Struct fastobo::ast::OboDoc

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pub struct OboDoc { /* private fields */ }

Expand description

A complete OBO document in format version 1.4.

Implementations§

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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);

pub fn new() -> Self

Create a new empty OBO document.

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pub fn with_header(header: HeaderFrame) -> Self

Create a new OBO document with the provided frame.

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

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

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

Create a new OBO document with the provided entity frames.

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

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

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impl OboDoc

Shared and mutable getters.

Get a reference to the header of the OBO document.

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

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

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

Get a reference to the entities of the OBO document.

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

Get a reference to the entities of the OBO document.

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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.

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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.

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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.

If all frames already have a namespace clause, this function will not check the contents of the header, return Ok(()). However, if a frame requires the assignment of the default namespace, then a CardinalityError may be raised depending on the header contents.

Example

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

[Term]
id: TST:01

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

doc.assign_namespaces().unwrap();
assert_eq!(doc.to_string(),
"default-namespace: test

[Term]
id: TST:01
namespace: test

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

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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.

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.