Struct fastobo::ast::OboDoc

pub struct OboDoc { /* fields omitted */ }

A complete OBO document in format version 1.4.

Implementations

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 = fastobo::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 = fastobo::from_reader(&mut r).unwrap();

// FIXME: threaded parser may not maintain ordering YET
// 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(Box::new("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.

impl OboDoc

Shared and mutable getters.

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.

pub fn is_empty(&self) -> bool

Check whether or not the document is empty.

An empty document has no header clauses and no entity frames.

impl OboDoc

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

The OBO 1.4 semantics are used to process header macros or to add the default OBO namespace to all the frames of the document.

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

Assign the ontology default namespace to all frames without one.

This function will not check the cardinality of namespace clauses in entity frames: it will only add a single namespace clause to all frames that have none.

Errors

• CardinalityError::MissingClause: if the header frame does not contain any default namespace definition.
• CardinalityError::DuplicateClauses if the header frame does contain more than one default namespace definition.

Example

let mut doc = OboDoc::from_str(
"default-namespace: TST

[Term]
id: TST:01

[Term]
id: PATO:0000001
namespace: quality
").unwrap();

doc.assign_namespaces().unwrap();

assert_eq!(doc.to_string(),
"default-namespace: TST

[Term]
id: TST:01
namespace: TST

[Term]
id: PATO:0000001
namespace: quality
");

pub fn treat_xrefs(&mut self)

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

Header macros are used to expand an ontology by overloading the actual semantics of xref clauses contained in several entity frames. In case the translated clauses are already present in the document, they won't be added a second time.

The following implicit macros will be processed even if they are not part of the document:

• treat-xrefs-as-equivalent: RO
• treat-xrefs-as-equivalent: BFO

Note

After processing the document, neither the original frame xrefs nor the treat-xrefs header clauses will be removed from the AST.

See also

• Header Macro Translation section of the syntax and semantics guide.

pub fn is_fully_labeled(&self) -> bool

Check if the OBO document is fully labeled.

An OBO ontology is fully labeled if every frame has exactly one name clause. This is equivalent to the definition in the OBO specification if we suppose an invalid OBO document is never fully labeled.

Trait Implementations

impl AsMut<Vec<EntityFrame, Global>> for OboDoc

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

Performs the conversion.

impl AsRef<[EntityFrame]> for OboDoc

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

Performs the conversion.

impl AsRef<Vec<EntityFrame, Global>> for OboDoc

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

Performs the conversion.

impl Clone for OboDoc

fn clone(&self) -> OboDoc

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for OboDoc

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

Formats the value using the given formatter.

impl Default for OboDoc

fn default() -> OboDoc

Returns the "default value" for a type.

impl Display for OboDoc

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

Formats the value using the given formatter.

impl Eq for OboDoc

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.

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

const RULE: Rule

The production rule the pair is expected to be obtained from.

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

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

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

Create a new instance from a Pair.

impl FromStr for OboDoc

type Err = SyntaxError

The associated error which can be returned from parsing.

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

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

impl Hash for OboDoc

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

Feeds this value into the given Hasher.

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

Feeds a slice of this type into the given Hasher.

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 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 StructuralEq for OboDoc

impl StructuralPartialEq for OboDoc

impl<B: BufRead> TryFrom<&'_ mut SequentialParser<B>> for OboDoc

type Error = Error

The type returned in the event of a conversion error.

fn try_from(parser: &mut SequentialParser<B>) -> Result<Self, Self::Error>

Performs the conversion.

impl<B: BufRead> TryFrom<&'_ mut ThreadedParser<B>> for OboDoc

type Error = Error

The type returned in the event of a conversion error.

fn try_from(reader: &mut ThreadedParser<B>) -> Result<Self, Self::Error>

Performs the conversion.

impl<B: BufRead> TryFrom<Box<SequentialParser<B>, Global>> for OboDoc

type Error = Error

The type returned in the event of a conversion error.

fn try_from(reader: Box<SequentialParser<B>>) -> Result<Self, Self::Error>

Performs the conversion.

impl<B: BufRead> TryFrom<Box<ThreadedParser<B>, Global>> for OboDoc

type Error = Error

The type returned in the event of a conversion error.

fn try_from(reader: Box<ThreadedParser<B>>) -> Result<Self, Self::Error>

Performs the conversion.

impl<B: BufRead> TryFrom<SequentialParser<B>> for OboDoc

type Error = Error

The type returned in the event of a conversion error.

fn try_from(parser: SequentialParser<B>) -> Result<Self, Self::Error>

Performs the conversion.

impl<B: BufRead> TryFrom<ThreadedParser<B>> for OboDoc

type Error = Error

The type returned in the event of a conversion error.

fn try_from(reader: ThreadedParser<B>) -> Result<Self, Self::Error>

Performs the conversion.