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virtual | ~MutablePathHandleGraph ()=default |
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virtual void | destroy_path (const path_handle_t &path)=0 |
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virtual path_handle_t | create_path_handle (const std::string &name, bool is_circular=false)=0 |
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virtual step_handle_t | append_step (const path_handle_t &path, const handle_t &to_append)=0 |
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virtual step_handle_t | prepend_step (const path_handle_t &path, const handle_t &to_prepend)=0 |
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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 |
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virtual void | set_circularity (const path_handle_t &path, bool circular)=0 |
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Public Member Functions inherited from handlegraph::PathHandleGraph |
virtual | ~PathHandleGraph ()=default |
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virtual size_t | get_path_count () const =0 |
| Returns the number of paths stored in the graph. More...
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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...
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virtual path_handle_t | get_path_handle (const std::string &path_name) const =0 |
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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...
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virtual bool | get_is_circular (const path_handle_t &path_handle) const =0 |
| Look up whether a path is circular. More...
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virtual size_t | get_step_count (const path_handle_t &path_handle) const =0 |
| Returns the number of node steps in the path. More...
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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...
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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...
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virtual step_handle_t | path_begin (const path_handle_t &path_handle) const =0 |
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virtual step_handle_t | path_end (const path_handle_t &path_handle) const =0 |
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virtual step_handle_t | path_back (const path_handle_t &path_handle) const =0 |
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virtual step_handle_t | path_front_end (const path_handle_t &path_handle) const =0 |
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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...
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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...
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virtual step_handle_t | get_next_step (const step_handle_t &step_handle) const =0 |
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virtual step_handle_t | get_previous_step (const step_handle_t &step_handle) const =0 |
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template<typename Iteratee > |
bool | for_each_path_handle (const Iteratee &iteratee) const |
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template<typename Iteratee > |
bool | for_each_step_on_handle (const handle_t &handle, const Iteratee &iteratee) const |
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virtual std::vector< step_handle_t > | steps_of_handle (const handle_t &handle, bool match_orientation=false) const |
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virtual bool | is_empty (const path_handle_t &path_handle) const |
| Returns true if the given path is empty, and false otherwise. More...
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PathForEachSocket | scan_path (const path_handle_t &path) const |
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template<typename Iteratee > |
bool | for_each_step_in_path (const path_handle_t &path, const Iteratee &iteratee) const |
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Public Member Functions inherited from handlegraph::HandleGraph |
virtual | ~HandleGraph ()=default |
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virtual bool | has_node (nid_t node_id) const =0 |
| Method to check if a node exists by ID. More...
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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...
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virtual nid_t | get_id (const handle_t &handle) const =0 |
| Get the ID from a handle. More...
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virtual bool | get_is_reverse (const handle_t &handle) const =0 |
| Get the orientation of a handle. More...
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virtual handle_t | flip (const handle_t &handle) const =0 |
| Invert the orientation of a handle (potentially without getting its ID) More...
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virtual size_t | get_length (const handle_t &handle) const =0 |
| Get the length of a node. More...
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virtual std::string | get_sequence (const handle_t &handle) const =0 |
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virtual size_t | get_node_count () const =0 |
| Return the number of nodes in the graph. More...
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virtual nid_t | min_node_id () const =0 |
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virtual nid_t | max_node_id () const =0 |
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template<typename Iteratee > |
bool | follow_edges (const handle_t &handle, bool go_left, const Iteratee &iteratee) const |
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template<typename Iteratee > |
bool | for_each_handle (const Iteratee &iteratee, bool parallel=false) const |
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virtual size_t | get_degree (const handle_t &handle, bool go_left) const |
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virtual bool | has_edge (const handle_t &left, const handle_t &right) const |
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bool | has_edge (const edge_t &edge) const |
| Convenient wrapper of has_edge for edge_t argument. More...
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virtual size_t | get_edge_count () const |
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virtual size_t | get_total_length () const |
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virtual char | get_base (const handle_t &handle, size_t index) const |
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virtual std::string | get_subsequence (const handle_t &handle, size_t index, size_t size) const |
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handle_t | forward (const handle_t &handle) const |
| Get the locally forward version of a handle. More...
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edge_t | edge_handle (const handle_t &left, const handle_t &right) const |
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handle_t | traverse_edge_handle (const edge_t &edge, const handle_t &left) const |
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template<typename Iteratee > |
bool | for_each_edge (const Iteratee &iteratee, bool parallel=false) const |
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This is the interface for a handle graph with embedded paths where the paths can be modified. Note that if the graph can also be modified, the implementation will also need to inherit from MutableHandleGraph, via the combination MutablePathMutableHandleGraph interface. TODO: This is a very limited interface at the moment. It will probably need to be extended.