Skip to content

Replace string formatting and appending with write! #20

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
bmesuere wants to merge 1 commit into
base: benchmark/2
Choose a base branch
from
Open

Replace string formatting and appending with write! #20

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
111 changes: 54 additions & 57 deletions src/gene.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
extern crate thiserror;
use thiserror::Error;

use std::io::Write;
use crate::dna::Nuc::{A, C, G, T};
use crate::dna::{trinucleotide, Nuc, ANTI_CODON_CODE, CODON_CODE};

Expand Down Expand Up @@ -40,7 +41,7 @@ impl ReadPrediction {

pub fn meta(&self, buf: &mut Vec<u8>) -> Result<(), GeneError> {
if !self.genes.is_empty() {
buf.append(&mut format!(">{}\n", std::str::from_utf8(&self.head)?).into_bytes())
write!(buf, ">{}\n", std::str::from_utf8(&self.head)?).unwrap();
}
for gene in &self.genes {
gene.meta(buf);
Expand Down Expand Up @@ -87,43 +88,41 @@ pub struct Gene {

impl Gene {
pub fn meta(&self, buf: &mut Vec<u8>) {
buf.append(
&mut format!(
"{}\t{}\t{}\t{}\t{:.6}\tI:{}\tD:{}\n",
self.start,
self.end,
if self.forward_strand { '+' } else { '-' },
self.frame,
self.score,
self.inserted
.iter()
.map(|i: &usize| { format!("{},", i) })
.collect::<String>(),
self.deleted
.iter()
.map(|i: &usize| { format!("{},", i) })
.collect::<String>()
)
.into_bytes(),
);
write!(
buf,
"{}\t{}\t{}\t{}\t{:.6}\tI:{}\tD:{}\n",
self.start,
self.end,
if self.forward_strand { '+' } else { '-' },
self.frame,
self.score,
self.inserted
.iter()
.map(|i: &usize| { format!("{},", i) })
.collect::<String>(),
self.deleted
.iter()
.map(|i: &usize| { format!("{},", i) })
.collect::<String>()
)
.unwrap();
}

pub fn gff(&self, buf: &mut Vec<u8>, head: &str) {
buf.append(
&mut format!(
"{}\tFGS\tCDS\t{}\t{}\t.\t{}\t{}\tID={}_{}_{}_{};product=predicted protein\n",
head,
self.start,
self.end,
if self.forward_strand { '+' } else { '-' },
self.frame - 1,
head,
self.start,
self.end,
if self.forward_strand { '+' } else { '-' }
)
.into_bytes(),
);
write!(
buf,
"{}\tFGS\tCDS\t{}\t{}\t.\t{}\t{}\tID={}_{}_{}_{};product=predicted protein\n",
head,
self.start,
self.end,
if self.forward_strand { '+' } else { '-' },
self.frame - 1,
head,
self.start,
self.end,
if self.forward_strand { '+' } else { '-' }
)
.unwrap();
}

pub fn dna(&self, buf: &mut Vec<u8>, head: &Vec<u8>, formatted: bool) -> Result<(), GeneError> {
Expand All @@ -145,17 +144,16 @@ impl Gene {
.collect(),
};

buf.append(
&mut format!(
">{}_{}_{}_{}\n{}\n",
std::str::from_utf8(head)?,
self.start,
self.end,
if self.forward_strand { '+' } else { '-' },
std::str::from_utf8(&dna)?,
)
.into_bytes(),
);
write!(
buf,
">{}_{}_{}_{}\n{}\n",
std::str::from_utf8(head)?,
self.start,
self.end,
if self.forward_strand { '+' } else { '-' },
std::str::from_utf8(&dna)?,
)
.unwrap();

Ok(())
}
Expand Down Expand Up @@ -202,17 +200,16 @@ impl Gene {
}
}

buf.append(
&mut format!(
">{}_{}_{}_{}\n{}\n",
std::str::from_utf8(head)?,
self.start,
self.end,
if self.forward_strand { '+' } else { '-' },
std::str::from_utf8(&protein)?,
)
.into_bytes(),
);
write!(
buf,
">{}_{}_{}_{}\n{}\n",
std::str::from_utf8(head)?,
self.start,
self.end,
if self.forward_strand { '+' } else { '-' },
std::str::from_utf8(&protein)?,
)
.unwrap();
Ok(())
}
}
Expand Down