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| PathSubgraphOverlay (const PathHandleGraph *backing, const unordered_set< nid_t > *node_subset) |
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virtual | ~PathSubgraphOverlay () |
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virtual size_t | get_path_count () const |
| Returns the number of paths stored in the graph. More...
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virtual bool | has_path (const std::string &path_name) const |
| 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 |
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virtual std::string | get_path_name (const path_handle_t &path_handle) const |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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virtual step_handle_t | path_end (const path_handle_t &path_handle) const |
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virtual step_handle_t | path_back (const path_handle_t &path_handle) const |
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virtual step_handle_t | path_front_end (const path_handle_t &path_handle) const |
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virtual bool | has_next_step (const step_handle_t &step_handle) const |
| 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 |
| 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 |
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virtual step_handle_t | get_previous_step (const step_handle_t &step_handle) const |
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| SubgraphOverlay (const HandleGraph *backing, const unordered_set< nid_t > *node_subset) |
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virtual | ~SubgraphOverlay () |
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virtual bool | has_node (nid_t node_id) const |
| 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 |
| 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 |
| Get the ID from a handle. More...
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virtual bool | get_is_reverse (const handle_t &handle) const |
| Get the orientation of a handle. More...
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virtual handle_t | flip (const handle_t &handle) const |
| 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 |
| Get the length of a node. More...
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virtual std::string | get_sequence (const handle_t &handle) const |
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virtual size_t | get_node_count () const |
| Return the number of nodes in the graph. More...
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virtual nid_t | min_node_id () const |
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virtual nid_t | max_node_id () const |
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Public Member Functions inherited from handlegraph::HandleGraph |
virtual | ~HandleGraph ()=default |
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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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Public Member Functions inherited from handlegraph::PathHandleGraph |
virtual | ~PathHandleGraph ()=default |
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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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Present a PathHandleGraph that is a backing HandleGraph but restricted to a subset of nodes.
Warning: we don't yet have a subgraph interface. So we only consider paths from the backing graph that are fully contained in the subgraph.