vg::JoinedSpliceGraph Class Reference
#include <splicing.hpp>
Inheritance diagram for vg::JoinedSpliceGraph:
Public Member Functions | |
| JoinedSpliceGraph (const HandleGraph &parent_graph, const IncrementalSubgraph &left_subgraph, handle_t left_splice_node, size_t left_splice_offset, const IncrementalSubgraph &right_subgraph, handle_t right_splice_node, size_t right_splice_offset) | |
| JoinedSpliceGraph ()=default | |
| ~JoinedSpliceGraph ()=default | |
| pair< size_t, size_t > | translate_node_ids (Path &path) const |
| Specialized interface. | |
| handle_t | left_seed_node () const |
| Get the handle corresponding to the seed node of the left subgraph. | |
| handle_t | right_seed_node () const |
| Get the handle corresponding to the seed node of the right subgraph. | |
| handle_t | left_splice_node () const |
| Get the handle corresponding to the left side of the splice join. | |
| handle_t | right_splice_node () const |
| Get the handle corresponding to the right side of the splice join. | |
| int64_t | min_link_length () const |
| Get the minimum length of a walk from the left seed to the right seed. | |
| int64_t | max_link_length () const |
| Get the maximum length of a walk from the left seed to the right seed. | |
| bool | has_node (id_t node_id) const |
| HandleGraph interface. | |
| handle_t | get_handle (const id_t &node_id, bool is_reverse=false) const |
| Look up the handle for the node with the given ID in the given orientation. | |
| id_t | get_id (const handle_t &handle) const |
| Get the ID from a handle. | |
| bool | get_is_reverse (const handle_t &handle) const |
| Get the orientation of a handle. | |
| handle_t | flip (const handle_t &handle) const |
| Invert the orientation of a handle (potentially without getting its ID). | |
| size_t | get_length (const handle_t &handle) const |
| Get the length of a node. | |
| string | get_sequence (const handle_t &handle) const |
| bool | follow_edges_impl (const handle_t &handle, bool go_left, const function< bool(const handle_t &)> &iteratee) const |
| bool | for_each_handle_impl (const function< bool(const handle_t &)> &iteratee, bool parallel=false) const |
| size_t | get_node_count () const |
| Return the number of nodes in the graph. | |
| id_t | min_node_id () const |
| id_t | max_node_id () const |
| char | get_base (const handle_t &handle, size_t index) const |
| Optional HandleGraph interface. | |
| string | get_subsequence (const handle_t &handle, size_t index, size_t size) const |
Private Member Functions | |
| pair< size_t, size_t > | underlying_interval (const handle_t &handle) const |
Private Attributes | |
| const HandleGraph * | parent_graph |
| const IncrementalSubgraph * | left_subgraph |
| const IncrementalSubgraph * | right_subgraph |
| vector< int64_t > | left_handle_trans |
| vector< int64_t > | right_handle_trans |
| size_t | left_splice_offset |
| size_t | right_splice_offset |
| vector< size_t > | handle_idxs |
| size_t | num_left_handles |
Constructor & Destructor Documentation
◆ JoinedSpliceGraph() [1/2]
| vg::JoinedSpliceGraph::JoinedSpliceGraph | ( | const HandleGraph & | parent_graph, |
| const IncrementalSubgraph & | left_subgraph, | ||
| handle_t | left_splice_node, | ||
| size_t | left_splice_offset, | ||
| const IncrementalSubgraph & | right_subgraph, | ||
| handle_t | right_splice_node, | ||
| size_t | right_splice_offset ) |
◆ JoinedSpliceGraph() [2/2]
|
default |
◆ ~JoinedSpliceGraph()
|
default |
Member Function Documentation
◆ flip()
Invert the orientation of a handle (potentially without getting its ID).
◆ follow_edges_impl()
| bool vg::JoinedSpliceGraph::follow_edges_impl | ( | const handle_t & | handle, |
| bool | go_left, | ||
| const function< bool(const handle_t &)> & | iteratee ) const |
Loop over all the handles to next/previous (right/left) nodes. Passes them to a callback which returns false to stop iterating and true to continue. Returns true if we finished and false if we stopped early.
