vg
tools for working with variation graphs
bdsg::ODGI Member List

This is the complete list of members for bdsg::ODGI, including all inherited members.

_deleted_node_countbdsg::ODGIprivate
_edge_countbdsg::ODGIprivate
_id_incrementbdsg::ODGIprivate
_max_node_rankbdsg::ODGIprivate
_min_node_rankbdsg::ODGIprivate
_node_countbdsg::ODGIprivate
_path_countbdsg::ODGIprivate
_path_rank_nextbdsg::ODGIprivate
add_to_number(const handle_t &handle, int64_t offset) constbdsg::ODGIprivate
append_step(const path_handle_t &path, const handle_t &to_append)bdsg::ODGIvirtual
apply_ordering(const std::vector< handle_t > &order, bool compact_ids=false)bdsg::ODGIvirtual
apply_orientation(const handle_t &handle)bdsg::ODGIvirtual
apply_path_ordering(const std::vector< path_handle_t > &order)bdsg::ODGI
canonicalize_edge(handle_t &left, handle_t &right) constbdsg::ODGIinlineprivate
clear(void)bdsg::ODGIvirtual
clear_paths(void)bdsg::ODGI
combine_handles(const std::vector< handle_t > &handles)bdsg::ODGI
create_edge(const handle_t &left, const handle_t &right)bdsg::ODGIvirtual
create_edge(const edge_t &edge)bdsg::ODGIinline
create_handle(const std::string &sequence)bdsg::ODGIvirtual
create_handle(const std::string &sequence, const nid_t &id)bdsg::ODGIvirtual
create_hidden_handle(const std::string &sequence)bdsg::ODGI
create_path_handle(const std::string &name, bool is_circular=false)bdsg::ODGIvirtual
create_step(const path_handle_t &path, const handle_t &handle)bdsg::ODGIprivate
decrement_rank(const step_handle_t &step_handle)bdsg::ODGIprivate
deleted_node_bvbdsg::ODGIprivate
deserialize(std::istream &in)handlegraph::SerializableHandleGraphinline
deserialize(const std::string &filename)handlegraph::SerializableHandleGraphinline
deserialize_members(std::istream &in)bdsg::ODGIprivatevirtual
destroy_edge(const handle_t &left, const handle_t &right)bdsg::ODGIvirtual
destroy_edge(const edge_t &edge)bdsg::ODGIinline
destroy_handle(const handle_t &handle)bdsg::ODGIvirtual
destroy_path(const path_handle_t &path)bdsg::ODGIvirtual
destroy_path_handle_records(uint64_t i)bdsg::ODGIprivate
destroy_step(const step_handle_t &step_handle, bool clean_up_empty_path=true)bdsg::ODGIprivate
display(void) constbdsg::ODGI
divide_handle(const handle_t &handle, const std::vector< size_t > &offsets)bdsg::ODGIvirtual
divide_handle(const handle_t &handle, size_t offset)bdsg::ODGIinline
edge_delta_to_id(uint64_t left, uint64_t delta) constbdsg::ODGIprivate
edge_handle(const handle_t &left, const handle_t &right) constbdsg::ODGI
edge_to_delta(const handle_t &left, const handle_t &right) constbdsg::ODGIprivate
find_metadata(const path_handle_t &path)bdsg::ODGIprivate
find_metadata(const path_handle_t &path) constbdsg::ODGIprivate
flip(const handle_t &handle) constbdsg::ODGIvirtual
follow_edges(const handle_t &handle, bool go_left, const Iteratee &iteratee) consthandlegraph::HandleGraph
follow_edges_impl(const handle_t &handle, bool go_left, const std::function< bool(const handle_t &)> &iteratee) constbdsg::ODGIprotectedvirtual
for_each_edge(const Iteratee &iteratee, bool parallel=false) consthandlegraph::HandleGraph
