Struct ChainMap 

pub struct ChainMap {
    pub map: FxHashMap<u32, Chain>,
}

A map of chains

Fields

map: FxHashMap<u32, Chain>

Implementations

impl ChainMap

pub fn new() -> Self

Create a new ChainMap

Returns

• ChainMap

Example

use chaintools::cmap::ChainMap;

let chains = ChainMap::new();

pub fn get(&self, key: &u32) -> Option<&Chain>

Get a chain from the map

Arguments

• key - A chain id

Returns

• Option<&Chain>

Example

use chaintools::cmap::ChainMap;
use chaintools::io::reader::Reader;

let chains = Reader::from_file("file.chain").unwrap();
let chain = chains.get(&123);
println!("{:?}", chain);

>>> Some(Chain { score: 0, refs: ChainHead { size: 0, start: 0, end: 0, strand: 0 },
query: ChainHead { size: 0, start: 0, end: 0, strand: 0 }, alinment: [], id: 123 })

pub fn get_mut(&mut self, key: &u32) -> Option<&mut Chain>

Get a mutable chain from the map

Arguments

• key - A chain id

Returns

• Option<&mut Chain>

Example

use chaintools::cmap::ChainMap;
use chaintools::io::reader::Reader;

let chains = Reader::from_file("file.chain").unwrap();
let chain = chains.get_mut(&123);
println!("{:?}", chain);

>>> Some(Chain { score: 0, refs: ChainHead { size: 0, start: 0, end: 0, strand: 0 },
query: ChainHead { size: 0, start: 0, end: 0, strand: 0 }, alinment: [], id: 123 })

pub fn filter<F>(&self, fc: F) -> Self

where F: Fn(&Chain) -> bool,

Generalized filtering function

Arguments

• fc - A closure that takes a reference to a Chain and returns a boolean

Returns

• ChainMap

Example

use chaintools::cmap::ChainMap;
use chaintools::cmap::chain::Chain;
use chaintools::io::reader::Reader;

let chains = Reader::from_file("file.chain").unwrap();
let filt_chains = chains.filter(|chain| chain.score > 100);

pub fn insert(&mut self, key: u32, value: Chain) -> &mut ChainMap

Insert a chain into a ChainMap

Arguments

• key - A chain id
• value - A Chain

Returns

• &mut ChainMap

Example

use chaintools::cmap::ChainMap;
use chaintools::io::reader::Reader;

let chains = Reader::from_file("file.chain").unwrap();
chains.insert(123, Chain{ score: 0, refs: ChainHead { size: 0, start: 0, end: 0, strand: 0 }, ..., id: 123});

pub fn remove(&mut self, key: &u32) -> &mut ChainMap

Remove a chain from a ChainMap

Arguments

• key - A chain id

Returns

• &mut ChainMap

Example

use chaintools::cmap::ChainMap;
use chaintools::io::reader::Reader;

let chains = Reader::from_file("file.chain").unwrap();
chains.remove(&123);

pub fn len(&self) -> usize

Sort the ChainMap by chain ids

Returns

• usize

Example

use chaintools::cmap::ChainMap;
use chaintools::io::reader::Reader;

let chains = Reader::from_file("file.chain").unwrap();
println!("Number of chains: {:?}", chains.len());

>>> 100

pub fn iter(&self) -> impl Iterator<Item = (&u32, &Chain)>

Iterate over the ChainMap

Returns

• Iterator<Item = (&u32, &Chain)>

Example

use chaintools::cmap::ChainMap;
use chaintools::io::reader::Reader;

let chains = Reader::from_file("file.chain").unwrap();
for (key, chain) in chains.iter() {
  println!("{:?} {:?}", key, chain);
  break;
}

pub fn iter_mut(&mut self) -> impl Iterator<Item = (&u32, &mut Chain)>

Iterate over mut ChainMap

Returns

• Iterator<Item = (&u32, &mut Chain)>

Example

use chaintools::cmap::ChainMap;
use chaintools::io::reader::Reader;

let chains = Reader::from_file("file.chain").unwrap();
for (key, chain) in chains.iter_mut() {
 println!("{:?} {:?}", key, chain);
 break;
}

pub fn keys(&self) -> impl Iterator<Item = &u32>

Iterate over the keys of the ChainMap

Returns

• Iterator<Item = &u32>

Example

use chaintools::cmap::ChainMap;
use chaintools::io::reader::Reader;

let chains = Reader::from_file("file.chain").unwrap();
for key in chains.keys() {
   println!("{:?}", key);
}

pub fn values(&self) -> impl Iterator<Item = &Chain>

Iterate over the values of the ChainMap

Returns

• Iterator<Item = &Chain>

Example

use chaintools::cmap::ChainMap;
use chaintools::io::reader::Reader;

let chains = Reader::from_file("file.chain").unwrap();
for chain in chains.values() {
  println!("{:?}", chain);
}

pub fn values_mut(&mut self) -> impl Iterator<Item = &mut Chain>

Iterate over mut values of the ChainMap

Returns

• Iterator<Item = &mut Chain>

Example

use chaintools::cmap::ChainMap;
use chaintools::io::reader::Reader;

let chains = Reader::from_file("file.chain").unwrap();
for chain in chains.values_mut() {
    println!("{:?}", chain);
    chain.score = 100;
    println!("{:?}", chain);
    break;
 }

pub fn filter_by_score(&self, score: i64) -> Self

Filter the ChainMap by score

Arguments

• score - An i64

Returns

• ChainMap

Example

use chaintools::cmap::ChainMap;
use chaintools::io::reader::Reader;

let chains = Reader::from_file("file.chain").unwrap();
let score = 1000;
let filt_chains = chains.filter_by_score(score);

pub fn filter_ref_by_size(&self, size: u64) -> Self

Filter the ChainMap by reference size

Arguments

• size - A u64

Returns

• ChainMap

Example

use chaintools::cmap::ChainMap;
use chaintools::io::reader::Reader;

let chains = Reader::from_file("file.chain").unwrap();
let size = 1000;
let filt_chains = chains.filter_query_by_size(size);

pub fn filter_query_by_size(&self, size: u64) -> Self

Filter the ChainMap by query size

Arguments

• size - A u64

Returns

• ChainMap

Example

use chaintools::cmap::ChainMap;
use chaintools::io::reader::Reader;

let chains = Reader::from_file("file.chain").unwrap();
let size = 1000;
let filt_chains = chains.filter_query_by_size(size);

pub fn filter_id(&self, ids: Vec<u32>) -> Self

Filter the ChainMap by chain ids

Arguments

• ids - A vector of chain ids

Returns

• ChainMap

Example

use chaintools::cmap::ChainMap;
use chaintools::io::reader::Reader;

let chains = Reader::from_file("file.chain").unwrap();
let ids = vec![123, 456];
let filt_chains = chains.filter(ids).len();
println!("{:?}", filt_chains);

>>> 2

Trait Implementations

impl Clone for ChainMap

fn clone(&self) -> ChainMap

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for ChainMap

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

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for ChainMap

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Serialize for ChainMap

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.