Fasta

bdb::traits

Trait Fasta 

Source 
pub trait Fasta: Sized {
    // Required methods
    fn to_fasta<T: Write>(
        &self,
        writer: &mut T,
    ) -> Result<(), Box<dyn StdError>>;
    fn from_fasta<T: BufRead>(reader: &mut T) -> Result<Self, Box<dyn StdError>>;

    // Provided methods
    fn estimate_fasta_size(&self) -> usize { ... }
    fn to_fasta_string(&self) -> Result<String, Box<dyn StdError>> { ... }
    fn to_fasta_file<P: AsRef<Path>>(
        &self,
        path: P,
    ) -> Result<(), Box<dyn StdError>> { ... }
    fn from_fasta_string(text: &str) -> Result<Self, Box<dyn StdError>> { ... }
    fn from_fasta_file<P: AsRef<Path>>(
        path: P,
    ) -> Result<Self, Box<dyn StdError>> { ... }
}
Expand description

Serialize to and from FASTA.

§Serialized Format

>sp|P46406|G3P_RABIT Glyceraldehyde-3-phosphate dehydrogenase OS=Oryctolagus cuniculus GN=GAPDH PE=1 SV=3
MVKVGVNGFGRIGRLVTRAAFNSGKVDVVAINDPFIDLHYMVYMFQYDSTHGKFHGTVKA
ENGKLVINGKAITIFQERDPANIKWGDAGAEYVVESTGVFTTMEKAGAHLKGGAKRVIIS
APSADAPMFVMGVNHEKYDNSLKIVSNASCTTNCLAPLAKVIHDHFGIVEGLMTTVHAIT
ATQKTVDGPSGKLWRDGRGAAQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTPNVSV
VDLTCRLEKAAKYDDIKKVVKQASEGPLKGILGYTEDQVVSCDFNSATHSSTFDAGAGIA
LNDHFVKLISWYDNEFGYSNRVVDLMVHMASKE

Required Methods§

Source

fn to_fasta<T: Write>(&self, writer: &mut T) -> Result<(), Box<dyn StdError>>

Export model to FASTA.

Note that many small writers are made to the writer, so the writer should be buffered.

Source

fn from_fasta<T: BufRead>(reader: &mut T) -> Result<Self, Box<dyn StdError>>

Import model from FASTA.

Provided Methods§

Source

fn estimate_fasta_size(&self) -> usize

Estimate the size of the resulting FASTA output to avoid reallocations.

Source

fn to_fasta_string(&self) -> Result<String, Box<dyn StdError>>

Export model to FASTA string.

Source

fn to_fasta_file<P: AsRef<Path>>( &self, path: P, ) -> Result<(), Box<dyn StdError>>

Export model to FASTA output file.

Source

fn from_fasta_string(text: &str) -> Result<Self, Box<dyn StdError>>

Import model from FASTA string.

Source

fn from_fasta_file<P: AsRef<Path>>(path: P) -> Result<Self, Box<dyn StdError>>

Import model from FASTA file.

Dyn Compatibility§

This trait is not dyn compatible.

In older versions of Rust, dyn compatibility was called "object safety", so this trait is not object safe.

Implementors§