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

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

append_path_name(const string &path_name)bdsg::PackedGraphprivate
append_step(const path_handle_t &path, const handle_t &to_append)bdsg::PackedGraphvirtual
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)=0handlegraph::MutableHandleGraphpure virtual
apply_orientation(const handle_t &handle)bdsg::PackedGraphvirtual
char_assignmentbdsg::PackedGraphprivate
clear(void)bdsg::PackedGraphvirtual
compact_ids(const vector< handle_t > &order)bdsg::PackedGraphprivate
complement_encoded_nucleotide(const uint64_t &val) constbdsg::PackedGraphinlineprivate
create_edge(const handle_t &left, const handle_t &right)bdsg::PackedGraphvirtual
handlegraph::MutablePathDeletableHandleGraph::create_edge(const edge_t &edge)handlegraph::MutableHandleGraphinline
create_handle(const std::string &sequence)bdsg::PackedGraphvirtual
create_handle(const std::string &sequence, const nid_t &id)bdsg::PackedGraphvirtual
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)=0handlegraph::MutablePathHandleGraphpure virtual
decode_nucleotide(const uint64_t &val) constbdsg::PackedGraphinlineprivate
decode_path_name(const int64_t &path_idx) constbdsg::PackedGraphprivate
decode_traversal(const uint64_t &val) constbdsg::PackedGraphinlineprivate
defrag_factorbdsg::PackedGraphprivatestatic
defragment(bool force=false)bdsg::PackedGraphprivate
defragment_path(const int64_t &path_idx, bool force=false)bdsg::PackedGraphprivate
deleted_basesbdsg::PackedGraphprivate
deleted_edge_recordsbdsg::PackedGraphprivate
deleted_membership_recordsbdsg::PackedGraphprivate
deleted_node_recordsbdsg::PackedGraphprivate
deleted_reversing_self_edge_recordsbdsg::PackedGraphprivate
deserialize(std::istream &in)handlegraph::SerializableHandleGraphinline
deserialize(const std::string &filename)handlegraph::SerializableHandleGraphinline
deserialize_members(istream &in)bdsg::PackedGraphprivatevirtual
destroy_edge(const handle_t &left, const handle_t &right)bdsg::PackedGraphvirtual
handlegraph::MutablePathDeletableHandleGraph::destroy_edge(const edge_t &edge)handlegraph::DeletableHandleGraphinline
destroy_handle(const handle_t &handle)bdsg::PackedGraphvirtual
destroy_path(const path_handle_t &path)bdsg::PackedGraphvirtual
divide_handle(const handle_t &handle, const std::vector< size_t > &offsets)bdsg::PackedGraphvirtual
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
edge_lists_ivbdsg::PackedGraphprivate
EDGE_NEXT_OFFSETbdsg::PackedGraphprivatestatic
EDGE_RECORD_SIZEbdsg::PackedGraphprivatestatic
EDGE_TRAV_OFFSETbdsg::PackedGraphprivatestatic
eject_deleted_paths()bdsg::PackedGraphprivate
encode_and_assign_path_name(const string &path_name)bdsg::PackedGraphprivate
encode_nucleotide(const char &nt) constbdsg::PackedGraphinlineprivate
encode_path_name(const string &path_name) constbdsg::PackedGraphprivate
encode_traversal(const handle_t &handle) constbdsg::PackedGraphinlineprivate
extract_encoded_path_name(const int64_t &path_idx) constbdsg::PackedGraphprivate
flip(const handle_t &handle) constbdsg::PackedGraphvirtual
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::PackedGraphvirtual
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::PackedGraphvirtual
for_each_path_handle(const Iteratee &iteratee) consthandlegraph::PathHandleGraph
for_each_path_handle_impl(const std::function< bool(const path_handle_t &)> &iteratee) constbdsg::PackedGraphvirtual
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::PackedGraph
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_assignment(const char &c) constbdsg::PackedGraphinlineprivate
get_base(const handle_t &handle, size_t index) constbdsg::PackedGraphvirtual
get_char(const uint64_t &assignment) constbdsg::PackedGraphinlineprivate
get_degree(const handle_t &handle, bool go_left) consthandlegraph::HandleGraphvirtual
