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pub mod comment;
pub mod evidence;
pub mod feature;
pub mod feature_location;
pub mod gene;
pub mod gene_location;
pub mod organism;
pub mod protein;
pub mod reference;
pub mod sequence;
mod db_reference;
mod keyword;
mod molecule;
mod property;
pub use self::db_reference::DbReference;
pub use self::keyword::Keyword;
pub use self::property::Property;
pub use self::molecule::Molecule;
use std::collections::HashSet;
use std::io::BufRead;
use std::str::FromStr;
use bytes::Bytes;
use quick_xml::Reader;
use quick_xml::events::BytesStart;
use crate::error::Error;
use crate::parser::FromXml;
use crate::parser::utils::attributes_to_hashmap;
use self::comment::Comment;
use self::evidence::Evidence;
use self::sequence::Sequence;
use self::feature::Feature;
use self::gene::Gene;
use self::gene_location::GeneLocation;
use self::organism::Organism;
use self::reference::Reference;
use self::protein::Protein;
use self::protein::ProteinExistence;
#[derive(Debug, Clone)]
pub struct Entry {
pub dataset: Dataset,
pub accessions: Vec<String>,
pub names: Vec<String>,
pub protein: Protein,
pub genes: Vec<Gene>,
pub organism: Organism,
pub organism_hosts: Vec<Organism>,
pub gene_location: Vec<GeneLocation>,
pub references: Vec<Reference>,
pub comments: Vec<Comment>,
pub db_references: Vec<DbReference>,
pub protein_existence: ProteinExistence,
pub keywords: Vec<Keyword>,
pub features: Vec<Feature>,
pub evidences: Vec<Evidence>,
pub sequence: Sequence,
}
impl Entry {
pub fn new(dataset: Dataset) -> Self {
Entry {
dataset,
accessions: Default::default(),
names: Default::default(),
protein: Default::default(),
genes: Default::default(),
organism: Default::default(),
organism_hosts: Default::default(),
gene_location: Default::default(),
references: Default::default(),
comments: Default::default(),
db_references: Default::default(),
protein_existence: Default::default(),
keywords: Default::default(),
features: Default::default(),
sequence: Default::default(),
evidences: Default::default(),
}
}
}
impl FromXml for Entry {
fn from_xml<B: BufRead>(
event: &BytesStart,
reader: &mut Reader<B>,
buffer: &mut Vec<u8>
) -> Result<Self, Error> {
debug_assert_eq!(event.local_name(), b"entry");
let attr = attributes_to_hashmap(event)?;
let dataset = match attr.get(&b"dataset"[..]).map(|a| &*a.value) {
Some(b"Swiss-Prot") => Dataset::SwissProt,
Some(b"TrEMBL") => Dataset::TrEmbl,
None => return Err(Error::MissingAttribute("dataset", "entry")),
Some(other) => return Err(Error::invalid_value("dataset", "entry", String::from_utf8_lossy(other)))
};
let mut entry = Entry::new(dataset);
parse_inner!{event, reader, buffer,
b"accession" => {
entry.accessions.push(reader.read_text(b"accession", buffer)?);
},
b"name" => {
entry.names.push(reader.read_text(b"name", buffer)?);
},
e @ b"protein" => {
entry.protein = FromXml::from_xml(&e, reader, buffer)?
},
e @ b"gene" => {
entry.genes.push(FromXml::from_xml(&e, reader, buffer)?);
},
e @ b"organism" => {
entry.organism = FromXml::from_xml(&e, reader, buffer)?;
},
e @ b"organismHost" => {
entry.organism_hosts.push(FromXml::from_xml(&e, reader, buffer)?);
},
e @ b"reference" => {
entry.references.push(FromXml::from_xml(&e, reader, buffer)?);
},
e @ b"comment" => {
entry.comments.push(FromXml::from_xml(&e, reader, buffer)?);
},
e @ b"dbReference" => {
entry.db_references.push(FromXml::from_xml(&e, reader, buffer)?);
},
e @ b"proteinExistence" => {
entry.protein_existence = FromXml::from_xml(&e, reader, buffer)?;
},
e @ b"keyword" => {
entry.keywords.push(FromXml::from_xml(&e, reader, buffer)?);
},
e @ b"feature" => {
entry.features.push(FromXml::from_xml(&e, reader, buffer)?);
},
e @ b"evidence" => {
entry.evidences.push(FromXml::from_xml(&e, reader, buffer)?);
},
e @ b"sequence" => {
entry.sequence = Sequence::from_xml(&e, reader, buffer)?;
},
e @ b"geneLocation" => {
entry.gene_location.push(FromXml::from_xml(&e, reader, buffer)?);
}
}
Ok(entry)
}
}
#[derive(Debug, Clone)]
pub enum Dataset {
SwissProt,
TrEmbl,
}