| append_path_name(const string &path_name) | bdsg::PackedGraph | private |
| append_step(const path_handle_t &path, const handle_t &to_append) | bdsg::PackedGraph | virtual |
| apply_ordering(const vector< handle_t > &order, bool compact_ids=false) | bdsg::PackedGraph | |
| handlegraph::MutablePathDeletableHandleGraph::apply_ordering(const std::vector< handle_t > &order, bool compact_ids=false)=0 | handlegraph::MutableHandleGraph | pure virtual |
| apply_orientation(const handle_t &handle) | bdsg::PackedGraph | virtual |
| char_assignment | bdsg::PackedGraph | private |
| clear(void) | bdsg::PackedGraph | virtual |
| compact_ids(const vector< handle_t > &order) | bdsg::PackedGraph | private |
| complement_encoded_nucleotide(const uint64_t &val) const | bdsg::PackedGraph | inlineprivate |
| create_edge(const handle_t &left, const handle_t &right) | bdsg::PackedGraph | virtual |
| handlegraph::MutablePathDeletableHandleGraph::create_edge(const edge_t &edge) | handlegraph::MutableHandleGraph | inline |
| create_handle(const std::string &sequence) | bdsg::PackedGraph | virtual |
| create_handle(const std::string &sequence, const nid_t &id) | bdsg::PackedGraph | virtual |
| create_path_handle(const string &name, bool is_circular=false) | bdsg::PackedGraph | |
| handlegraph::MutablePathDeletableHandleGraph::create_path_handle(const std::string &name, bool is_circular=false)=0 | handlegraph::MutablePathHandleGraph | pure virtual |
| decode_nucleotide(const uint64_t &val) const | bdsg::PackedGraph | inlineprivate |
| decode_path_name(const int64_t &path_idx) const | bdsg::PackedGraph | private |
| decode_traversal(const uint64_t &val) const | bdsg::PackedGraph | inlineprivate |
| defrag_factor | bdsg::PackedGraph | privatestatic |
| defragment(bool force=false) | bdsg::PackedGraph | private |
| defragment_path(const int64_t &path_idx, bool force=false) | bdsg::PackedGraph | private |
| deleted_bases | bdsg::PackedGraph | private |
| deleted_edge_records | bdsg::PackedGraph | private |
| deleted_membership_records | bdsg::PackedGraph | private |
| deleted_node_records | bdsg::PackedGraph | private |
| deleted_reversing_self_edge_records | bdsg::PackedGraph | private |
| deserialize(std::istream &in) | handlegraph::SerializableHandleGraph | inline |
| deserialize(const std::string &filename) | handlegraph::SerializableHandleGraph | inline |
| deserialize_members(istream &in) | bdsg::PackedGraph | privatevirtual |
| destroy_edge(const handle_t &left, const handle_t &right) | bdsg::PackedGraph | virtual |
| handlegraph::MutablePathDeletableHandleGraph::destroy_edge(const edge_t &edge) | handlegraph::DeletableHandleGraph | inline |
| destroy_handle(const handle_t &handle) | bdsg::PackedGraph | virtual |
| destroy_path(const path_handle_t &path) | bdsg::PackedGraph | virtual |
| divide_handle(const handle_t &handle, const std::vector< size_t > &offsets) | bdsg::PackedGraph | virtual |
| handlegraph::MutablePathDeletableHandleGraph::divide_handle(const handle_t &handle, size_t offset) | handlegraph::MutableHandleGraph | inline |
| edge_handle(const handle_t &left, const handle_t &right) const | handlegraph::HandleGraph | |
| edge_lists_iv | bdsg::PackedGraph | private |
| EDGE_NEXT_OFFSET | bdsg::PackedGraph | privatestatic |
| EDGE_RECORD_SIZE | bdsg::PackedGraph | privatestatic |
| EDGE_TRAV_OFFSET | bdsg::PackedGraph | privatestatic |
| eject_deleted_paths() | bdsg::PackedGraph | private |
| encode_and_assign_path_name(const string &path_name) | bdsg::PackedGraph | private |
| encode_nucleotide(const char &nt) const | bdsg::PackedGraph | inlineprivate |
| encode_path_name(const string &path_name) const | bdsg::PackedGraph | private |
| encode_traversal(const handle_t &handle) const | bdsg::PackedGraph | inlineprivate |
