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use crate::IntSpan;
use regex::Regex;
use std::collections::{BTreeMap, HashMap};
#[derive(Default, Clone)]
pub struct Range {
name: String,
chr: String,
strand: String,
start: i32,
end: i32,
others: BTreeMap<String, String>,
}
impl Range {
// Immutable accessors
pub fn name(&self) -> &String {
&self.name
}
pub fn chr(&self) -> &String {
&self.chr
}
pub fn strand(&self) -> &String {
&self.strand
}
pub fn start(&self) -> &i32 {
&self.start
}
pub fn end(&self) -> &i32 {
&self.end
}
// Mutable accessors
pub fn strand_mut(&mut self) -> &mut String {
&mut self.strand
}
pub fn new() -> Self {
Self {
name: "".to_string(),
chr: "".to_string(),
strand: "".to_string(),
start: 0,
end: 0,
others: BTreeMap::new(),
}
}
/// Constructed from chr, start and end
///
/// ```
/// # use intspan::Range;
/// let range = Range::from("I", 1, 100);
/// # assert_eq!(*range.chr(), "I");
/// # assert_eq!(*range.start(), 1);
/// # assert_eq!(*range.end(), 100);
/// ```
pub fn from<S>(chr: S, start: i32, end: i32) -> Self
where
S: Into<String>,
{
let s = chr.into();
Self {
name: "".to_string(),
chr: s,
strand: "".to_string(),
start,
end,
others: BTreeMap::new(),
}
}
/// Constructed from string
///
/// ```
/// # use intspan::Range;
/// let range = Range::from_str("I:1-100");
/// # assert_eq!(*range.chr(), "I");
/// # assert_eq!(*range.start(), 1);
/// # assert_eq!(*range.end(), 100);
/// # assert_eq!(range.to_string(), "I:1-100");
/// let range = Range::from_str("I:100");
/// # assert_eq!(*range.chr(), "I");
/// # assert_eq!(*range.start(), 100);
/// # assert_eq!(*range.end(), 100);
/// # assert_eq!(range.to_string(), "I:100");
/// let range = Range::from_str("S288c.I(-):27070-29557");
/// # assert_eq!(*range.name(), "S288c");
/// # assert_eq!(*range.strand(), "-");
/// # assert_eq!(range.to_string(), "S288c.I(-):27070-29557");
/// ```
pub fn from_str<S>(range: S) -> Self
where
S: Into<String>,
{
let s = range.into();
let mut new = Self::new();
new.decode(&s);
new
}
/// To string
///
/// ```
/// # use intspan::Range;
/// let range = Range::from("I", 1, 100);
/// assert_eq!(range.to_string(), "I:1-100");
/// let range = Range::from("I", 100, 100);
/// assert_eq!(range.to_string(), "I:100");
/// ```
pub fn to_string(&self) -> String {
self.encode()
}
/// Valid or not
///
/// ```
/// # use intspan::Range;
/// let range = Range::from("I", 1, 100);
/// assert!(range.is_valid());
/// let range = Range::from_str("I:100");
/// assert!(range.is_valid());
/// let range = Range::from_str("invalid");
/// assert!(!range.is_valid());
/// ```
pub fn is_valid(&self) -> bool {
self.start != 0
}
/// IntSpan
///
/// ```
/// # use intspan::Range;
/// let range = Range::from("I", 1, 100);
/// assert_eq!(range.intspan().to_string(), "1-100");
/// let range = Range::from_str("I:100");
/// assert_eq!(range.intspan().to_string(), "100");
/// ```
pub fn intspan(&self) -> IntSpan {
let mut intspan = IntSpan::new();
intspan.add_pair(self.start, self.end);
intspan
}
fn decode(&mut self, header: &String) {
lazy_static! {
static ref RE: Regex = Regex::new(
r"(?xi)
(?:(?P<name>[\w_]+)\.)?
(?P<chr>[\w/-]+)
(?:\((?P<strand>.+)\))?
[:] # spacer
(?P<start>\d+)
[_\-]? # spacer
(?P<end>\d+)?
",
)
.unwrap();
}
let caps = match RE.captures(header.as_str()) {
Some(x) => x,
None => {
self.chr = header.split(' ').next().unwrap().to_string();
return;
}
};
let dict: HashMap<String, String> = RE
.capture_names()
.flatten()
.filter_map(|n| Some((n.to_string(), caps.name(n)?.as_str().to_string())))
.collect();
for key in dict.keys() {
match key.as_str() {
"name" => self.name = dict.get(key).unwrap().to_owned(),
"chr" => self.chr = dict.get(key).unwrap().to_owned(),
"strand" => self.strand = dict.get(key).unwrap().to_owned(),
"start" => self.start = dict.get(key).unwrap().parse::<i32>().unwrap(),
"end" => self.end = dict.get(key).unwrap().parse::<i32>().unwrap(),
_ => {}
}
}
if self.start != 0 && self.end == 0 {
self.end = self.start;
}
// eprintln!("{:#?}", &dict);
}
fn encode(&self) -> String {
let mut header = String::new();
if !self.name.is_empty() {
header += self.name.as_str();
if !self.chr.is_empty() {
header += ".";
header += self.chr.as_str();
}
} else if !self.chr.is_empty() {
header += self.chr.as_str();
}
if !self.strand.is_empty() {
header += "(";
header += self.strand.as_str();
header += ")";
}
if self.start != 0 {
header += ":";
header += self.start.to_string().as_str();
if self.end != self.start {
header += "-";
header += self.end.to_string().as_str();
}
}
header
}
}
#[test]
fn fa_headers() {
let tests = vec![
("S288c", "S288c"),
("S288c The baker's yeast", "S288c"),
("1:-100", "1:-100"),
("infile_0/1/0_514:19-25", "infile_0/1/0_514:19-25"),
];
for (header, expected) in tests {
eprintln!("{:#?}", header);
let range = Range::from_str(header);
assert_eq!(range.to_string(), expected);
}
}