vg
tools for working with variation graphs
handlegraph::MutablePathMutableHandleGraph Member List

This is the complete list of members for handlegraph::MutablePathMutableHandleGraph, including all inherited members.

append_step(const path_handle_t &path, const handle_t &to_append)=0handlegraph::MutablePathHandleGraphpure virtual
apply_ordering(const std::vector< handle_t > &order, bool compact_ids=false)=0handlegraph::MutableHandleGraphpure virtual
apply_orientation(const handle_t &handle)=0handlegraph::MutableHandleGraphpure virtual
ASSEMBLY_OR_NAME_MATCHhandlegraph::PathMetadataprivatestatic
create_edge(const handle_t &left, const handle_t &right)=0handlegraph::MutableHandleGraphpure virtual
create_edge(const edge_t &edge)handlegraph::MutableHandleGraphinline
create_handle(const std::string &sequence)=0handlegraph::MutableHandleGraphpure virtual
create_handle(const std::string &sequence, const nid_t &id)=0handlegraph::MutableHandleGraphpure virtual
create_path(const PathSense &sense, const std::string &sample, const std::string &locus, const size_t &haplotype, const size_t &phase_block, const subrange_t &subrange, bool is_circular=false)handlegraph::MutablePathMetadatavirtual
create_path_handle(const std::string &name, bool is_circular=false)=0handlegraph::MutablePathHandleGraphpure virtual
create_path_name(const PathSense &sense, const std::string &sample, const std::string &locus, const size_t &haplotype, const size_t &phase_block, const subrange_t &subrange)handlegraph::PathMetadatastatic
destroy_path(const path_handle_t &path_handle)=0handlegraph::MutablePathHandleGraphpure virtual
destroy_paths(const std::vector< path_handle_t > &paths)handlegraph::MutablePathHandleGraphvirtual
divide_handle(const handle_t &handle, const std::vector< size_t > &offsets)=0handlegraph::MutableHandleGraphpure virtual
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) const =0handlegraph::HandleGraphpure virtual
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) const =0handlegraph::HandleGraphprotectedpure virtual
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) const =0handlegraph::HandleGraphprotectedpure virtual
for_each_path_handle(const Iteratee &iteratee) consthandlegraph::PathHandleGraph
for_each_path_handle_impl(const std::function< bool(const path_handle_t &)> &iteratee) const =0handlegraph::PathHandleGraphprotectedpure virtual
for_each_path_matching(const std::unordered_set< PathSense > *senses, const std::unordered_set< std::string > *samples, const std::unordered_set< std::string > *loci, const Iteratee &iteratee) consthandlegraph::PathMetadata
for_each_path_matching(const std::unordered_set< PathSense > &senses, const std::unordered_set< std::string > &samples, const std::unordered_set< std::string > &loci, const Iteratee &iteratee) consthandlegraph::PathMetadata
for_each_path_matching_impl(const std::unordered_set< PathSense > *senses, const std::unordered_set< std::string > *samples, const std::unordered_set< std::string > *loci, const std::function< bool(const path_handle_t &)> &iteratee) consthandlegraph::PathMetadataprotectedvirtual
for_each_path_of_sample(const std::string &sample, const Iteratee &iteratee) consthandlegraph::PathMetadata
for_each_path_of_sense(const PathSense &sense, const Iteratee &iteratee) consthandlegraph::PathMetadata
for_each_step_in_path(const path_handle_t &path, const Iteratee &iteratee) consthandlegraph::PathHandleGraph
for_each_step_of_sense(const handle_t &visited, const PathSense &sense, const Iteratee &iteratee) consthandlegraph::PathMetadata
for_each_step_of_sense_impl(const handle_t &visited, const PathSense &sense, const std::function< bool(const step_handle_t &)> &iteratee) consthandlegraph::PathMetadataprotectedvirtual
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) const =0handlegraph::PathHandleGraphprotectedpure virtual
FORMAThandlegraph::PathMetadataprivatestatic
forward(const handle_t &handle) consthandlegraph::HandleGraph
get_base(const handle_t &handle, size_t index) consthandlegraph::HandleGraphvirtual
get_degree(const handle_t &handle, bool go_left) consthandlegraph::HandleGraphvirtual
get_edge_count() consthandlegraph::HandleGraphvirtual
get_handle(const nid_t &node_id, bool is_reverse=false) const =0handlegraph::HandleGraphpure virtual
get_handle_of_step(const step_handle_t &step_handle) const =0handlegraph::PathHandleGraphpure virtual
get_haplotype(const path_handle_t &handle) consthandlegraph::PathMetadatavirtual
get_id(const handle_t &handle) const =0handlegraph::HandleGraphpure virtual
get_is_circular(const path_handle_t &path_handle) const =0handlegraph::PathHandleGraphpure virtual
get_is_reverse(const handle_t &handle) const =0handlegraph::HandleGraphpure virtual
get_length(const handle_t &handle) const =0handlegraph::HandleGraphpure virtual
get_locus_name(const path_handle_t &handle) consthandlegraph::PathMetadatavirtual
get_next_step(const step_handle_t &step_handle) const =0handlegraph::PathHandleGraphpure virtual
get_node_count() const =0handlegraph::HandleGraphpure virtual
get_path_count() const =0handlegraph::PathHandleGraphpure virtual
