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 |