vg
tools for working with variation graphs
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#include <path_handle_graph.hpp>
Public Member Functions | |
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 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 |
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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 |
Protected Member Functions | |
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 |
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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 |
This is the interface for a handle graph that stores embedded paths.
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virtualdefault |
bool handlegraph::PathHandleGraph::for_each_path_handle | ( | const Iteratee & | iteratee | ) | const |
Execute a function on each path_handle_t in the graph. If it returns bool, and it returns false, stop iteration. Returns true if we finished and false if we stopped early.
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protectedpure virtual |
Execute a function on each path in the graph. If it returns false, stop iteration. Returns true if we finished and false if we stopped early.
Implemented in xg::XG, bdsg::PackedGraph, bdsg::HashGraph, vg::PathSubgraphOverlay, bdsg::ODGI, and vg::MemoizingGraph.
bool handlegraph::PathHandleGraph::for_each_step_in_path | ( | const path_handle_t & | path, |
const Iteratee & | iteratee | ||
) | const |
Loop over all the steps (step_handle_t) along a path. In a non-circular path, iterates from first through last step. In a circular path, iterates from the step returned by path_begin forward around to the step immediately before it. If the iteratee returns bool, and it returns false, stop. Returns true if we finished and false if we stopped early.
bool handlegraph::PathHandleGraph::for_each_step_on_handle | ( | const handle_t & | handle, |
const Iteratee & | iteratee | ||
) | const |
Execute a function on each step (step_handle_t) of a handle in any path. If it returns bool and returns false, stop iteration. Returns true if we finished and false if we stopped early.
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protectedpure virtual |
Execute a function on each step of a handle in any path. If it returns false, stop iteration. Returns true if we finished and false if we stopped early.
Implemented in xg::XG, vg::PathSubgraphOverlay, bdsg::ODGI, and vg::MemoizingGraph.
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pure virtual |
Get a node handle (node ID and orientation) from a handle to an step on a path.
Implemented in xg::XG, bdsg::PackedGraph, bdsg::HashGraph, bdsg::ODGI, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.
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pure virtual |
Look up whether a path is circular.
Implemented in xg::XG, bdsg::ODGI, bdsg::PackedGraph, bdsg::HashGraph, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.
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pure virtual |
Returns a handle to the next step on the path. If the given step is the final step of a non-circular path, this method has undefined behavior. In a circular path, the "last" step will loop around to the "first" step.
Implemented in xg::XG, bdsg::PackedGraph, bdsg::HashGraph, bdsg::ODGI, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.
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pure virtual |
Returns the number of paths stored in the graph.
Implemented in xg::XG, bdsg::ODGI, bdsg::PackedGraph, bdsg::HashGraph, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.
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pure virtual |
Look up the path handle for the given path name. The path with that name must exist.
Implemented in xg::XG, bdsg::PackedGraph, bdsg::HashGraph, bdsg::ODGI, vg::PathSubgraphOverlay, and vg::MemoizingGraph.
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pure virtual |
Returns a handle to the path that an step is on.
Implemented in xg::XG, bdsg::PackedGraph, bdsg::ODGI, bdsg::HashGraph, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.
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pure virtual |
Look up the name of a path from a handle to it.
Implemented in xg::XG, bdsg::PackedGraph, bdsg::HashGraph, vg::VG, bdsg::ODGI, vg::PathSubgraphOverlay, and vg::MemoizingGraph.
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pure virtual |
Returns a handle to the previous step on the path. If the given step is the first step of a non-circular path, this method has undefined behavior. In a circular path, it will loop around from the "first" step (i.e. the one returned by path_begin) to the "last" step.
Implemented in xg::XG, bdsg::PackedGraph, bdsg::HashGraph, bdsg::ODGI, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.
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pure virtual |
Returns the number of node steps in the path.
Implemented in xg::XG, bdsg::PackedGraph, bdsg::HashGraph, vg::VG, bdsg::ODGI, vg::PathSubgraphOverlay, and vg::MemoizingGraph.
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pure virtual |
Returns true if the step is not the last step in a non-circular path.
Implemented in xg::XG, bdsg::PackedGraph, bdsg::ODGI, bdsg::HashGraph, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.
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pure virtual |
Determine if a path name exists and is legal to get a path handle for.
Implemented in xg::XG, bdsg::PackedGraph, bdsg::HashGraph, bdsg::ODGI, vg::PathSubgraphOverlay, and vg::MemoizingGraph.
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pure virtual |
Returns true if the step is not the first step in a non-circular path.
Implemented in xg::XG, bdsg::PackedGraph, bdsg::ODGI, bdsg::HashGraph, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.
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virtual |
Returns true if the given path is empty, and false otherwise.
Reimplemented in bdsg::ODGI, and vg::MemoizingGraph.
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pure virtual |
Get a handle to the last step, which will be an arbitrary step in a circular path that we consider "last" based on our construction of the path. If the path is empty then the implementation must return the same value as path_front_end().
Implemented in xg::XG, bdsg::PackedGraph, bdsg::HashGraph, bdsg::ODGI, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.
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pure virtual |
Get a handle to the first step, which will be an arbitrary step in a circular path that we consider "first" based on our construction of the path. If the path is empty, then the implementation must return the same value as path_end().
Implemented in xg::XG, bdsg::PackedGraph, bdsg::HashGraph, bdsg::ODGI, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.
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pure virtual |
Get a handle to a fictitious position past the end of a path. This position is returned by get_next_step for the final step in a path in a non-circular path. Note: get_next_step will NEVER return this value for a circular path.
Implemented in xg::XG, bdsg::PackedGraph, bdsg::HashGraph, bdsg::ODGI, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.
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pure virtual |
Get a handle to a fictitious position before the beginning of a path. This position is return by get_previous_step for the first step in a path in a non-circular path. Note: get_previous_step will NEVER return this value for a circular path.
Implemented in xg::XG, bdsg::PackedGraph, bdsg::HashGraph, bdsg::ODGI, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.
PathForEachSocket handlegraph::PathHandleGraph::scan_path | ( | const path_handle_t & | path | ) | const |
Returns a class with an STL-style iterator interface that can be used directly in a for each loop like: for (handle_t handle : graph->scan_path(path)) { }
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virtual |
Returns a vector of all steps of a node on paths. Optionally restricts to steps that match the handle in orientation.
Reimplemented in bdsg::ODGI, and vg::MemoizingGraph.