Struct fastobo::ast::OboDoc

pub struct OboDoc { /* fields omitted */ }

A complete OBO document in format version 1.4.

Methods

impl OboDoc

Constructors and builder methods.

Parser

Use from_file to parse a file on the local filesystem, or from_stream to parse a BufRead implementor (BufRead is needed instead of Read as the parser is line-based):

let doc1 = OboDoc::from_file("tests/data/ms.obo").unwrap();

// This is equivalent to (but with the file path set in eventual errors):
let mut r = BufReader::new(File::open("tests/data/ms.obo").unwrap());
let doc2 = OboDoc::from_stream(&mut r).unwrap();

assert_eq!(doc1, doc2);

Builder Pattern

The builder pattern makes it easy to create an OboDoc from an interator of EntityFrame, in order to add an HeaderFrame after all the entities where collected:

use std::iter::FromIterator;

let entities = vec![TermFrame::new(ClassIdent::from(PrefixedIdent::new("TEST", "001")))];
let doc = OboDoc::from_iter(entities.into_iter())
    .and_header(HeaderFrame::from(HeaderClause::FormatVersion("1.4".into())));

pub fn new() -> Self

Create a new empty OBO document.

pub fn with_header(header: HeaderFrame) -> Self

Create a new OBO document with the provided frame.

pub fn and_header(self, header: HeaderFrame) -> Self

Use the provided frame as the header of the OBO document.

pub fn with_entities(entities: Vec<EntityFrame>) -> Self

Create a new OBO document with the provided entity frames.

pub fn and_entities(self, entities: Vec<EntityFrame>) -> Self

Use the provided entity frames as the content of the OBO document.

pub fn from_stream<B>(stream: &mut B) -> Result<Self> where
    B: BufRead, 

Consume a buffered stream containing an OBO document into an AST.

pub fn from_file<P>(path: P) -> Result<Self> where
    P: AsRef<Path>, 

Read an OBO file located somwhere in the filesystem.

impl OboDoc

pub fn header(&self) -> &HeaderFrame

Get a reference to the header of the OBO document.

pub fn header_mut(&mut self) -> &mut HeaderFrame

Get a mutable reference to the header of the OBO document.

pub fn entities(&self) -> &Vec<EntityFrame>

Get a reference to the entities of the OBO document.

pub fn entities_mut(&mut self) -> &mut Vec<EntityFrame>

Get a reference to the entities of the OBO document.

Trait Implementations

impl<'i> FromPair<'i> for OboDoc

const RULE: Rule

unsafe fn from_pair_unchecked(pair: Pair<'i, Rule>) -> Result<Self>

Create a new instance from a Pair without checking the rule.

fn from_pair(pair: Pair<'i, Rule>) -> Result<Self, Error>

Create a new instance from a Pair.

impl Orderable for OboDoc

fn sort(&mut self)

Sort the document in the right serialization order.

fn is_sorted(&self) -> bool

Check if the document is sorted in the right serialization order.

impl OboSemantics for OboDoc

Additional methods for OboDoc that can be used to edit the syntax tree.

fn assign_namespaces(&mut self) -> Result<(), CardinalityError>

Assign the ontology default namespace to all frames without one.

fn treat_xrefs(&mut self)

Process macros in the header frame, adding clauses to relevant entities.

impl AsRef<[EntityFrame]> for OboDoc

fn as_ref(&self) -> &[EntityFrame]

Performs the conversion.

impl AsRef<Vec<EntityFrame>> for OboDoc

fn as_ref(&self) -> &Vec<EntityFrame>

Performs the conversion.

impl AsMut<Vec<EntityFrame>> for OboDoc

fn as_mut(&mut self) -> &mut Vec<EntityFrame>

Performs the conversion.

impl PartialEq<OboDoc> for OboDoc

fn eq(&self, other: &OboDoc) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &OboDoc) -> bool

This method tests for !=.

impl Eq for OboDoc

impl Clone for OboDoc

fn clone(&self) -> OboDoc

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Default for OboDoc

fn default() -> OboDoc

Returns the "default value" for a type.

impl Hash for OboDoc

fn hash<__H: Hasher>(&self, state: &mut __H)

Feeds this value into the given [Hasher].

fn hash_slice<H>(data: &[Self], state: &mut H) where
    H: Hasher, 

Feeds a slice of this type into the given [Hasher].

impl Debug for OboDoc

fn fmt(&self, f: &mut Formatter) -> Result

Formats the value using the given formatter.

impl Display for OboDoc

fn fmt(&self, f: &mut Formatter) -> FmtResult

Formats the value using the given formatter.

impl FromStr for OboDoc

type Err = Error

The associated error which can be returned from parsing.

fn from_str(s: &str) -> Result<Self>

Parses a string s to return a value of this type.

impl<E> FromIterator<E> for OboDoc where
    E: Into<EntityFrame>, 

fn from_iter<T>(iter: T) -> Self where
    T: IntoIterator<Item = E>, 

Creates a value from an iterator.