#include <mutable_handle_graph.hpp>
Public Member Functions | |
| 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::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 |
Additional Inherited Members | |
| 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 |
Detailed Description
This is the interface for a handle graph that supports addition of new graph material.
Constructor & Destructor Documentation
◆ ~MutableHandleGraph()
|
virtualdefault |
Member Function Documentation
◆ apply_ordering()
|
pure virtual |
Reorder the graph's internal structure to match that given. This sets the order that is used for iteration in functions like for_each_handle. If compact_ids is true, may (but will not necessarily) compact the id space of the graph to match the ordering, from 1->|ordering|. In other cases, node IDs will be preserved. This may be a no-op in the case of graph implementations that do not have any mechanism to maintain an ordering. This may invalidate outstanding handles. Returns true if node IDs actually were adjusted to match the given order, and false if they remain unchanged.
Implemented in vg::VG.
◆ apply_orientation()
|
pure virtual |
Alter the node that the given handle corresponds to so the orientation indicated by the handle becomes the node's local forward orientation. Rewrites all edges pointing to the node and the node's sequence to reflect this. Invalidates all handles to the node (including the one passed). Returns a new, valid handle to the node in its new forward orientation. Note that it is possible for the node's ID to change. Does not update any stored paths. May change the ordering of the underlying graph.
Implemented in vg::VG.
◆ create_edge() [1/2]
|
inline |
Convenient wrapper for create_edge.
◆ create_edge() [2/2]
|
pure virtual |
Create an edge connecting the given handles in the given order and orientations. Ignores existing edges.
Implemented in vg::VG.
◆ create_handle() [1/2]
|
pure virtual |
Create a new node with the given sequence and return the handle. The sequence may not be empty.
◆ create_handle() [2/2]
|
pure virtual |
Create a new node with the given id and sequence, then return the handle. The sequence may not be empty. The ID must be strictly greater than 0.
◆ divide_handle() [1/2]
|
pure virtual |
Split a handle's underlying node at the given offsets in the handle's orientation. Returns all of the handles to the parts. Other handles to the node being split may be invalidated. The split pieces stay in the same local forward orientation as the original node, but the returned handles come in the order and orientation appropriate for the handle passed in. Updates stored paths. This invalidates the passed handles, but not other handles.
◆ divide_handle() [2/2]
|
inline |
Specialization of divide_handle for a single division point.
◆ increment_node_ids() [1/2]
|
virtual |
This specialization for long appears to be needed to avoid confusion about nid_t.
◆ increment_node_ids() [2/2]
|
virtual |
Add the given value to all node IDs. Has a default implementation in terms of reassign_node_ids, but can be implemented more efficiently in some graphs.
Reimplemented in vg::VG.
◆ optimize()
|
pure virtual |
Adjust the representation of the graph in memory to improve performance. Optionally, allow the node IDs to be reassigned to further improve performance. Note: Ideally, this method is called one time once there is expected to be few graph modifications in the future. This may invalidate outstanding handles.
Implemented in vg::VG.
◆ reassign_node_ids()
|
pure virtual |
Renumber all node IDs using the given function, which, given an old ID, returns the new ID. Modifies the graph in place. Invalidates all outstanding handles. If the graph supports paths, they also must be updated. The mapping function may return 0. In this case, the input ID will remain unchanged. The mapping function should not return any ID for which it would return 0.
Implemented in vg::VG.
◆ set_id_increment()
|
pure virtual |
Set a minimum id to increment the id space by, used as a hint during construction. May have no effect on a backing implementation.
Implemented in vg::VG.
The documentation for this class was generated from the following files:
- deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp
- deps/libhandlegraph/src/mutable_handle_graph.cpp
