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

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

append_step(const path_handle_t &path, const handle_t &to_append)bdsg::HashGraphvirtual
apply_ordering(const vector< handle_t > &order, bool compact_ids=false)bdsg::HashGraph
handlegraph::MutablePathDeletableHandleGraph::apply_ordering(const std::vector< handle_t > &order, bool compact_ids=false)=0handlegraph::MutableHandleGraphpure virtual
apply_orientation(const handle_t &handle)bdsg::HashGraphvirtual
clear(void)bdsg::HashGraphvirtual
create_edge(const handle_t &left, const handle_t &right)bdsg::HashGraphvirtual
handlegraph::MutablePathDeletableHandleGraph::create_edge(const edge_t &edge)handlegraph::MutableHandleGraphinline
create_handle(const std::string &sequence)bdsg::HashGraphvirtual
create_handle(const std::string &sequence, const nid_t &id)bdsg::HashGraphvirtual
create_path_handle(const string &name, bool is_circular=false)bdsg::HashGraph
handlegraph::MutablePathDeletableHandleGraph::create_path_handle(const std::string &name, bool is_circular=false)=0handlegraph::MutablePathHandleGraphpure virtual
deserialize(std::istream &in)handlegraph::SerializableHandleGraphinline
deserialize(const std::string &filename)handlegraph::SerializableHandleGraphinline
deserialize_members(istream &in)bdsg::HashGraphprivatevirtual
destroy_edge(const handle_t &left, const handle_t &right)bdsg::HashGraphvirtual
handlegraph::MutablePathDeletableHandleGraph::destroy_edge(const edge_t &edge)handlegraph::DeletableHandleGraphinline
destroy_handle(const handle_t &handle)bdsg::HashGraphvirtual
destroy_path(const path_handle_t &path)bdsg::HashGraphvirtual
divide_handle(const handle_t &handle, const std::vector< size_t > &offsets)bdsg::HashGraphvirtual
handlegraph::MutablePathDeletableHandleGraph::divide_handle(const handle_t &handle, size_t offset)handlegraph::MutableHandleGraphinline
edge_handle(const handle_t &left, const handle_t &right) consthandlegraph::HandleGraph
flip(const handle_t &handle) constbdsg::HashGraphvirtual
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::HashGraphvirtual
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::HashGraphvirtual
for_each_path_handle(const Iteratee &iteratee) consthandlegraph::PathHandleGraph
for_each_path_handle_impl(const std::function< bool(const path_handle_t &)> &iteratee) constbdsg::HashGraphvirtual
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 function< bool(const step_handle_t &)> &iteratee) constbdsg::HashGraph
handlegraph::MutablePathDeletableHandleGraph::for_each_step_on_handle_impl(const handle_t &handle, const std::function< bool(const step_handle_t &)> &iteratee) const =0handlegraph::PathHandleGraphprotectedpure virtual
forward(const handle_t &handle) consthandlegraph::HandleGraph
get_base(const handle_t &handle, size_t index) constbdsg::HashGraphvirtual
get_degree(const handle_t &handle, bool go_left) constbdsg::HashGraphvirtual
get_edge_count() consthandlegraph::HandleGraphvirtual
get_handle(const nid_t &node_id, bool is_reverse=false) constbdsg::HashGraphvirtual
get_handle_of_step(const step_handle_t &step_handle) constbdsg::HashGraphvirtual
get_id(const handle_t &handle) constbdsg::HashGraphvirtual
get_is_circular(const path_handle_t &path_handle) constbdsg::HashGraphvirtual
get_is_reverse(const handle_t &handle) constbdsg::HashGraphvirtual
get_length(const handle_t &handle) constbdsg::HashGraphvirtual
get_magic_number() constbdsg::HashGraphvirtual
get_next_step(const step_handle_t &step_handle) constbdsg::HashGraphvirtual
get_node_count(void) constbdsg::HashGraphvirtual
