#include <mutable_path_deletable_handle_graph.hpp>
Inheritance diagram for handlegraph::MutablePathDeletableHandleGraph:
Public Member Functions | |
| virtual | ~MutablePathDeletableHandleGraph ()=default |
| virtual handle_t | change_sequence (const handle_t &handle, const std::string &sequence) |
 Public Member Functions inherited from handlegraph::MutablePathMutableHandleGraph | |
| virtual | ~MutablePathMutableHandleGraph ()=default |
| Public Member Functions inherited from handlegraph::MutablePathHandleGraph | |
| virtual | ~MutablePathHandleGraph ()=default |
| virtual void | destroy_path (const path_handle_t &path_handle)=0 |
| virtual void | destroy_paths (const std::vector< path_handle_t > &paths) |
| virtual path_handle_t | create_path_handle (const std::string &name, bool is_circular=false)=0 |
| virtual path_handle_t | rename_path (const path_handle_t &path_handle, const std::string &new_name) |
| virtual step_handle_t | append_step (const path_handle_t &path, const handle_t &to_append)=0 |
| virtual step_handle_t | prepend_step (const path_handle_t &path, const handle_t &to_prepend)=0 |
| virtual void | pop_front_step (const path_handle_t &path_handle) |
| virtual void | pop_back_step (const path_handle_t &path_handle) |
| virtual std::pair< step_handle_t, step_handle_t > | rewrite_segment (const step_handle_t &segment_begin, const step_handle_t &segment_end, const std::vector< handle_t > &new_segment)=0 |
| virtual void | set_circularity (const path_handle_t &path, bool circular)=0 |
| Public Member Functions inherited from handlegraph::PathHandleGraph | |
| virtual | ~PathHandleGraph ()=default |
| virtual size_t | get_path_count () const =0 |
| Returns the number of paths stored in the graph. More... | |
| virtual bool | has_path (const std::string &path_name) const =0 |
| Determine if a path name exists and is legal to get a path handle for. More... | |
| virtual path_handle_t | get_path_handle (const std::string &path_name) const =0 |
| virtual std::string | get_path_name (const path_handle_t &path_handle) const =0 |
| Look up the name of a path from a handle to it. More... | |
| virtual bool | get_is_circular (const path_handle_t &path_handle) const =0 |
| Look up whether a path is circular. More... | |
| virtual size_t | get_step_count (const path_handle_t &path_handle) const =0 |
| Returns the number of node steps in the path. More... | |
| virtual size_t | get_step_count (const handle_t &handle) const |
| Returns the number of node steps on a handle. More... | |
| virtual handle_t | get_handle_of_step (const step_handle_t &step_handle) const =0 |
| Get a node handle (node ID and orientation) from a handle to an step on a path. More... | |
| virtual path_handle_t | get_path_handle_of_step (const step_handle_t &step_handle) const =0 |
| Returns a handle to the path that an step is on. More... | |
| virtual step_handle_t | path_begin (const path_handle_t &path_handle) const =0 |
| virtual step_handle_t | path_end (const path_handle_t &path_handle) const =0 |
| virtual step_handle_t | path_back (const path_handle_t &path_handle) const =0 |
| virtual step_handle_t | path_front_end (const path_handle_t &path_handle) const =0 |
| virtual bool | has_next_step (const step_handle_t &step_handle) const =0 |
| Returns true if the step is not the last step in a non-circular path. More... | |
| virtual bool | has_previous_step (const step_handle_t &step_handle) const =0 |
| Returns true if the step is not the first step in a non-circular path. More... | |
| virtual step_handle_t | get_next_step (const step_handle_t &step_handle) const =0 |
| virtual step_handle_t | get_previous_step (const step_handle_t &step_handle) const =0 |
| template<typename Iteratee > | |
| bool | for_each_path_handle (const Iteratee &iteratee) const |
| template<typename Iteratee > | |
| bool | for_each_step_on_handle (const handle_t &handle, const Iteratee &iteratee) const |
| virtual std::vector< step_handle_t > | steps_of_handle (const handle_t &handle, bool match_orientation=false) const |
| virtual bool | is_empty (const path_handle_t &path_handle) const |
| Returns true if the given path is empty, and false otherwise. More... | |
| PathForEachSocket | scan_path (const path_handle_t &path) const |
| template<typename Iteratee > | |
| bool | for_each_step_in_path (const path_handle_t &path, const Iteratee &iteratee) const |
