▼ seqan3 | |
▼ alignment | |
► aligned_sequence | |
aligned_sequence_concept.hpp | Includes the aligned_sequence_concept and the related insert_gap and erase_gap functions to enable stl container support |
all.hpp | Meta-header for the aligned sequence in the alignment module |
► configuration | |
align_config_band.hpp | Provides seqan3::detail::align_config_band |
align_config_band_static.hpp | Provides seqan3::band_static |
align_config_edit.hpp | Provides seqan3::align_cfg::edit |
align_config_gap.hpp | Provides gap configurations |
align_config_global.hpp | Provides global alignment configurations |
align_config_max_error.hpp | Provides seqan3::align_cfg::max_error configuration |
align_config_output.hpp | Provides configuration for alignment output |
align_config_score.hpp | Provides scoring configurations |
align_config_sequence_ends.hpp | Provides the free ends gap configuration |
all.hpp | Meta-header for the alignment configuration module |
utility.hpp | Provides functionality to access get function by enum values |
► matrix | |
alignment_coordinate.hpp | Provides seqan3::detail::alignment_coordinate |
alignment_matrix_formatter.hpp | Contains seqan3::detail::alignment_matrix_formatter and seqan3::detail::alignment_matrix_format |
alignment_score_matrix.hpp | Contains the declaration of seqan3::detail::alignment_score_matrix |
alignment_trace_algorithms.hpp | Contains algorithms that operate on seqan3::detail::alignment_trace_matrix |
alignment_trace_matrix.hpp | Contains the declaration of seqan3::detail::alignment_trace_matrix |
all.hpp | |
matrix_concept.hpp | Contains seqan3::detail::matrix_concept |
row_wise_matrix.hpp | Contains seqan3::detail::row_wise_matrix |
trace_directions.hpp | Contains the declaration of seqan3::detail::trace_directions |
► pairwise | |
► execution | |
alignment_executor_two_way.hpp | Provides seqan3::detail::alignment_executor_two_way |
alignment_range.hpp | Provides seqan3::detail::alignment_range |
all.hpp | Meta-header for the pairwise execution submodule |
execution_handler_sequential.hpp | Provides seqan3::detail::execution_handler_sequential |
align_pairwise.hpp | Provides pairwise alignment function |
align_result.hpp | Provides seqan3::align_result |
alignment_selector.hpp | Provides seqan3::detail::alignment_selector |
all.hpp | Meta-header for the pairwise submodule |
edit_distance_unbanded.hpp | Contains a pairwise alignment algorithm for edit distance but without band |
► scoring | |
all.hpp | Meta-header for the Scoring sub-module |
aminoacid_scoring_scheme.hpp | Provides seqan3::aminoacid_scoring_scheme |
gap_scheme.hpp | Provides seqan3::gap_scheme |
nucleotide_scoring_scheme.hpp | Provides seqan3::nucleotide_scoring_scheme |
scoring_scheme_base.hpp | Provides seqan3::scoring_scheme_base |
scoring_scheme_concept.hpp | Provides seqan3::scoring_scheme_concept |
all.hpp | Meta-header for the alignment module |
exception.hpp | Includes customized exception types for the alignment module |
▼ alphabet | |
► adaptation | |
all.hpp | Meta-header for the adaptation submodule; includes all headers from alphabet/adaptation/ |
char.hpp | Provides alphabet adaptations for standard char types |
concept.hpp | Provides seqan3::char_adaptation_concept and seqan3::uint_adaptation_concept |
pre.hpp | |
uint.hpp | Provides alphabet adaptations for standard uint types |
► aminoacid | |
aa20.hpp | Contains seqan3::aa20, container aliases and string literals |
aa27.hpp | Contains seqan3::aa27, container aliases and string literals |
all.hpp | Meta-header for the aminoacid submodule; includes all headers from alphabet/aminoacid/ |
aminoacid_base.hpp | Free function/metafunction wrappers for alphabets with member functions/types |
concept.hpp | Provides seqan3::aminoacid_concept |
translation.hpp | Contains functions for translating a triplet of nucleotides into an amino acid |