get_edge_count() constbdsg::PackedGraphvirtual
get_edge_target(const uint64_t &edge_index) constbdsg::PackedGraphinlineprivate
get_handle(const nid_t &node_id, bool is_reverse=false) constbdsg::PackedGraphvirtual
get_handle_of_step(const step_handle_t &step_handle) constbdsg::PackedGraphvirtual
get_id(const handle_t &handle) constbdsg::PackedGraphvirtual
get_is_circular(const path_handle_t &path_handle) constbdsg::PackedGraphvirtual
get_is_reverse(const handle_t &handle) constbdsg::PackedGraphvirtual
get_length(const handle_t &handle) constbdsg::PackedGraphvirtual
get_magic_number() constbdsg::PackedGraphvirtual
get_membership_path(const uint64_t &membership_index) constbdsg::PackedGraphinlineprivate
get_membership_step(const uint64_t &membership_index) constbdsg::PackedGraphinlineprivate
get_next_edge_index(const uint64_t &edge_index) constbdsg::PackedGraphinlineprivate
get_next_membership(const uint64_t &membership_index) constbdsg::PackedGraphinlineprivate
get_next_step(const step_handle_t &step_handle) constbdsg::PackedGraphvirtual
get_node_count(void) constbdsg::PackedGraphvirtual
get_or_make_assignment(const char &c)bdsg::PackedGraphinlineprivate
get_path_count() constbdsg::PackedGraphvirtual
get_path_handle(const std::string &path_name) constbdsg::PackedGraphvirtual
get_path_handle_of_step(const step_handle_t &step_handle) constbdsg::PackedGraphvirtual
get_path_name(const path_handle_t &path_handle) constbdsg::PackedGraphvirtual
get_previous_step(const step_handle_t &step_handle) constbdsg::PackedGraphvirtual
get_sequence(const handle_t &handle) constbdsg::PackedGraphvirtual
get_step_count(const path_handle_t &path_handle) constbdsg::PackedGraphvirtual
get_step_next(const PackedPath &path, const uint64_t &step_index) constbdsg::PackedGraphinlineprivate
get_step_prev(const PackedPath &path, const uint64_t &step_index) constbdsg::PackedGraphinlineprivate
get_step_trav(const PackedPath &path, const uint64_t &step_index) constbdsg::PackedGraphinlineprivate
get_subsequence(const handle_t &handle, size_t index, size_t size) constbdsg::PackedGraphvirtual
get_total_length() constbdsg::PackedGraphvirtual
GRAPH_END_EDGES_OFFSETbdsg::PackedGraphprivatestatic
graph_index_to_node_member_index(const size_t &graph_index) constbdsg::PackedGraphinlineprivate
graph_index_to_seq_len_index(const size_t &graph_index) constbdsg::PackedGraphinlineprivate
graph_index_to_seq_start_index(const size_t &graph_index) constbdsg::PackedGraphinlineprivate
graph_ivbdsg::PackedGraphprivate
graph_iv_index(const handle_t &handle) constbdsg::PackedGraphinlineprivate
GRAPH_RECORD_SIZEbdsg::PackedGraphprivatestatic
GRAPH_START_EDGES_OFFSETbdsg::PackedGraphprivatestatic
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::PackedGraphvirtual
has_node(nid_t node_id) constbdsg::PackedGraphvirtual
has_path(const std::string &path_name) constbdsg::PackedGraphvirtual
has_previous_step(const step_handle_t &step_handle) constbdsg::PackedGraphvirtual
increment_node_ids(nid_t increment)bdsg::PackedGraphvirtual
inverse_char_assignmentbdsg::PackedGraphprivate
is_empty(const path_handle_t &path_handle) consthandlegraph::PathHandleGraphvirtual
max_idbdsg::PackedGraphprivate
max_node_id(void) constbdsg::PackedGraphvirtual
MEMBERSHIP_ID_RECORD_SIZEbdsg::PackedGraphprivatestatic
MEMBERSHIP_NEXT_RECORD_SIZEbdsg::PackedGraphprivatestatic
MEMBERSHIP_OFFSET_RECORD_SIZEbdsg::PackedGraphprivatestatic
min_idbdsg::PackedGraphprivate
min_node_id(void) constbdsg::PackedGraphvirtual
NARROW_PAGE_WIDTHbdsg::PackedGraphprivatestatic
new_node_record(nid_t node_id)bdsg::PackedGraphprivate
nid_to_graph_ivbdsg::PackedGraphprivate
NODE_MEMBER_RECORD_SIZEbdsg::PackedGraphprivatestatic
optimize(bool allow_id_reassignment=true)bdsg::PackedGraphvirtual
PackedGraph()bdsg::PackedGraph
PackedGraph(istream &in)bdsg::PackedGraph
path_back(const path_handle_t &path_handle) constbdsg::PackedGraphvirtual