| Public Member Functions inherited from handlegraph::HandleGraph | |
| virtual | ~HandleGraph ()=default |
| virtual bool | has_node (nid_t node_id) const =0 |
| Method to check if a node exists by ID. More... | |
| virtual handle_t | get_handle (const nid_t &node_id, bool is_reverse=false) const =0 |
| Look up the handle for the node with the given ID in the given orientation. More... | |
| virtual nid_t | get_id (const handle_t &handle) const =0 |
| Get the ID from a handle. More... | |
| virtual bool | get_is_reverse (const handle_t &handle) const =0 |
| Get the orientation of a handle. More... | |
| virtual handle_t | flip (const handle_t &handle) const =0 |
| Invert the orientation of a handle (potentially without getting its ID) More... | |
| virtual size_t | get_length (const handle_t &handle) const =0 |
| Get the length of a node. More... | |
| virtual std::string | get_sequence (const handle_t &handle) const =0 |
| virtual size_t | get_node_count () const =0 |
| Return the number of nodes in the graph. More... | |
| virtual nid_t | min_node_id () const =0 |
| virtual nid_t | max_node_id () const =0 |
| template<typename Iteratee > | |
| bool | follow_edges (const handle_t &handle, bool go_left, const Iteratee &iteratee) const |
| template<typename Iteratee > | |
| bool | for_each_handle (const Iteratee &iteratee, bool parallel=false) const |
| virtual size_t | get_degree (const handle_t &handle, bool go_left) const |
| virtual bool | has_edge (const handle_t &left, const handle_t &right) const |
| bool | has_edge (const edge_t &edge) const |
| Convenient wrapper of has_edge for edge_t argument. More... | |
| virtual size_t | get_edge_count () const |
| virtual size_t | get_total_length () const |
| virtual char | get_base (const handle_t &handle, size_t index) const |
| virtual std::string | get_subsequence (const handle_t &handle, size_t index, size_t size) const |
| handle_t | forward (const handle_t &handle) const |
| Get the locally forward version of a handle. More... | |
| edge_t | edge_handle (const handle_t &left, const handle_t &right) const |
| handle_t | traverse_edge_handle (const edge_t &edge, const handle_t &left) const |
| template<typename Iteratee > | |
| bool | for_each_edge (const Iteratee &iteratee, bool parallel=false) const |
| Public Member Functions inherited from handlegraph::PathMetadata | |
| virtual | ~PathMetadata ()=default |
| virtual PathSense | get_sense (const path_handle_t &handle) const |
| What is the given path meant to be representing? More... | |
| virtual std::string | get_sample_name (const path_handle_t &handle) const |
| virtual std::string | get_locus_name (const path_handle_t &handle) const |
| virtual size_t | get_haplotype (const path_handle_t &handle) const |
| virtual size_t | get_phase_block (const path_handle_t &handle) const |
| virtual subrange_t | get_subrange (const path_handle_t &handle) const |
| template<typename Iteratee > | |
| bool | for_each_path_of_sense (const PathSense &sense, const Iteratee &iteratee) const |
| template<typename Iteratee > | |
| bool | for_each_path_of_sample (const std::string &sample, const Iteratee &iteratee) const |
| template<typename Iteratee > | |
| bool | 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) const |
| template<typename Iteratee > | |
| bool | 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) const |
| template<typename Iteratee > | |
| bool | for_each_step_of_sense (const handle_t &visited, const PathSense &sense, const Iteratee &iteratee) const |
| Public Member Functions inherited from handlegraph::MutablePathMetadata | |
| virtual | ~MutablePathMetadata ()=default |
| virtual path_handle_t | 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) |
| Public Member Functions inherited from handlegraph::MutableHandleGraph | |
| virtual | ~MutableHandleGraph ()=default |
| virtual handle_t | create_handle (const std::string &sequence)=0 |
| virtual handle_t | create_handle (const std::string &sequence, const nid_t &id)=0 |
| virtual void | create_edge (const handle_t &left, const handle_t &right)=0 |
| void | create_edge (const edge_t &edge) |
| Convenient wrapper for create_edge. More... | |
| virtual handle_t | apply_orientation (const handle_t &handle)=0 |
| virtual std::vector< handle_t > | divide_handle (const handle_t &handle, const std::vector< size_t > &offsets)=0 |