| extract_encoded_path_name(const int64_t &path_idx) const | bdsg::PackedGraph | private |
| flip(const handle_t &handle) const | bdsg::PackedGraph | virtual |
| follow_edges(const handle_t &handle, bool go_left, const Iteratee &iteratee) const | handlegraph::HandleGraph | |
| follow_edges_impl(const handle_t &handle, bool go_left, const std::function< bool(const handle_t &)> &iteratee) const | bdsg::PackedGraph | virtual |
| for_each_edge(const Iteratee &iteratee, bool parallel=false) const | handlegraph::HandleGraph | |
| for_each_handle(const Iteratee &iteratee, bool parallel=false) const | handlegraph::HandleGraph | |
| for_each_handle_impl(const std::function< bool(const handle_t &)> &iteratee, bool parallel=false) const | bdsg::PackedGraph | virtual |
| for_each_path_handle(const Iteratee &iteratee) const | handlegraph::PathHandleGraph | |
| for_each_path_handle_impl(const std::function< bool(const path_handle_t &)> &iteratee) const | bdsg::PackedGraph | virtual |
| for_each_step_in_path(const path_handle_t &path, const Iteratee &iteratee) const | handlegraph::PathHandleGraph | |
| for_each_step_on_handle(const handle_t &handle, const Iteratee &iteratee) const | handlegraph::PathHandleGraph | |
| for_each_step_on_handle_impl(const handle_t &handle, const function< bool(const step_handle_t &)> &iteratee) const | bdsg::PackedGraph | |
| handlegraph::MutablePathDeletableHandleGraph::for_each_step_on_handle_impl(const handle_t &handle, const std::function< bool(const step_handle_t &)> &iteratee) const =0 | handlegraph::PathHandleGraph | protectedpure virtual |
| forward(const handle_t &handle) const | handlegraph::HandleGraph | |
| get_assignment(const char &c) const | bdsg::PackedGraph | inlineprivate |
| get_base(const handle_t &handle, size_t index) const | bdsg::PackedGraph | virtual |
| get_char(const uint64_t &assignment) const | bdsg::PackedGraph | inlineprivate |
| get_degree(const handle_t &handle, bool go_left) const | handlegraph::HandleGraph | virtual |
| get_edge_count() const | bdsg::PackedGraph | virtual |
| get_edge_target(const uint64_t &edge_index) const | bdsg::PackedGraph | inlineprivate |
| get_handle(const nid_t &node_id, bool is_reverse=false) const | bdsg::PackedGraph | virtual |
| get_handle_of_step(const step_handle_t &step_handle) const | bdsg::PackedGraph | virtual |
| get_id(const handle_t &handle) const | bdsg::PackedGraph | virtual |
| get_is_circular(const path_handle_t &path_handle) const | bdsg::PackedGraph | virtual |
| get_is_reverse(const handle_t &handle) const | bdsg::PackedGraph | virtual |
| get_length(const handle_t &handle) const | bdsg::PackedGraph | virtual |
| get_magic_number() const | bdsg::PackedGraph | virtual |
| get_membership_path(const uint64_t &membership_index) const | bdsg::PackedGraph | inlineprivate |
| get_membership_step(const uint64_t &membership_index) const | bdsg::PackedGraph | inlineprivate |
| get_next_edge_index(const uint64_t &edge_index) const | bdsg::PackedGraph | inlineprivate |
| get_next_membership(const uint64_t &membership_index) const | bdsg::PackedGraph | inlineprivate |
| get_next_step(const step_handle_t &step_handle) const | bdsg::PackedGraph | virtual |
| get_node_count(void) const | bdsg::PackedGraph | virtual |
| get_or_make_assignment(const char &c) | bdsg::PackedGraph | inlineprivate |
| get_path_count() const | bdsg::PackedGraph | virtual |
| get_path_handle(const std::string &path_name) const | bdsg::PackedGraph | virtual |
| get_path_handle_of_step(const step_handle_t &step_handle) const | bdsg::PackedGraph | virtual |
| get_path_name(const path_handle_t &path_handle) const | bdsg::PackedGraph | virtual |
| get_previous_step(const step_handle_t &step_handle) const | bdsg::PackedGraph | virtual |
| get_sequence(const handle_t &handle) const | bdsg::PackedGraph | virtual |