translation_details.hpp | Contains translation details for nucleotide to aminoacid translation |
translation_genetic_code.hpp | Genetic codes used for translating a triplet of nucleotides into an amino acid |
► composition | |
all.hpp | Meta-header for the composition submodule; includes all headers from alphabet/composition/ |
cartesian_composition.hpp | Provides seqan3::cartesian_composition |
detail.hpp | Provides implementation detail for seqan3::union_composition and seqan3::cartesian_composition |
union_composition.hpp | Contains seqan3::union_composition |
► detail | |
alphabet_base.hpp | Provides seqan3::alphabet_base |
alphabet_proxy.hpp | Free function/metafunction wrappers for alphabets with member functions/types |
convert.hpp | |
hash.hpp | Provides overloads for std::hash |
member_exposure.hpp | Free function/metafunction wrappers for alphabets with member functions/types |
► gap | |
all.hpp | Meta-header for the gap submodule; includes all headers from alphabet/gap/ |
gap.hpp | Contains seqan3::gap |
gapped.hpp | Contains seqan3::gapped |
► mask | |
all.hpp | Meta-header for the mask submodule; includes all headers from alphabet/mask/ |
mask.hpp | Create a mask composition which can be applied with another alphabet |
masked.hpp | Extends a given alphabet with the mask alphabet |
► nucleotide | |
all.hpp | Meta-header for the nucleotide submodule; includes all headers from alphabet/nucleotide/ |
concept.hpp | Provides seqan3::nucleotide_concept |
dna15.hpp | Contains seqan3::dna15, container aliases and string literals |
dna4.hpp | Contains seqan3::dna4, container aliases and string literals |
dna5.hpp | Contains seqan3::dna5, container aliases and string literals |
nucleotide_base.hpp | Provides seqan3::nucleotide_base |
rna15.hpp | Provides seqan3::rna15, container aliases and string literals |
rna4.hpp | Contains seqan3::rna4, container aliases and string literals |
rna5.hpp | Contains seqan3::rna5, container aliases and string literals |
► quality | |
aliases.hpp | Contains aliases for qualified |
all.hpp | Meta-header that includes all headers from alphabet/quality/ |
concept.hpp | Quality alphabet concept |
phred42.hpp | Contains seqan3::phred42 quality scores |
phred63.hpp | Contains seqan3::phred63 quality scores |
phred68legacy.hpp | Contains seqan3::phred68legacy quality scores |
qualified.hpp | Contains quality alphabet compositions |
quality_base.hpp | Contains seqan3::phred42 quality scores |
► structure | |
all.hpp | Meta-header for the structure module. It includes all headers from alphabet/structure/ |
dot_bracket3.hpp | Contains the dot bracket format for RNA structure |
dssp9.hpp | Contains the dssp format for protein structure |
rna_structure_concept.hpp | Provides seqan3::rna_structure_concept |
structured_aa.hpp | Contains the composition of aminoacid with structure alphabets |
structured_rna.hpp | Contains the composition of nucleotide with structure alphabets |
wuss.hpp | Contains the WUSS format for RNA structure |
all.hpp | Meta-header for the alphabet module |
concept.hpp | Core alphabet concept and free function/metafunction wrappers |
concept_pre.hpp | Seqan3::alphabet_concept metafunction base classes |
▼ argument_parser | |
► detail | |
format_base.hpp | Contains the format_base struct containing all helper functions that are needed in all formats |
format_help.hpp | Contains the format_help struct that print the help page to the command line and the two child formats (format_version, format_short_help) that print short help messages to the command line |
format_html.hpp | Contains the format_html struct and its helper functions |
format_man.hpp | Contains the format_man struct and its helper functions |
format_parse.hpp | Contains the format_parse class |
all.hpp | Meta-Header for the argument parser module |
argument_parser.hpp | Contains seqan3::argument_parser class |
