#include <source_sink_overlay.hpp>
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| handle_t | from_backing (const handle_t &backing_handle) const |
| | Convert a backing graph handle to our handle to the same node.
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| handle_t | to_backing (const handle_t &our_handle) const |
| | Convert our handle to a backing graph node into a backing graph handle to the same node.
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| bool | is_ours (const handle_t &our_handle) const |
| | Determine if a handle points to an overlay-added node or not.
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Present a HandleGraph that is a backing HandleGraph with all its head nodes connected to a single source node, and all its tail nodes connected to a single sink node.
◆ SourceSinkOverlay()
| vg::SourceSinkOverlay::SourceSinkOverlay |
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const HandleGraph * | backing, |
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size_t | length = 1024, |
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id_t | source_id = 0, |
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id_t | sink_id = 0, |
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bool | break_disconnected = true ) |
Make a new SourceSinkOverlay. The backing graph must not be modified while the overlay exists.
The overlay will project a source node consisting of '#' characters, and a sink node consisting of '$' characters. The lengths of the nodes may be specified, and default to 1024, the max length that GCSA2 supports. The IDs of the nodes will be autodetected from the backing graph's max ID if not specified (or given as 0). If either is specified, both must be specified.
Also breaks into disconnected components with no tips, unless break_disconnected is false. When breaking into such a component, we choose an arbitrary node, link the source node to its start, and link everything that also went to its start to the sink node.
◆ flip()
Invert the orientation of a handle (potentially without getting its ID).
◆ follow_edges_impl()
| bool vg::SourceSinkOverlay::follow_edges_impl |
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const handle_t & | handle, |
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bool | go_left, |
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const function< bool(const handle_t &)> & | iteratee ) const |
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virtual |
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::SourceSinkOverlay::for_each_handle_impl |
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const function< bool(const handle_t &)> & | iteratee, |
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bool | parallel = false ) const |
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Loop over all the nodes in the graph in their local forward orientations, in their internal stored order. Stop if the iteratee returns false.
◆ from_backing()
| handle_t vg::SourceSinkOverlay::from_backing |
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const handle_t & | backing_handle | ) |
const |
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inlineprotected |
Convert a backing graph handle to our handle to the same node.
◆ get_degree()
| size_t vg::SourceSinkOverlay::get_degree |
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const handle_t & | handle, |
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bool | go_left ) const |
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Compute the degree of one side of a handle in O(1) time, if the backing graph also provides this facility in O(1) time. Takes O(n) time otherwise in the returned degree.
◆ get_handle()
| handle_t vg::SourceSinkOverlay::get_handle |
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const id_t & | node_id, |
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bool | is_reverse ) const |
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Look up the handle for the node with the given ID in the given orientation.
◆ get_id()
| id_t vg::SourceSinkOverlay::get_id |
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const handle_t & | handle | ) |
const |
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virtual |
Get the ID from a handle.
◆ get_is_reverse()
| bool vg::SourceSinkOverlay::get_is_reverse |
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const handle_t & | handle | ) |
const |
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Get the orientation of a handle.
◆ get_length()
| size_t vg::SourceSinkOverlay::get_length |
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const handle_t & | handle | ) |
const |
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Get the length of a node.
◆ get_node_count()
| size_t vg::SourceSinkOverlay::get_node_count |
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const |
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Return the number of nodes in the graph.
◆ get_sequence()
| string vg::SourceSinkOverlay::get_sequence |
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const handle_t & | handle | ) |
const |
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virtual |
Get the sequence of a node, presented in the handle's local forward orientation.
◆ get_sink_handle()
| handle_t vg::SourceSinkOverlay::get_sink_handle |
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const |
Expose the handle to the synthetic sink.
◆ get_source_handle()
| handle_t vg::SourceSinkOverlay::get_source_handle |
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const |
Expose the handle to the synthetic source.
◆ get_underlying_handle()
| handle_t vg::SourceSinkOverlay::get_underlying_handle |
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const handle_t & | handle | ) |
const |
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virtual |
Get the handle in the underlying graph that corresponds to the handle in the overlay. Throws an error if called on either the source or sink node
◆ has_node()
| bool vg::SourceSinkOverlay::has_node |
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id_t | node_id | ) |
const |
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Check if a node exists by ID.
◆ is_ours()
| bool vg::SourceSinkOverlay::is_ours |
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const handle_t & | our_handle | ) |
const |
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inlineprotected |
Determine if a handle points to an overlay-added node or not.
◆ max_node_id()
| id_t vg::SourceSinkOverlay::max_node_id |
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const |
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Return the largest ID in the graph.
◆ min_node_id()
| id_t vg::SourceSinkOverlay::min_node_id |
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const |
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Return the smallest ID in the graph.
◆ to_backing()
Convert our handle to a backing graph node into a backing graph handle to the same node.
◆ backing
What backing graph do we overlay?
◆ backing_heads
| unordered_set<handle_t> vg::SourceSinkOverlay::backing_heads |
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protected |
We keep a set of backing graph head handles, in backing graph handle space. This also includes anything else we need to hook up to our source node to break into tipless components.
◆ backing_tails
| unordered_set<handle_t> vg::SourceSinkOverlay::backing_tails |
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And similarly for the tails. These handles read out of their components.
◆ node_length
| size_t vg::SourceSinkOverlay::node_length |
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How long are the projected nodes?
◆ sink_fwd
| const handle_t vg::SourceSinkOverlay::sink_fwd = as_handle(2) |
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◆ sink_id
| id_t vg::SourceSinkOverlay::sink_id |
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What is our projected sink node ID?
◆ sink_rev
| const handle_t vg::SourceSinkOverlay::sink_rev = as_handle(3) |
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◆ source_fwd
| const handle_t vg::SourceSinkOverlay::source_fwd = as_handle(0) |
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◆ source_id
| id_t vg::SourceSinkOverlay::source_id |
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What is our projected source node ID?
◆ source_rev
| const handle_t vg::SourceSinkOverlay::source_rev = as_handle(1) |
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The documentation for this class was generated from the following files:
1.17.0