get_path_count() constbdsg::HashGraphvirtual
get_path_handle(const std::string &path_name) constbdsg::HashGraphvirtual
get_path_handle_of_step(const step_handle_t &step_handle) constbdsg::HashGraphvirtual
get_path_name(const path_handle_t &path_handle) constbdsg::HashGraphvirtual
get_previous_step(const step_handle_t &step_handle) constbdsg::HashGraphvirtual
get_sequence(const handle_t &handle) constbdsg::HashGraphvirtual
get_step_count(const path_handle_t &path_handle) constbdsg::HashGraphvirtual
get_subsequence(const handle_t &handle, size_t index, size_t size) constbdsg::HashGraphvirtual
get_total_length() consthandlegraph::HandleGraphvirtual
graphbdsg::HashGraphprivate
has_edge(const handle_t &left, const handle_t &right) consthandlegraph::HandleGraphvirtual
has_edge(const edge_t &edge) consthandlegraph::HandleGraphinline
has_next_step(const step_handle_t &step_handle) constbdsg::HashGraphvirtual
has_node(nid_t node_id) constbdsg::HashGraphvirtual
has_path(const std::string &path_name) constbdsg::HashGraphvirtual
has_previous_step(const step_handle_t &step_handle) constbdsg::HashGraphvirtual
HashGraph()bdsg::HashGraph
HashGraph(istream &in)bdsg::HashGraph
increment_node_ids(nid_t increment)bdsg::HashGraphvirtual
is_empty(const path_handle_t &path_handle) consthandlegraph::PathHandleGraphvirtual
max_idbdsg::HashGraphprivate
max_node_id(void) constbdsg::HashGraphvirtual
min_idbdsg::HashGraphprivate
min_node_id(void) constbdsg::HashGraphvirtual
next_path_idbdsg::HashGraphprivate
optimize(bool allow_id_reassignment=true)bdsg::HashGraphvirtual
path_back(const path_handle_t &path_handle) constbdsg::HashGraphvirtual
path_begin(const path_handle_t &path_handle) constbdsg::HashGraphvirtual
path_end(const path_handle_t &path_handle) constbdsg::HashGraphvirtual
path_front_end(const path_handle_t &path_handle) constbdsg::HashGraphvirtual
path_idbdsg::HashGraphprivate
pathsbdsg::HashGraphprivate
prepend_step(const path_handle_t &path, const handle_t &to_prepend)bdsg::HashGraphvirtual
reassign_node_ids(const std::function< nid_t(const nid_t &)> &get_new_id)bdsg::HashGraphvirtual
rewrite_segment(const step_handle_t &segment_begin, const step_handle_t &segment_end, const std::vector< handle_t > &new_segment)bdsg::HashGraphvirtual
scan_path(const path_handle_t &path) consthandlegraph::PathHandleGraph
serialize(std::ostream &out) consthandlegraph::SerializableHandleGraphinline
serialize(const std::string &filename) consthandlegraph::SerializableHandleGraphinline
serialize_members(ostream &out) constbdsg::HashGraphprivatevirtual
set_circularity(const path_handle_t &path, bool circular)bdsg::HashGraphvirtual
set_id(const handle_t &internal, nid_t new_id)bdsg::HashGraphprivatestatic
set_id_increment(const nid_t &min_id)bdsg::HashGraphvirtual
steps_of_handle(const handle_t &handle, bool match_orientation=false) consthandlegraph::PathHandleGraphvirtual
traverse_edge_handle(const edge_t &edge, const handle_t &left) consthandlegraph::HandleGraph
~DeletableHandleGraph()=defaulthandlegraph::DeletableHandleGraphvirtual
~HandleGraph()=defaulthandlegraph::HandleGraphvirtual
~HashGraph()bdsg::HashGraph
~MutableHandleGraph()=defaulthandlegraph::MutableHandleGraphvirtual
~MutablePathDeletableHandleGraph()=defaulthandlegraph::MutablePathDeletableHandleGraphvirtual
~MutablePathHandleGraph()=defaulthandlegraph::MutablePathHandleGraphvirtual
~MutablePathMutableHandleGraph()=defaulthandlegraph::MutablePathMutableHandleGraphvirtual
~PathHandleGraph()=defaulthandlegraph::PathHandleGraphvirtual
~SerializableHandleGraph()=defaulthandlegraph::SerializableHandleGraphvirtual