path_begin(const path_handle_t &path_handle) constbdsg::PackedGraphvirtual
path_deleted_steps_ivbdsg::PackedGraphprivate
path_end(const path_handle_t &path_handle) constbdsg::PackedGraphvirtual
path_front_end(const path_handle_t &path_handle) constbdsg::PackedGraphvirtual
path_head_ivbdsg::PackedGraphprivate
path_idbdsg::PackedGraphprivate
path_is_circular_ivbdsg::PackedGraphprivate
path_is_deleted_ivbdsg::PackedGraphprivate
path_membership_id_ivbdsg::PackedGraphprivate
path_membership_next_ivbdsg::PackedGraphprivate
path_membership_node_ivbdsg::PackedGraphprivate
path_membership_offset_ivbdsg::PackedGraphprivate
path_name_length_ivbdsg::PackedGraphprivate
path_name_start_ivbdsg::PackedGraphprivate
path_names_ivbdsg::PackedGraphprivate
PATH_NEXT_OFFSETbdsg::PackedGraphprivatestatic
PATH_PREV_OFFSETbdsg::PackedGraphprivatestatic
PATH_RECORD_SIZEbdsg::PackedGraphprivatestatic
PATH_RESIZE_FACTORbdsg::PackedGraphprivatestatic
path_tail_ivbdsg::PackedGraphprivate
pathsbdsg::PackedGraphprivate
prepend_step(const path_handle_t &path, const handle_t &to_prepend)bdsg::PackedGraphvirtual
reassign_node_ids(const std::function< nid_t(const nid_t &)> &get_new_id)bdsg::PackedGraphvirtual
remove_edge_reference(const handle_t &on, const handle_t &to)bdsg::PackedGraphprivate
report_memory(ostream &out, bool individual_paths=false) constbdsg::PackedGraph
reversing_self_edge_recordsbdsg::PackedGraphprivate
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)=0handlegraph::MutablePathHandleGraphpure virtual
scan_path(const path_handle_t &path) consthandlegraph::PathHandleGraph
seq_ivbdsg::PackedGraphprivate
seq_length_ivbdsg::PackedGraphprivate
SEQ_LENGTH_RECORD_SIZEbdsg::PackedGraphprivatestatic
seq_start_ivbdsg::PackedGraphprivate
SEQ_START_RECORD_SIZEbdsg::PackedGraphprivatestatic
serialize(std::ostream &out) consthandlegraph::SerializableHandleGraphinline
serialize(const std::string &filename) consthandlegraph::SerializableHandleGraphinline
serialize_members(ostream &out) constbdsg::PackedGraphprivatevirtual
set_circularity(const path_handle_t &path, bool circular)bdsg::PackedGraphvirtual
set_edge_target(const uint64_t &edge_index, const handle_t &handle)bdsg::PackedGraphinlineprivate
set_id_increment(const nid_t &min_id)bdsg::PackedGraphvirtual
set_membership_path(const uint64_t &membership_index, const uint64_t &path)bdsg::PackedGraphinlineprivate
set_membership_step(const uint64_t &membership_index, const uint64_t &step)bdsg::PackedGraphinlineprivate
set_next_membership(const uint64_t &membership_index, const uint64_t &next)bdsg::PackedGraphinlineprivate
set_step_next(PackedPath &path, const uint64_t &step_index, const uint64_t &next_index)bdsg::PackedGraphinlineprivate
set_step_prev(PackedPath &path, const uint64_t &step_index, const uint64_t &prev_index)bdsg::PackedGraphinlineprivate
set_step_trav(PackedPath &path, const uint64_t &step_index, const uint64_t &trav)bdsg::PackedGraphinlineprivate
STEP_RECORD_SIZEbdsg::PackedGraphprivatestatic
steps_of_handle(const handle_t &handle, bool match_orientation=false) consthandlegraph::PathHandleGraphvirtual
tighten(void)bdsg::PackedGraphprivate
traverse_edge_handle(const edge_t &edge, const handle_t &left) consthandlegraph::HandleGraph
WIDE_PAGE_WIDTHbdsg::PackedGraphprivatestatic
~DeletableHandleGraph()=defaulthandlegraph::DeletableHandleGraphvirtual
~HandleGraph()=defaulthandlegraph::HandleGraphvirtual
~MutableHandleGraph()=defaulthandlegraph::MutableHandleGraphvirtual
~MutablePathDeletableHandleGraph()=defaulthandlegraph::MutablePathDeletableHandleGraphvirtual
~MutablePathHandleGraph()=defaulthandlegraph::MutablePathHandleGraphvirtual
~MutablePathMutableHandleGraph()=defaulthandlegraph::MutablePathMutableHandleGraphvirtual
~PackedGraph()bdsg::PackedGraph
~PathHandleGraph()=defaulthandlegraph::PathHandleGraphvirtual
~SerializableHandleGraph()=defaulthandlegraph::SerializableHandleGraphvirtual