for_each_handle(const Iteratee &iteratee, bool parallel=false) consthandlegraph::HandleGraph
for_each_handle_impl(const std::function< bool(const handle_t &)> &iteratee, bool parallel=false) constbdsg::ODGIprotectedvirtual
for_each_path_handle(const Iteratee &iteratee) consthandlegraph::PathHandleGraph
for_each_path_handle_impl(const std::function< bool(const path_handle_t &)> &iteratee) constbdsg::ODGIprotectedvirtual
for_each_step_in_path(const path_handle_t &path, const std::function< void(const step_handle_t &)> &iteratee) constbdsg::ODGI
handlegraph::MutablePathDeletableHandleGraph::for_each_step_in_path(const path_handle_t &path, const Iteratee &iteratee) consthandlegraph::PathHandleGraph
for_each_step_on_handle(const handle_t &handle, const Iteratee &iteratee) consthandlegraph::PathHandleGraph
for_each_step_on_handle_impl(const handle_t &handle, const std::function< bool(const step_handle_t &)> &iteratee) constbdsg::ODGIprotectedvirtual
forward(const handle_t &handle) constbdsg::ODGI
get_base(const handle_t &handle, size_t index) consthandlegraph::HandleGraphvirtual
get_degree(const handle_t &handle, bool go_left) constbdsg::ODGIvirtual
get_edge_count() consthandlegraph::HandleGraphvirtual
get_handle(const nid_t &node_id, bool is_reverse=false) constbdsg::ODGIvirtual
get_handle_of_step(const step_handle_t &step_handle) constbdsg::ODGIvirtual
get_id(const handle_t &handle) constbdsg::ODGIvirtual
get_is_circular(const path_handle_t &path_handle) constbdsg::ODGIvirtual
get_is_reverse(const handle_t &handle) constbdsg::ODGIvirtual
get_length(const handle_t &handle) constbdsg::ODGIvirtual
get_magic_number() constbdsg::ODGIvirtual
get_next_step(const step_handle_t &step_handle) constbdsg::ODGIvirtual
get_node_count(void) constbdsg::ODGIvirtual
get_path_count(void) constbdsg::ODGIvirtual
get_path_handle(const std::string &path_name) constbdsg::ODGIvirtual
get_path_handle_of_step(const step_handle_t &step_handle) constbdsg::ODGIvirtual
get_path_name(const path_handle_t &path_handle) constbdsg::ODGIvirtual
get_previous_step(const step_handle_t &step_handle) constbdsg::ODGIvirtual
get_sequence(const handle_t &handle) constbdsg::ODGIvirtual
get_step_count(const path_handle_t &path_handle) constbdsg::ODGIvirtual
get_step_count(const handle_t &handle) constbdsg::ODGI
get_subsequence(const handle_t &handle, size_t index, size_t size) consthandlegraph::HandleGraphvirtual
get_total_length() consthandlegraph::HandleGraphvirtual
graph_id_hidden_setbdsg::ODGIprivate
has_edge(const handle_t &left, const handle_t &right) constbdsg::ODGIvirtual
handlegraph::MutablePathDeletableHandleGraph::has_edge(const edge_t &edge) consthandlegraph::HandleGraphinline
has_linear_next_step(const step_handle_t &step_handle) constbdsg::ODGIprotected
has_linear_previous_step(const step_handle_t &step_handle) constbdsg::ODGIprotected
has_next_step(const step_handle_t &step_handle) constbdsg::ODGIvirtual
has_node(nid_t node_id) constbdsg::ODGIvirtual
has_path(const std::string &path_name) constbdsg::ODGIvirtual
has_previous_step(const step_handle_t &step_handle) constbdsg::ODGIvirtual
id_to_rank(const nid_t &node_id) constbdsg::ODGIprivate
increment_node_ids(nid_t increment)bdsg::ODGIvirtual