| get_step_count(const path_handle_t &path_handle) const | bdsg::PackedGraph | virtual |
| get_step_next(const PackedPath &path, const uint64_t &step_index) const | bdsg::PackedGraph | inlineprivate |
| get_step_prev(const PackedPath &path, const uint64_t &step_index) const | bdsg::PackedGraph | inlineprivate |
| get_step_trav(const PackedPath &path, const uint64_t &step_index) const | bdsg::PackedGraph | inlineprivate |
| get_subsequence(const handle_t &handle, size_t index, size_t size) const | bdsg::PackedGraph | virtual |
| get_total_length() const | bdsg::PackedGraph | virtual |
| GRAPH_END_EDGES_OFFSET | bdsg::PackedGraph | privatestatic |
| graph_index_to_node_member_index(const size_t &graph_index) const | bdsg::PackedGraph | inlineprivate |
| graph_index_to_seq_len_index(const size_t &graph_index) const | bdsg::PackedGraph | inlineprivate |
| graph_index_to_seq_start_index(const size_t &graph_index) const | bdsg::PackedGraph | inlineprivate |
| graph_iv | bdsg::PackedGraph | private |
| graph_iv_index(const handle_t &handle) const | bdsg::PackedGraph | inlineprivate |
| GRAPH_RECORD_SIZE | bdsg::PackedGraph | privatestatic |
| GRAPH_START_EDGES_OFFSET | bdsg::PackedGraph | privatestatic |
| has_edge(const handle_t &left, const handle_t &right) const | handlegraph::HandleGraph | virtual |
| has_edge(const edge_t &edge) const | handlegraph::HandleGraph | inline |
| has_next_step(const step_handle_t &step_handle) const | bdsg::PackedGraph | virtual |
| has_node(nid_t node_id) const | bdsg::PackedGraph | virtual |
| has_path(const std::string &path_name) const | bdsg::PackedGraph | virtual |
| has_previous_step(const step_handle_t &step_handle) const | bdsg::PackedGraph | virtual |
| increment_node_ids(nid_t increment) | bdsg::PackedGraph | virtual |
| inverse_char_assignment | bdsg::PackedGraph | private |
| is_empty(const path_handle_t &path_handle) const | handlegraph::PathHandleGraph | virtual |
| max_id | bdsg::PackedGraph | private |
| max_node_id(void) const | bdsg::PackedGraph | virtual |
| MEMBERSHIP_ID_RECORD_SIZE | bdsg::PackedGraph | privatestatic |
| MEMBERSHIP_NEXT_RECORD_SIZE | bdsg::PackedGraph | privatestatic |
| MEMBERSHIP_OFFSET_RECORD_SIZE | bdsg::PackedGraph | privatestatic |
| min_id | bdsg::PackedGraph | private |
| min_node_id(void) const | bdsg::PackedGraph | virtual |
| NARROW_PAGE_WIDTH | bdsg::PackedGraph | privatestatic |
| new_node_record(nid_t node_id) | bdsg::PackedGraph | private |
| nid_to_graph_iv | bdsg::PackedGraph | private |
| NODE_MEMBER_RECORD_SIZE | bdsg::PackedGraph | privatestatic |
| optimize(bool allow_id_reassignment=true) | bdsg::PackedGraph | virtual |
| PackedGraph() | bdsg::PackedGraph | |
| PackedGraph(istream &in) | bdsg::PackedGraph | |
| path_back(const path_handle_t &path_handle) const | bdsg::PackedGraph | virtual |
| path_begin(const path_handle_t &path_handle) const | bdsg::PackedGraph | virtual |
| path_deleted_steps_iv | bdsg::PackedGraph | private |
| path_end(const path_handle_t &path_handle) const | bdsg::PackedGraph | virtual |
| path_front_end(const path_handle_t &path_handle) const | bdsg::PackedGraph | virtual |
| path_head_iv | bdsg::PackedGraph | private |
| path_id | bdsg::PackedGraph | private |
| path_is_circular_iv | bdsg::PackedGraph | private |
| path_is_deleted_iv | bdsg::PackedGraph | private |
| path_membership_id_iv | bdsg::PackedGraph | private |
| path_membership_next_iv | bdsg::PackedGraph | private |
| path_membership_node_iv | bdsg::PackedGraph | private |
| path_membership_offset_iv | bdsg::PackedGraph | private |
| path_name_length_iv | bdsg::PackedGraph | private |
| path_name_start_iv | bdsg::PackedGraph | private |
| path_names_iv | bdsg::PackedGraph | private |
| PATH_NEXT_OFFSET | bdsg::PackedGraph | privatestatic |