auxiliary.hpp | Contains auxiliary information |
exceptions.hpp | Contains parser related exceptions |
validators.hpp | Contains some standard validators for (positional) options |
▼ contrib | |
► stream | |
bz2_istream.hpp | |
bz2_ostream.hpp | |
gz_istream.hpp | |
gz_ostream.hpp | |
▼ core | |
► algorithm | |
all.hpp | Meta-Header for components of the algorithm submodule |
concept.hpp | Provides concepts for the configuration classes |
configuration.hpp | Provides seqan3::detail::configuration and utility functions |
deferred_config_element_base.hpp | Provides seqan3::detail::deferred_config_element_base |
parameter_pack.hpp | |
► concept | |
all.hpp | Meta-include for custom concepts |
cereal.hpp | Adaptions of concepts from the Cereal library |
core_language.hpp | Provides concepts for core language types and relations that don't have concepts in C++20 (yet) |
tuple.hpp | Provides seqan3::tuple_like_concept |
► detail | |
all.hpp | Meta-header for implementation details in the core module |
int_types.hpp | Contains metaprogramming utilities for integer types |
reflection.hpp | Static reflection for arbitrary types |
strong_type.hpp | Contains basic data structure for strong types |
terminal.hpp | Checks if program is run interactively and retrieves dimensions of terminal (Transferred from seqan2) |
► metafunction | |
all.hpp | Provides various metafunctions |
basic.hpp | Provides various metafunctions on generic types |
deferred_crtp_base.hpp | Provides seqan3::detail::deferred_crtp_base |
function.hpp | Provides various metafunctions for use on functions |
iterator.hpp | Provides various metafunctions for use on iterators |
pack.hpp | Provides various metafunctions on a set of types, usually provided as template argument pack |
pre.hpp | Provides various metafunctions base templates and shortcuts |
range.hpp | Provides various metafunctions used by the range module |
template_inspection.hpp | Provides seqan3::type_list and auxiliary metafunctions |
transformation_trait_or.hpp | Provides seqan3::detail::transformation_trait_or |
► simd | |
► detail | |
builtin_simd.hpp | Provides seqan3::detail::builtin_simd, seqan3::detail::is_builtin_simd and seqan3::simd::simd_traits<builtin_simd_t> |
default_simd_backend.hpp | Contains seqan3::detail::default_simd_backend |
default_simd_length.hpp | Contains seqan3::detail::default_simd_length and seqan3::detail::default_simd_max_length |
all.hpp | Meta-header for the simd module |
concept.hpp | Contains seqan3::simd::simd_concept |
simd.hpp | Contains seqan3::simd::simd_type |
simd_algorithm.hpp | Contains algorithms to modify seqan3::simd::simd_type |
simd_debug_stream.hpp | Provides seqan3::debug_stream overload for seqan3::simd::simd_type |
simd_traits.hpp | Contains seqan3::simd::simd_traits |
add_enum_bitwise_operators.hpp | Provides seqan3::add_enum_bitwise_operators |
all.hpp | Meta-header for the core module |
bit_manipulation.hpp | Provides utility functions for bit twiddling |
platform.hpp | Contains platform and dependency checks |
pod_tuple.hpp | Contains seqan3::pod_tuple |
tuple_utility.hpp | Provides utility functions for tuple like interfaces |
type_list.hpp | Provides seqan3::type_list and auxiliary metafunctions |
▼ io | |
► alignment_file | |
all.hpp | Meta-include for the alignment IO submodule |
detail.hpp | Auxiliary functions for the alignment IO |
format_sam.hpp | Provides the seqan3::alignment_file_format_sam class |
header.hpp | Provides the seqan3::alignment_file_header class |
input_options.hpp | Provides seqan3::alignment_file_in_options |
output.hpp | Provides seqan3::alignment_file_output and corresponding traits classes |
output_format_concept.hpp | Provides seqan3::alignment_file_output_format_concept and auxiliary classes |
output_options.hpp | Provides seqan3::alignment_file_output_options |
