Namespace fwdpp::ts

Tree sequence Kelleher2018-fu support.

Namespaces

• Namespace fwdpp::ts::detail

• Namespace fwdpp::ts::io

• Namespace fwdpp::ts::simplification

Classes

• Struct all_mutations

• Struct birth_data

• Struct convert_sample_index_to_nodes_t

• Struct edge

• Struct mut_rec_intermediates

• Struct mutation_record

• Struct new_variant_record

• Struct node

• Struct node_traversal_order

• Struct nodes_preorder

• Struct parent_location

• Struct sample_group_map

• Struct selected_variants_only

• Struct site

• Template Struct table_collection

• Struct update_samples_list_t

• Class child_iterator

• Class marginal_tree

• Class node_iterator

• Class node_traversal_preorder

• Class root_iterator

• Class samples_error

• Class samples_iterator

• Template Class site_visitor

• Template Class table_simplifier

• Class tables_error

• Template Class tree_visitor

Enums

• Enum simplification_flags

Functions

• Template Function fwdpp::ts::copy_births_since_last_simplification

• Template Function fwdpp::ts::count_mutations(const TableCollectionType&, const MutationContainerType&, SAMPLES&&, std::vector<std::uint32_t>&)

• Template Function fwdpp::ts::count_mutations(const TableCollectionType&, const MutationContainerType&, SAMPLES&&, std::vector<std::uint32_t>&, std::vector<std::uint32_t>&)

• Template Function fwdpp::ts::decapitate

• Template Function fwdpp::ts::edge_table_minimally_sorted

• Template Function fwdpp::ts::edge_table_strictly_sorted

• Template Function fwdpp::ts::end

• Template Function fwdpp::ts::find_pre_existing_edges

• Template Function fwdpp::ts::flag_mutations_for_recycling

• Template Function fwdpp::ts::generate_data_matrix(const TableCollectionType&, Samples&&, const bool, const bool, const bool, const double, const double)

• Template Function fwdpp::ts::generate_data_matrix(const TableCollectionType&, Samples&&, const bool, const bool, const bool)

• Template Function fwdpp::ts::generate_offspring

• Function fwdpp::ts::get_children

• Template Function fwdpp::ts::get_edge_sort_cmp

• Template Function fwdpp::ts::get_minimal_edge_sort_cmp

• Template Function fwdpp::ts::get_nodes(const marginal_tree&, ORDER)

• Template Function fwdpp::ts::get_nodes(const marginal_tree&, table_index_t, ORDER)

• Function fwdpp::ts::get_parent_ids

• Function fwdpp::ts::get_roots

• Function fwdpp::ts::get_samples

• Template Function fwdpp::ts::handle_pre_existing_edges

• Function fwdpp::ts::make_mut_queue(const std::vector<std::uint32_t>&, const std::vector<std::uint32_t>&)

• Function fwdpp::ts::make_mut_queue(const std::vector<std::size_t>&, const std::size_t)

• Template Function fwdpp::ts::make_simplifier_state

• Template Function fwdpp::ts::make_table_simplifier

• Template Function fwdpp::ts::mark_multiple_roots

• Template Function fwdpp::ts::mutate_tables

• Function fwdpp::ts::node_traversal_dispatch

• Function fwdpp::ts::num_children

• Function fwdpp::ts::num_nodes

• Function fwdpp::ts::num_roots

• Function fwdpp::ts::num_samples

• Function fwdpp::ts::operator<

• Function fwdpp::ts::operator==(const mutation_record&, const mutation_record&)

• Function fwdpp::ts::operator==(const node&, const node&)

• Function fwdpp::ts::operator==(const site&, const site&)

• Function fwdpp::ts::operator==(const edge&, const edge&)

• Template Function fwdpp::ts::process_children

• Template Function fwdpp::ts::process_nodes(const marginal_tree&, ORDER, const F&)

• Template Function fwdpp::ts::process_nodes(const marginal_tree&, table_index_t, ORDER, const F&)

• Template Function fwdpp::ts::process_roots

• Template Function fwdpp::ts::process_samples

• Template Function fwdpp::ts::rebuild_site_table

• Template Function fwdpp::ts::record_diploid_offspring(const std::vector<double>&, const std::tuple<table_index_t, table_index_t>&, const std::int32_t, const double, TableCollectionType&)

• Template Function fwdpp::ts::record_diploid_offspring(const std::vector<double>&, const std::tuple<table_index_t, table_index_t>&, const std::int32_t, const double, TableCollectionType&, edge_buffer&)

• Template Function fwdpp::ts::record_mutations_infinite_sites

• Template Function fwdpp::ts::record_site_during_rebuild

• Template Function fwdpp::ts::remove_fixations_from_haploid_genomes

• Template Function fwdpp::ts::simplify_tables(const NodeVector&, const simplification_flags, simplification::simplifier_internal_state<TableCollectionType>&, TableCollectionType&, NodeVector&, PreservedVariantIndexes&)

• Template Function fwdpp::ts::simplify_tables(const NodeVector&, TableCollectionType&, simplification_flags, NodeVector&, PreservedVariantIndexes&)

• Template Function fwdpp::ts::simplify_tables(const NodeVector&, const simplification_flags, TableCollectionType&)

• Template Function fwdpp::ts::simplify_tables(const NodeVector&, const NodeVector&, simplification_flags, simplification::simplifier_internal_state<TableCollectionType>&, TableCollectionType&, edge_buffer&, NodeVector&, PreservedVariantIndexes&)

• Template Function fwdpp::ts::sort_edge_table(std::ptrdiff_t, TableCollectionType&)

• Template Function fwdpp::ts::sort_edge_table(TableCollectionType&)

• Template Function fwdpp::ts::sort_mutation_table

• Template Function fwdpp::ts::sort_mutation_table_and_rebuild_site_table

• Template Function fwdpp::ts::sort_tables

• Template Function fwdpp::ts::sort_tables_for_simplification

• Template Function fwdpp::ts::split_breakpoints

• Template Function fwdpp::ts::split_breakpoints_add_edges

• Template Function fwdpp::ts::stitch_together_edges

• Function fwdpp::ts::total_time

• Template Function fwdpp::ts::visit_sites

Typedefs

• Typedef fwdpp::ts::convert_sample_index_to_nodes

• Typedef fwdpp::ts::edge_buffer

• Typedef fwdpp::ts::std_table_collection

• Typedef fwdpp::ts::table_index_t

• Typedef fwdpp::ts::update_samples_list

Variables

• Variable fwdpp::ts::default_ancestral_state

• Variable fwdpp::ts::default_derived_state

• Variable fwdpp::ts::NULL_INDEX