insert_step(const step_handle_t &before, const step_handle_t &after, const handle_t &to_insert)bdsg::ODGI
is_empty(const path_handle_t &path_handle) constbdsg::ODGIvirtual
is_path_end(const step_handle_t &step_handle) constbdsg::ODGI
is_path_front_end(const step_handle_t &step_handle) constbdsg::ODGI
link_steps(const step_handle_t &from, const step_handle_t &to)bdsg::ODGIprivate
load(std::istream &in)bdsg::ODGI
max_node_id(void) constbdsg::ODGIvirtual
min_node_id(void) constbdsg::ODGIvirtual
node_vbdsg::ODGIprivate
ODGI(void)bdsg::ODGIinline
optimize(bool allow_id_reassignment=true)bdsg::ODGIvirtual
path_back(const path_handle_t &path_handle) constbdsg::ODGIvirtual
path_begin(const path_handle_t &path_handle) constbdsg::ODGIvirtual
path_end(const path_handle_t &path_handle) constbdsg::ODGIvirtual
path_front_end(const path_handle_t &path_handle) constbdsg::ODGIvirtual
path_metadata_vbdsg::ODGIprivate
path_name_mapbdsg::ODGIprivate
path_to_rank(const path_handle_t &path) constbdsg::ODGIprivate
prepend_step(const path_handle_t &path, const handle_t &to_append)bdsg::ODGIvirtual
rank_to_id(const uint64_t &rank) constbdsg::ODGIprivate
rank_to_path(size_t rank) constbdsg::ODGIprivate
reassign_node_ids(const std::function< nid_t(const nid_t &)> &get_new_id)bdsg::ODGIvirtual
rewrite_segment(const step_handle_t &segment_begin, const step_handle_t &segment_end, const std::vector< handle_t > &new_segment)bdsg::ODGIvirtual
scan_path(const path_handle_t &path) consthandlegraph::PathHandleGraph
serialize(std::ostream &out) consthandlegraph::SerializableHandleGraphinline
serialize(const std::string &filename) consthandlegraph::SerializableHandleGraphinline
serialize_and_measure(std::ostream &out) constbdsg::ODGI
serialize_members(std::ostream &out) constbdsg::ODGIprivatevirtual
set_circularity(const path_handle_t &path_handle, bool circular)bdsg::ODGIvirtual
set_handle_of_step(step_handle_t &step_handle, const handle_t &handle) constbdsg::ODGIprivate
set_handle_sequence(const handle_t &handle, const std::string &seq)bdsg::ODGIprivate
set_id_increment(const nid_t &min_id)bdsg::ODGIvirtual
set_step(const step_handle_t &step_handle, const handle_t &handle)bdsg::ODGI
steps_of_handle(const handle_t &handle, bool match_orientation=false) constbdsg::ODGIvirtual
swap_handles(const handle_t &a, const handle_t &b)bdsg::ODGI
to_gfa(std::ostream &out) constbdsg::ODGI
to_gfa(const string &filename) constbdsg::ODGI
to_gfa() constbdsg::ODGI
traverse_edge_handle(const edge_t &edge, const handle_t &left) constbdsg::ODGI
~DeletableHandleGraph()=defaulthandlegraph::DeletableHandleGraphvirtual
~HandleGraph()=defaulthandlegraph::HandleGraphvirtual
~MutableHandleGraph()=defaulthandlegraph::MutableHandleGraphvirtual
~MutablePathDeletableHandleGraph()=defaulthandlegraph::MutablePathDeletableHandleGraphvirtual
~MutablePathHandleGraph()=defaulthandlegraph::MutablePathHandleGraphvirtual
~MutablePathMutableHandleGraph()=defaulthandlegraph::MutablePathMutableHandleGraphvirtual
~ODGI(void)bdsg::ODGIinline
~PathHandleGraph()=defaulthandlegraph::PathHandleGraphvirtual
~SerializableHandleGraph()=defaulthandlegraph::SerializableHandleGraphvirtual