sam_tag_dictionary.hpp | Provides the seqan3::sam_tag_dictionary class and auxiliaries |
► detail | |
ignore_output_iterator.hpp | Provides seqan3::detail::ignore_output_iterator for writing to null stream |
in_file_iterator.hpp | Provides the seqan3::detail::in_file_iterator class template |
misc.hpp | Provides various utility functions |
out_file_iterator.hpp | Provides the seqan3::detail::out_file_iterator class template |
record.hpp | |
► sequence_file | |
all.hpp | Meta-include for the sequence IO submodule |
format_fasta.hpp | Provides the seqan3::sequence_file_format_fasta class |
format_fastq.hpp | Provides the seqan3::sequence_file_format_fastq class |
input.hpp | Provides seqan3::sequence_file_input and corresponding traits classes |
input_format_concept.hpp | Provides seqan3::sequence_file_input_format_concept and auxiliary classes |
input_options.hpp | Provides seqan3::sequence_file_input_options |
output.hpp | Provides seqan3::sequence_file_output and corresponding traits classes |
output_format_concept.hpp | Provides seqan3::sequence_file_format_out_concept and auxiliary classes |
output_options.hpp | Provides seqan3::sequence_file_output_options |
► stream | |
all.hpp | Meta-header for all stream related functionality |
char_operations.hpp | Provides utilities for modifying characters |
concept.hpp | Stream concepts |
debug_stream.hpp | Provides seqan3::debug_stream and related types |
parse_condition.hpp | Provides parse conditions for tokenization |
parse_condition_detail.hpp | Provides parse conditions for tokenization |
► structure_file | |
all.hpp | Meta-include for the structure IO submodule |
detail.hpp | Helper functions (e.g. conversions) for the structure IO submodule |
format_vienna.hpp | Provides the seqan3::structure_file_format_vienna class |
input.hpp | Provides seqan3::structure_file_in and corresponding traits classes |
input_format_concept.hpp | Provides seqan3::structure_file_input_format_concept |
input_options.hpp | Provides seqan3::structure_file_input_options |
output.hpp | Provides seqan3::structure_file_out and corresponding traits classes |
output_format_concept.hpp | Provides seqan3::structure_file_output_format_concept and auxiliary classes |
output_options.hpp | Provides seqan3::structure_file_output_options |
all.hpp | Meta-header for all IO related functionality |
exception.hpp | Provides exceptions used in the I/O module |
filesystem.hpp | This header includes C++17 filesystem support and imports it into namespace seqan3::filesystem (independent of whether it is marked as "experimental") |
record.hpp | Provides the seqan3::record template and the seqan3::field enum |
▼ range | |
► container | |
aligned_allocator.hpp | Contains seqan3::aligned_allocator |
all.hpp | Meta-header for the container submodule |
bitcompressed_vector.hpp | Provides seqan3::bitcompressed_vector |
concatenated_sequences.hpp | Provides seqan3::concatenated_sequences |
concept.hpp | Adaptations of concepts from the standard library |
constexpr_string.hpp | A constexpr string implementation to manipulate string literals at compile time |
► decorator | |
all.hpp | Meta-header for the decorator submodule |
► detail | |
inherited_iterator_base.hpp | Provides the seqan3::detail::inherited_iterator_base template |
misc.hpp | Provides various utility functions |
random_access_iterator.hpp | Provides the seqan3::detail::random_access_iterator class |
► view | |
all.hpp | Meta-header for the view submodule |
char_to.hpp | Provides seqan3::view::char_to |
complement.hpp | Provides seqan3::view::complement |
convert.hpp | Provides seqan3::view::convert |
deep.hpp | Provides seqan3::view::deep |
detail.hpp | Auxiliary header for the view submodule |
get.hpp | Provides seqan3::view::get |
kmer_hash.hpp | Provides seqan3::view::kmer_hash |
persist.hpp | Provides seqan3::view::persist |
rank_to.hpp | Provides seqan3::view::rank_to |