get_path_handle(const std::string &path_name) const =0handlegraph::PathHandleGraphpure virtual
get_path_handle_of_step(const step_handle_t &step_handle) const =0handlegraph::PathHandleGraphpure virtual
get_path_name(const path_handle_t &path_handle) const =0handlegraph::PathHandleGraphpure virtual
get_phase_block(const path_handle_t &handle) consthandlegraph::PathMetadatavirtual
get_previous_step(const step_handle_t &step_handle) const =0handlegraph::PathHandleGraphpure virtual
get_sample_name(const path_handle_t &handle) consthandlegraph::PathMetadatavirtual
get_sense(const path_handle_t &handle) consthandlegraph::PathMetadatavirtual
get_sequence(const handle_t &handle) const =0handlegraph::HandleGraphpure virtual
get_step_count(const path_handle_t &path_handle) const =0handlegraph::PathHandleGraphpure virtual
get_step_count(const handle_t &handle) consthandlegraph::PathHandleGraphvirtual
get_subrange(const path_handle_t &handle) consthandlegraph::PathMetadatavirtual
get_subsequence(const handle_t &handle, size_t index, size_t size) consthandlegraph::HandleGraphvirtual
get_total_length() consthandlegraph::HandleGraphvirtual
HAPLOTYPE_MATCHhandlegraph::PathMetadataprivatestatic
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) const =0handlegraph::PathHandleGraphpure virtual
has_node(nid_t node_id) const =0handlegraph::HandleGraphpure virtual
has_path(const std::string &path_name) const =0handlegraph::PathHandleGraphpure virtual
has_previous_step(const step_handle_t &step_handle) const =0handlegraph::PathHandleGraphpure virtual
increment_node_ids(nid_t increment)handlegraph::MutableHandleGraphvirtual
increment_node_ids(long increment)handlegraph::MutableHandleGraphvirtual
is_empty(const path_handle_t &path_handle) consthandlegraph::PathHandleGraphvirtual
LOCUS_MATCH_ANYhandlegraph::PathMetadataprivatestatic
LOCUS_MATCH_NUMERICAL_WITHOUT_HAPLOTYPEhandlegraph::PathMetadataprivatestatic
max_node_id() const =0handlegraph::HandleGraphpure virtual
min_node_id() const =0handlegraph::HandleGraphpure virtual
NO_END_POSITIONhandlegraph::PathMetadatastatic
NO_HAPLOTYPEhandlegraph::PathMetadatastatic
NO_LOCUS_NAMEhandlegraph::PathMetadatastatic
NO_PHASE_BLOCKhandlegraph::PathMetadatastatic
NO_SAMPLE_NAMEhandlegraph::PathMetadatastatic
NO_SUBRANGEhandlegraph::PathMetadatastatic
optimize(bool allow_id_reassignment=true)=0handlegraph::MutableHandleGraphpure virtual
parse_haplotype(const std::string &path_name)handlegraph::PathMetadatastatic
parse_locus_name(const std::string &path_name)handlegraph::PathMetadatastatic
parse_path_name(const std::string &path_name, PathSense &sense, std::string &sample, std::string &locus, size_t &haplotype, size_t &phase_block, subrange_t &subrange)handlegraph::PathMetadatastatic
parse_phase_block(const std::string &path_name)handlegraph::PathMetadatastatic
parse_sample_name(const std::string &path_name)handlegraph::PathMetadatastatic
parse_sense(const std::string &path_name)handlegraph::PathMetadatastatic
parse_subrange(const std::string &path_name)handlegraph::PathMetadatastatic
path_back(const path_handle_t &path_handle) const =0handlegraph::PathHandleGraphpure virtual
path_begin(const path_handle_t &path_handle) const =0handlegraph::PathHandleGraphpure virtual
path_end(const path_handle_t &path_handle) const =0handlegraph::PathHandleGraphpure virtual
path_front_end(const path_handle_t &path_handle) const =0handlegraph::PathHandleGraphpure virtual
PHASE_BLOCK_MATCHhandlegraph::PathMetadataprivatestatic
pop_back_step(const path_handle_t &path_handle)handlegraph::MutablePathHandleGraphvirtual
pop_front_step(const path_handle_t &path_handle)handlegraph::MutablePathHandleGraphvirtual
prepend_step(const path_handle_t &path, const handle_t &to_prepend)=0handlegraph::MutablePathHandleGraphpure virtual
RANGE_END_MATCHhandlegraph::PathMetadataprivatestatic
RANGE_END_SEPARATORhandlegraph::PathMetadataprivatestatic
RANGE_START_MATCHhandlegraph::PathMetadataprivatestatic
RANGE_START_SEPARATORhandlegraph::PathMetadataprivatestatic
RANGE_TERMINATORhandlegraph::PathMetadataprivatestatic
reassign_node_ids(const std::function< nid_t(const nid_t &)> &get_new_id)=0handlegraph::MutableHandleGraphpure virtual
rename_path(const path_handle_t &path_handle, const std::string &new_name)handlegraph::MutablePathHandleGraphvirtual
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
SEPARATORhandlegraph::PathMetadataprivatestatic
set_circularity(const path_handle_t &path, bool circular)=0handlegraph::MutablePathHandleGraphpure virtual
set_id_increment(const nid_t &min_id)=0handlegraph::MutableHandleGraphpure virtual
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
~HandleGraph()=defaulthandlegraph::HandleGraphvirtual
~MutableHandleGraph()=defaulthandlegraph::MutableHandleGraphvirtual
~MutablePathHandleGraph()=defaulthandlegraph::MutablePathHandleGraphvirtual
~MutablePathMetadata()=defaulthandlegraph::MutablePathMetadatavirtual
~MutablePathMutableHandleGraph()=defaulthandlegraph::MutablePathMutableHandleGraphvirtual
~PathHandleGraph()=defaulthandlegraph::PathHandleGraphvirtual
~PathMetadata()=defaulthandlegraph::PathMetadatavirtual