◆ for_each_handle_impl()
| bool vg::JoinedSpliceGraph::for_each_handle_impl | ( | const function< bool(const handle_t &)> & | iteratee, |
| bool | parallel = false ) const |
Loop over all the nodes in the graph in their local forward orientations, in their internal stored order. Stop if the iteratee returns false. Can be told to run in parallel, in which case stopping after a false return value is on a best-effort basis and iteration order is not defined.
◆ get_base()
| char vg::JoinedSpliceGraph::get_base | ( | const handle_t & | handle, |
| size_t | index ) const |
Optional HandleGraph interface.
Returns one base of a handle's sequence, in the orientation of the handle.
◆ get_handle()
Look up the handle for the node with the given ID in the given orientation.
◆ get_id()
◆ get_is_reverse()
| bool vg::JoinedSpliceGraph::get_is_reverse | ( | const handle_t & | handle | ) | const |
Get the orientation of a handle.
◆ get_length()
| size_t vg::JoinedSpliceGraph::get_length | ( | const handle_t & | handle | ) | const |
Get the length of a node.
◆ get_node_count()
| size_t vg::JoinedSpliceGraph::get_node_count | ( | ) | const |
Return the number of nodes in the graph.
◆ get_sequence()
| string vg::JoinedSpliceGraph::get_sequence | ( | const handle_t & | handle | ) | const |
Get the sequence of a node, presented in the handle's local forward orientation.
◆ get_subsequence()
| string vg::JoinedSpliceGraph::get_subsequence | ( | const handle_t & | handle, |
| size_t | index, | ||
| size_t | size ) const |
Returns a substring of a handle's sequence, in the orientation of the handle. If the indicated substring would extend beyond the end of the handle's sequence, the return value is truncated to the sequence's end.
◆ has_node()
| bool vg::JoinedSpliceGraph::has_node | ( | id_t | node_id | ) | const |
HandleGraph interface.
Method to check if a node exists by ID
◆ left_seed_node()
| handle_t vg::JoinedSpliceGraph::left_seed_node | ( | ) | const |
Get the handle corresponding to the seed node of the left subgraph.
◆ left_splice_node()
| handle_t vg::JoinedSpliceGraph::left_splice_node | ( | ) | const |
Get the handle corresponding to the left side of the splice join.
◆ max_link_length()
| int64_t vg::JoinedSpliceGraph::max_link_length | ( | ) | const |
Get the maximum length of a walk from the left seed to the right seed.
◆ max_node_id()
| id_t vg::JoinedSpliceGraph::max_node_id | ( | ) | const |
Return the largest ID in the graph, or some larger number if the largest ID is unavailable. Return value is unspecified if the graph is empty.
◆ min_link_length()
| int64_t vg::JoinedSpliceGraph::min_link_length | ( | ) | const |
Get the minimum length of a walk from the left seed to the right seed.
◆ min_node_id()
| id_t vg::JoinedSpliceGraph::min_node_id | ( | ) | const |
Return the smallest ID in the graph, or some smaller number if the smallest ID is unavailable. Return value is unspecified if the graph is empty.
◆ right_seed_node()
| handle_t vg::JoinedSpliceGraph::right_seed_node | ( | ) | const |
Get the handle corresponding to the seed node of the right subgraph.
◆ right_splice_node()
| handle_t vg::JoinedSpliceGraph::right_splice_node | ( | ) | const |
Get the handle corresponding to the right side of the splice join.
◆ translate_node_ids()
| pair< size_t, size_t > vg::JoinedSpliceGraph::translate_node_ids | ( | Path & | path | ) | const |
Specialized interface.
Translates an aligned path to the underlying graph of the two incremental subgraphs Also returns the indexes of the left and right splice points. If either is not present, the corresponding index is set to numeric_limits<size_t>::max()
◆ underlying_interval()
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private |
Member Data Documentation
◆ handle_idxs
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private |
◆ left_handle_trans
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private |
◆ left_splice_offset
|
private |
◆ left_subgraph
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private |
◆ num_left_handles
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private |
◆ parent_graph
|
private |
◆ right_handle_trans
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private |
◆ right_splice_offset
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private |
◆ right_subgraph
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private |
The documentation for this class was generated from the following files:
- src/splicing.hpp
- src/splicing.cpp
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