| std::pair< handle_t, handle_t > | divide_handle (const handle_t &handle, size_t offset) |
| Specialization of divide_handle for a single division point. More... | |
| virtual void | optimize (bool allow_id_reassignment=true)=0 |
| virtual bool | apply_ordering (const std::vector< handle_t > &order, bool compact_ids=false)=0 |
| virtual void | set_id_increment (const nid_t &min_id)=0 |
| virtual void | increment_node_ids (nid_t increment) |
| virtual void | increment_node_ids (long increment) |
| This specialization for long appears to be needed to avoid confusion about nid_t. More... | |
| virtual void | reassign_node_ids (const std::function< nid_t(const nid_t &)> &get_new_id)=0 |
| Public Member Functions inherited from handlegraph::DeletableHandleGraph | |
| virtual | ~DeletableHandleGraph ()=default |
| virtual void | destroy_handle (const handle_t &handle)=0 |
| virtual void | destroy_edge (const handle_t &left, const handle_t &right)=0 |
| virtual handle_t | truncate_handle (const handle_t &handle, bool trunc_left, size_t offset) |
| void | destroy_edge (const edge_t &edge) |
| Convenient wrapper for destroy_edge. More... | |
| virtual void | clear ()=0 |
| Remove all nodes and edges. May also remove all paths, if applicable. More... | |
Additional Inherited Members | |
| Static Public Member Functions inherited from handlegraph::PathMetadata | |
| static PathSense | parse_sense (const std::string &path_name) |
| static std::string | parse_sample_name (const std::string &path_name) |
| static std::string | parse_locus_name (const std::string &path_name) |
| static size_t | parse_haplotype (const std::string &path_name) |
| static size_t | parse_phase_block (const std::string &path_name) |
| static subrange_t | parse_subrange (const std::string &path_name) |
| static void | 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) |
| Decompose a formatted path name into metadata. More... | |
| static std::string | 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) |
| Static Public Attributes inherited from handlegraph::PathMetadata | |
| static const std::string | NO_SAMPLE_NAME = "" |
| static const std::string | NO_LOCUS_NAME = "" |
| static const size_t | NO_HAPLOTYPE = std::numeric_limits<size_t>::max() |
| static const size_t | NO_PHASE_BLOCK = std::numeric_limits<size_t>::max() |
| static const subrange_t | NO_SUBRANGE {PathMetadata::NO_END_POSITION, PathMetadata::NO_END_POSITION} |
| static const offset_t | NO_END_POSITION = std::numeric_limits<offset_t>::max() |
| Protected Member Functions inherited from handlegraph::PathHandleGraph | |
| virtual bool | for_each_path_handle_impl (const std::function< bool(const path_handle_t &)> &iteratee) const =0 |
| virtual bool | for_each_step_on_handle_impl (const handle_t &handle, const std::function< bool(const step_handle_t &)> &iteratee) const =0 |
| Protected Member Functions inherited from handlegraph::HandleGraph | |
| virtual bool | follow_edges_impl (const handle_t &handle, bool go_left, const std::function< bool(const handle_t &)> &iteratee) const =0 |
| virtual bool | for_each_handle_impl (const std::function< bool(const handle_t &)> &iteratee, bool parallel=false) const =0 |
| Protected Member Functions inherited from handlegraph::PathMetadata | |
| virtual bool | 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) const |
| virtual bool | for_each_step_of_sense_impl (const handle_t &visited, const PathSense &sense, const std::function< bool(const step_handle_t &)> &iteratee) const |
Detailed Description
This is the interface for a graph which is deletable and which has paths which are also mutable.
Constructor & Destructor Documentation
◆ ~MutablePathDeletableHandleGraph()
|
virtualdefault |
Member Function Documentation
◆ change_sequence()
|
virtual |
Change the sequence of handle's forward orientation to a new sequence. Returns a (possibly altered) handle to the node with the new sequence. The returned handle has the same orientation as the handle provided as an argument. May invalidate existing handles to the node. Updates paths to follow the new node if called through a class inheriting a MutablePathHandleGraph interface.
Reimplemented from handlegraph::DeletableHandleGraph.
The documentation for this class was generated from the following files:
- deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp
- deps/libhandlegraph/src/mutable_path_deletable_handle_graph.cpp
