Struct demes::GraphBuilder

pub struct GraphBuilder { /* private fields */ }

This type allows building a Graph using code rather then using text input.

Notes

• A “builder” in rust will never be as convenient as one in, say, Python or Juilia. The lack of a rust REPL and the strong type checking are the primary reasons.
• All error checks are delayed until resolution.

Implementations

impl GraphBuilder

pub fn new( time_units: TimeUnits, generation_time: Option<InputGenerationTime>, defaults: Option<GraphDefaults> ) -> Self

Constructor

Returns

This function returns an “builder” containing an unresolved Graph.

pub fn new_generations(defaults: Option<GraphDefaults>) -> Self

Construct a builder with time units in generations.

This function works by calling GraphBuilder::new.

pub fn add_deme<I: IntoIterator<Item = UnresolvedEpoch>>( &mut self, name: &str, epochs: I, history: UnresolvedDemeHistory, description: Option<&str> )

Add a Deme to the graph.

Examples

let start_size = demes::InputDemeSize::from(100.);
let epoch = demes::UnresolvedEpoch{start_size: Some(start_size), ..Default::default()};
let history = demes::UnresolvedDemeHistory::default();
let mut b = demes::GraphBuilder::new_generations(None);
b.add_deme("A", vec![epoch], history, Some("this is deme A"));
b.resolve().unwrap();

Notes

pub fn add_migration(&mut self, migration: UnresolvedMigration)

Add a migration to the graph.

Examples

Adding an asymmetric migration

See UnresolvedMigration.

let start_size = demes::InputDemeSize::from(100.);
let epoch = demes::UnresolvedEpoch{start_size: Some(start_size), ..Default::default()};
let history = demes::UnresolvedDemeHistory::default();
let mut b = demes::GraphBuilder::new_generations(None);
b.add_deme("A", vec![epoch], history.clone(), Some("this is deme A"));
b.add_deme("B", vec![epoch], history, Some("this is deme B"));
let migration = demes::UnresolvedMigration::default().set_source("A").set_dest("B").set_rate(1e-4);
b.add_migration(migration);
b.resolve().unwrap();

Adding a symmetric migration

See UnresolvedMigration.

let start_size = demes::InputDemeSize::from(100.);
let epoch = demes::UnresolvedEpoch{start_size: Some(start_size), ..Default::default()};
let history = demes::UnresolvedDemeHistory::default();
let mut b = demes::GraphBuilder::new_generations(None);
b.add_deme("A", vec![epoch], history.clone(), Some("this is deme A"));
b.add_deme("B", vec![epoch], history, Some("this is deme B"));
let migration = demes::UnresolvedMigration::default().set_demes(["A","B"].as_slice()).set_rate(1e-4);
b.add_migration(migration);
b.resolve().unwrap();

We can also use a Vec instead of an array:

let migration = demes::UnresolvedMigration::default().set_demes(vec!["A","B"]).set_rate(1e-4);
b.add_migration(migration);

pub fn add_pulse<T: Into<InputTime>, P: Into<InputProportion>, I: IntoIterator<Item = P>>( &mut self, sources: Option<&[&str]>, dest: Option<&str>, time: Option<T>, proportions: Option<I> )

Add an UnresolvedPulse to the graph.

Examples

let start_size = demes::InputDemeSize::from(100.);
let epoch = demes::UnresolvedEpoch{start_size: Some(start_size), ..Default::default()};
let history = demes::UnresolvedDemeHistory::default();
let mut b = demes::GraphBuilder::new_generations(None);
b.add_deme("A", vec![epoch], history.clone(), Some("this is deme A"));
b.add_deme("B", vec![epoch], history, Some("this is deme B"));
b.add_pulse(Some(&["A"]),
            Some("B"),
            Some(50.0),
            Some([0.5].as_slice()));
b.resolve().unwrap();

pub fn resolve(self) -> Result<Graph, DemesError>

Generate and return a resolved Graph.

Errors

Returns `DemesError’ if any of the data are invalid.

pub fn set_toplevel_metadata<T: Serialize>( &mut self, metadata: &T ) -> Result<(), BuilderError>

Set top-level metadata

Parameters

• metadata: the metadata type

Note

Repeated calls will overwrite existing metadata.

Errors

• BuilderError if serialization to YAML fails.

Example

#[derive(serde::Serialize, serde::Deserialize)]
struct MyMetaData {
   foo: i32,
   bar: String
}
builder.set_toplevel_metadata(&MyMetaData{foo: 3, bar: "string".to_owned()}).unwrap();