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use core::io::{stdin,Reader,ReaderUtil};
use str = core::str;
const EOF: char = -1 as char;
struct FASTAReader {
in: Reader,
priv peeked: char,
}
impl FASTAReader {
static fn new() -> FASTAReader {
FASTAReader { in: stdin(), peeked: EOF }
}
fn read_line(&mut self) -> ~str {
let mut line = self.in.read_line();
if self.peeked != '>' {
str::unshift_char(&mut line, self.peeked);
}
self.peeked = self.in.read_char();
line
}
fn read_sequence(&mut self) -> (~str, ~str) {
if self.peeked == EOF {
self.peeked = self.in.read_char();
}
let name = self.read_line();
let mut dna = ~"";
while !self.in.eof() && self.peeked != '>' {
let line = self.read_line();
str::push_str(&mut dna, line);
}
(name, dna)
}
pub fn each_sequence(&mut self, cb: &fn(~str, ~str) -> bool) {
while !self.in.eof() {
let (name, dna) = self.read_sequence();
cb(name, dna);
}
}
pub fn sequences(&mut self) -> (~[~str], ~[~str]) {
let mut names = ~[];
let mut dnas = ~[];
for self.each_sequence |name, dna| {
names.push(name);
dnas.push(dna);
}
(names, dnas)
}
}
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