| PATH_PREV_OFFSET | bdsg::PackedGraph | privatestatic |
| PATH_RECORD_SIZE | bdsg::PackedGraph | privatestatic |
| PATH_RESIZE_FACTOR | bdsg::PackedGraph | privatestatic |
| path_tail_iv | bdsg::PackedGraph | private |
| paths | bdsg::PackedGraph | private |
| prepend_step(const path_handle_t &path, const handle_t &to_prepend) | bdsg::PackedGraph | virtual |
| reassign_node_ids(const std::function< nid_t(const nid_t &)> &get_new_id) | bdsg::PackedGraph | virtual |
| remove_edge_reference(const handle_t &on, const handle_t &to) | bdsg::PackedGraph | private |
| report_memory(ostream &out, bool individual_paths=false) const | bdsg::PackedGraph | |
| reversing_self_edge_records | bdsg::PackedGraph | private |
| rewrite_segment(const step_handle_t &segment_begin, const step_handle_t &segment_end, const vector< handle_t > &new_segment) | bdsg::PackedGraph | |
| handlegraph::MutablePathDeletableHandleGraph::rewrite_segment(const step_handle_t &segment_begin, const step_handle_t &segment_end, const std::vector< handle_t > &new_segment)=0 | handlegraph::MutablePathHandleGraph | pure virtual |
| scan_path(const path_handle_t &path) const | handlegraph::PathHandleGraph | |
| seq_iv | bdsg::PackedGraph | private |
| seq_length_iv | bdsg::PackedGraph | private |
| SEQ_LENGTH_RECORD_SIZE | bdsg::PackedGraph | privatestatic |
| seq_start_iv | bdsg::PackedGraph | private |
| SEQ_START_RECORD_SIZE | bdsg::PackedGraph | privatestatic |
| serialize(std::ostream &out) const | handlegraph::SerializableHandleGraph | inline |
| serialize(const std::string &filename) const | handlegraph::SerializableHandleGraph | inline |
| serialize_members(ostream &out) const | bdsg::PackedGraph | privatevirtual |
| set_circularity(const path_handle_t &path, bool circular) | bdsg::PackedGraph | virtual |
| set_edge_target(const uint64_t &edge_index, const handle_t &handle) | bdsg::PackedGraph | inlineprivate |
| set_id_increment(const nid_t &min_id) | bdsg::PackedGraph | virtual |
| set_membership_path(const uint64_t &membership_index, const uint64_t &path) | bdsg::PackedGraph | inlineprivate |
| set_membership_step(const uint64_t &membership_index, const uint64_t &step) | bdsg::PackedGraph | inlineprivate |
| set_next_membership(const uint64_t &membership_index, const uint64_t &next) | bdsg::PackedGraph | inlineprivate |
| set_step_next(PackedPath &path, const uint64_t &step_index, const uint64_t &next_index) | bdsg::PackedGraph | inlineprivate |
| set_step_prev(PackedPath &path, const uint64_t &step_index, const uint64_t &prev_index) | bdsg::PackedGraph | inlineprivate |
| set_step_trav(PackedPath &path, const uint64_t &step_index, const uint64_t &trav) | bdsg::PackedGraph | inlineprivate |
| STEP_RECORD_SIZE | bdsg::PackedGraph | privatestatic |
| steps_of_handle(const handle_t &handle, bool match_orientation=false) const | handlegraph::PathHandleGraph | virtual |
| tighten(void) | bdsg::PackedGraph | private |
| traverse_edge_handle(const edge_t &edge, const handle_t &left) const | handlegraph::HandleGraph | |
| WIDE_PAGE_WIDTH | bdsg::PackedGraph | privatestatic |
| ~DeletableHandleGraph()=default | handlegraph::DeletableHandleGraph | virtual |
| ~HandleGraph()=default | handlegraph::HandleGraph | virtual |
| ~MutableHandleGraph()=default | handlegraph::MutableHandleGraph | virtual |
| ~MutablePathDeletableHandleGraph()=default | handlegraph::MutablePathDeletableHandleGraph | virtual |
| ~MutablePathHandleGraph()=default | handlegraph::MutablePathHandleGraph | virtual |
| ~MutablePathMutableHandleGraph()=default | handlegraph::MutablePathMutableHandleGraph | virtual |
| ~PackedGraph() | bdsg::PackedGraph | |
| ~PathHandleGraph()=default | handlegraph::PathHandleGraph | virtual |
| ~SerializableHandleGraph()=default | handlegraph::SerializableHandleGraph | virtual |