single_pass_input.hpp | Provides seqan3::single_pass_input_view |
take.hpp | Provides seqan3::view::take |
take_exactly.hpp | Provides seqan3::view::take_exactly and seqan3::view::take_exactly_or_throw |
take_line.hpp | Provides seqan3::view::take_line and seqan3::view::take_line_or_throw |
take_until.hpp | Provides seqan3::view::take_until and seqan3::view::take_until_or_throw |
to_char.hpp | Provides seqan3::view::to_char |
to_rank.hpp | Provides seqan3::view::to_rank |
translation.hpp | Provides seqan3::view::translate and seqan3::view::translate_single |
trim.hpp | Provides seqan3::view::trim |
all.hpp | Meta-header for the range module |
concept.hpp | Additional non-standard concepts for ranges |
shortcuts.hpp | Contains various shortcuts for common std::ranges functions |
▼ search | |
► algorithm | |
► configuration | |
all.hpp | Meta-header for the search configuration module |
max_error.hpp | Provides the configuration for maximum number of errors for all error types |
max_error_common.hpp | Provides the error types for maximum number of errors |
max_error_rate.hpp | Provides the configuration for maximum number of errors in percent of the query length across all error types |
mode.hpp | Provides the mode configuration to define the search modes "all", "all_best", "best" and "strata" |
output.hpp | Provides the configuration for returning positions in the text |
utility.hpp | Provides functionality to access get function by enum values |
► detail | |
search.hpp | Provides the public interface for search algorithms |
search_common.hpp | Provides data structures used by different search algorithms |
search_scheme_algorithm.hpp | Provides the algorithm to search in an index using search schemes |
search_scheme_precomputed.hpp | Provides the data structures and precomputed instances for (optimum) search schemes |
search_trivial.hpp | Provides an approximate string matching algorithm based on simple backtracking. This should only be used as a reference for unit testing |
all.hpp | Meta-header for the Search Algorithm module |
search.hpp | Provides the public interface for search algorithms |
► fm_index | |
► detail | |
csa_alphabet_strategy.hpp | Provides an alphabet mapping that implements an identity map (i.e. each character is mapped to its rank) |
fm_index_iterator.hpp | Provides the internal representation of a node of the seqan3::fm_index_iterator |
all.hpp | Meta-header for the FM index module |
bi_fm_index.hpp | Provides the bidirectional seqan3::bi_fm_index |
bi_fm_index_iterator.hpp | Provides the seqan3::bi_fm_index_iterator for searching in the bidirectional seqan3::bi_fm_index |
concept.hpp | Provides the concepts for seqan3::fm_index and seqan3::bi_fm_index and its traits and iterators |
fm_index.hpp | Provides the unidirectional seqan3::fm_index |
fm_index_iterator.hpp | Provides the seqan3::fm_index_iterator for searching in the unidirectional seqan3::fm_index |
all.hpp | Meta-header for the search module |
▼ std | |
► view | |
all.hpp | Meta-include for standard library views |
common.hpp | Provides seqan3::view::common |
filter.hpp | Provides seqan3::view::filter |
reverse.hpp | Provides seqan3::view::reverse |
subrange.hpp | Provides seqan3::view::subrange |
transform.hpp | Provides seqan3::view::transform |
view_all.hpp | Provides seqan3::view::all |
charconv | Provides std::from_chars and std::to_chars if not defined in the stl <charconv> header |
charconv_detail.hpp | Provides LLVM's implementation of std::from_chars and std::to_chars for integral types and a custom solution for floating points types |
concepts | The Concepts library |
iterator | Provides C++20 additions to the <iterator> header |
ranges | Adaptations of concepts from the Ranges TS |
type_traits | Provides C++20 additions to the type_traits header |
version.hpp | Contains SeqAn version macros and global variables |