seqan3::detail::align_config_id::output_sequence1_id
@ output_sequence1_id
ID for the sequence1 id output option.
seqan3::detail::align_config_id::result_type
@ result_type
ID for the result_type option.
seqan3::detail::align_config_id::global
@ global
ID for the global alignment option.
seqan3::detail::align_config_id::output_begin_position
@ output_begin_position
ID for the begin position output option.
seqan3::detail::align_config_id::debug
@ debug
ID for the debug option.
seqan3::detail::align_config_id::min_score
@ min_score
ID for the min_score option.
seqan3::detail::align_config_id::vectorised
@ vectorised
ID for the vectorised option.
seqan3::detail::align_config_id::gap
@ gap
ID for the gap_cost_affine option.
seqan3::detail::align_config_id::scoring
@ scoring
ID for the scoring_scheme option.
seqan3::detail::align_config_id::score_type
@ score_type
ID for the score_type option.
seqan3::detail::align_config_id::local
@ local
ID for the local alignment option.
seqan3::detail
The internal SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29