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use fnv::FnvHashMap;
use gfa::{
gfa::{Link, Segment, GFA},
optfields::OptFields,
};
use crate::pathhandlegraph::MutableGraphPaths;
use crate::{
handle::{Edge, Handle, NodeId},
handlegraph::*,
mutablehandlegraph::*,
pathhandlegraph::PathId,
};
use super::{Node, Path};
#[derive(Debug)]
pub struct HashGraph {
pub max_id: NodeId,
pub min_id: NodeId,
pub graph: FnvHashMap<NodeId, Node>,
pub path_id: FnvHashMap<Vec<u8>, PathId>,
pub paths: FnvHashMap<PathId, Path>,
}
impl Default for HashGraph {
fn default() -> HashGraph {
HashGraph {
max_id: NodeId::from(0),
min_id: NodeId::from(std::u64::MAX),
graph: Default::default(),
path_id: Default::default(),
paths: Default::default(),
}
}
}
impl HashGraph {
pub fn new() -> HashGraph {
Default::default()
}
fn add_gfa_segment<'a, 'b, T: OptFields>(
&'a mut self,
seg: &'b Segment<usize, T>,
) {
self.create_handle(&seg.sequence, seg.name as u64);
}
fn add_gfa_link<T: OptFields>(&mut self, link: &Link<usize, T>) {
let left = Handle::new(link.from_segment as u64, link.from_orient);
let right = Handle::new(link.to_segment as u64, link.to_orient);
self.create_edge(Edge(left, right));
}
fn add_gfa_path<T: OptFields>(&mut self, path: &gfa::gfa::Path<usize, T>) {
let path_id = self.create_path(&path.path_name, false).unwrap();
for (name, orient) in path.iter() {
self.path_append_step(path_id, Handle::new(name as u64, orient));
}
}
pub fn from_gfa<T: OptFields>(gfa: &GFA<usize, T>) -> HashGraph {
let mut graph = Self::new();
gfa.segments.iter().for_each(|s| graph.add_gfa_segment(s));
gfa.links.iter().for_each(|l| graph.add_gfa_link(l));
gfa.paths.iter().for_each(|p| graph.add_gfa_path(p));
graph
}
pub fn print_path(&self, path_id: &PathId) {
let path = self.paths.get(&path_id).unwrap();
println!("Path\t{}", path_id.0);
for (ix, handle) in path.nodes.iter().enumerate() {
let node = self.get_node(&handle.id()).unwrap();
if ix != 0 {
print!(" -> ");
}
let seq_str = std::str::from_utf8(&node.sequence).unwrap();
print!("{}", seq_str);
}
println!();
}
pub fn print_occurrences(&self) {
self.handles().for_each(|h| {
let node = self.get_node(&h.id()).unwrap();
let seq_str = std::str::from_utf8(&node.sequence).unwrap();
println!("{} - {:?}", seq_str, node.occurrences);
});
}
pub fn get_node(&self, node_id: &NodeId) -> Option<&Node> {
self.graph.get(node_id)
}
pub fn get_node_unchecked(&self, node_id: &NodeId) -> &Node {
self.graph.get(node_id).unwrap_or_else(|| {
panic!("Tried getting a node that doesn't exist, ID: {:?}", node_id)
})
}
pub fn get_node_mut(&mut self, node_id: &NodeId) -> Option<&mut Node> {
self.graph.get_mut(node_id)
}
pub fn get_path(&self, path_id: &PathId) -> Option<&Path> {
self.paths.get(path_id)
}
pub fn get_path_unchecked(&self, path_id: &PathId) -> &Path {
self.paths
.get(path_id)
.unwrap_or_else(|| panic!("Tried to look up nonexistent path:"))
}
}