Struct NCGfa 

pub struct NCGfa<T: OptFields> {
    pub header: Header,
    pub nodes: Vec<NCNode<T>>,
    pub paths: Vec<NCPath>,
    pub edges: Option<Vec<NCEdge<T>>>,
    pub mapper: Vec<String>,
}

The graph contains of nodes, path and edges. NCGfa = NumericCompactGfa This is a compact graph representation of the GFA file.

Comment: Implementation here are much faster and do include some derivates of parser and data structures that are not parsing the whole file and/or are faster with the downside of more memory.

Fields

header: Header

nodes: Vec<NCNode<T>>

paths: Vec<NCPath>

edges: Option<Vec<NCEdge<T>>>

mapper: Vec<String>

Implementations

impl<T: OptFields> NCGfa<T>

pub fn new() -> Self

NGraph constructor

Example

use gfa_reader::NCGfa;
let graph: NCGfa<()> = NCGfa::new();

pub fn parse_gfa_file_direct(&mut self, file_name: &str, edge: bool)

Read the graph from a file

Example

use gfa_reader::Gfa;
let mut graph = Gfa::new();
graph.parse_gfa_file("/path/to/graph");
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pub fn parse_gfa_file_and_convert(&mut self, file_name: &str, edges: bool)

Read the graph from a file

Example

use gfa_reader::Gfa;
let mut graph = Gfa::new();
graph.parse_gfa_file("/path/to/graph");
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pub fn make_mapper(&mut self, graph: &Gfa<T>) -> HashMap<String, usize>

Creat a map from string node id -> numeric node id

pub fn convert_with_mapper( &mut self, mapper: HashMap<String, usize>, graph: &Gfa<T>, )

Convert the “old” graph with the mapper

Using the mapper from “make_mapper”

pub fn get_old_node(&self, node_id: &usize) -> &String

Get original (string) node

pub fn to_file(self, file_name: &str)

Write the graph to a file

pub fn check_numeric(&self) -> bool

Check if the graph is really numeric

pub fn remove_mapper(&mut self)

Remove the mapper if not needed

Trait Implementations

impl<T: Clone + OptFields> Clone for NCGfa<T>

fn clone(&self) -> NCGfa<T>

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl<T: Debug + OptFields> Debug for NCGfa<T>

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.