Module fastobo::visit

Visitor traits for the OBO syntax tree.

Visit can be used to implement an algorithm that can traverse an OBO AST without editing it, e.g. for validation purposes. This reduces the boilerplate needed for functions that only require to work on specific parts of an OBO document.

Example

The following visitor will collect all synonym types of an OBO document and can be used to return a set of references to the undeclared ones:

extern crate fastobo;

use std::collections::HashSet;
use fastobo::ast::*;
use fastobo::visit::Visit;

#[derive(Default)]
struct SynTypeChecker<'ast> {
    declared: HashSet<&'ast SynonymTypeIdent>,
    used: HashSet<&'ast SynonymTypeIdent>,
}

impl<'ast> Visit<'ast> for SynTypeChecker<'ast> {
    fn visit_header_clause(&mut self, clause: &'ast HeaderClause) {
        if let HeaderClause::SynonymTypedef(ty, _, _) = clause {
            self.declared.insert(ty);
        }
    }

    fn visit_synonymtype_ident(&mut self, id: &'ast SynonymTypeIdent) {
        self.used.insert(id);
    }
}

pub fn undeclared_synonym_types(doc: &OboDoc) -> HashSet<&SynonymTypeIdent> {
    let mut checker = SynTypeChecker::default();
    checker.visit_doc(doc);
    checker.used.difference(&checker.declared).cloned().collect()
}

let doc = fastobo::from_file("tests/data/ms.obo").unwrap();
assert!(undeclared_synonym_types(&doc).is_empty());

See also

• The Visitor design pattern in rust-unofficial/patterns.

Modules

visit	Default implementation of Visit trait methods.
visit_mut	Default implementation of VisitMut trait methods.

Structs

IdCompactor	A visitor that will compact identifiers in an OBO document.
IdDecompactor	A visitor that will decompact identifiers in an OBO document.

Traits

Visit	Syntax tree traversal to walk a shared borrow of an OBO syntax tree.
VisitMut	Syntax tree traversal to walk a mutable borrow of an OBO syntax tree.