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#![allow(non_upper_case_globals)]
#![allow(non_camel_case_types)]
#![allow(non_snake_case)]
#![cfg_attr(doc_cfg, feature(doc_cfg))]
#[allow(deref_nullptr)]
#[allow(rustdoc::broken_intra_doc_links)]
pub mod bindings;
mod _macros; mod edge_table;
pub mod error;
mod flags;
mod individual_table;
pub mod metadata;
mod migration_table;
mod mutation_table;
mod node_table;
mod population_table;
pub mod prelude;
mod site_table;
mod table_collection;
mod table_iterator;
pub mod table_views;
mod traits;
mod tree_interface;
mod trees;
pub mod types;
mod util;
pub use bindings::TSK_NODE_IS_SAMPLE;
pub use bindings::tsk_flags_t;
use bindings::tsk_id_t;
use bindings::tsk_size_t;
#[repr(transparent)]
#[derive(Copy, Clone, Debug, Eq, PartialEq, Ord, PartialOrd, std::hash::Hash)]
pub struct NodeId(tsk_id_t);
#[repr(transparent)]
#[derive(Copy, Clone, Debug, Eq, PartialEq, Ord, PartialOrd, std::hash::Hash)]
pub struct IndividualId(tsk_id_t);
#[repr(transparent)]
#[derive(Copy, Clone, Debug, Eq, PartialEq, Ord, PartialOrd, std::hash::Hash)]
pub struct PopulationId(tsk_id_t);
#[repr(transparent)]
#[derive(Copy, Clone, Debug, Eq, PartialEq, Ord, PartialOrd, std::hash::Hash)]
pub struct SiteId(tsk_id_t);
#[repr(transparent)]
#[derive(Copy, Clone, Debug, Eq, PartialEq, Ord, PartialOrd, std::hash::Hash)]
pub struct MutationId(tsk_id_t);
#[repr(transparent)]
#[derive(Copy, Clone, Debug, Eq, PartialEq, Ord, PartialOrd, std::hash::Hash)]
pub struct MigrationId(tsk_id_t);
#[repr(transparent)]
#[derive(Copy, Clone, Debug, Eq, PartialEq, Ord, PartialOrd, std::hash::Hash)]
pub struct EdgeId(tsk_id_t);
impl_id_traits!(NodeId);
impl_id_traits!(IndividualId);
impl_id_traits!(PopulationId);
impl_id_traits!(SiteId);
impl_id_traits!(MutationId);
impl_id_traits!(MigrationId);
impl_id_traits!(EdgeId);
impl_size_type_comparisons_for_row_ids!(NodeId);
impl_size_type_comparisons_for_row_ids!(EdgeId);
impl_size_type_comparisons_for_row_ids!(SiteId);
impl_size_type_comparisons_for_row_ids!(MutationId);
impl_size_type_comparisons_for_row_ids!(PopulationId);
impl_size_type_comparisons_for_row_ids!(MigrationId);
#[derive(Copy, Clone, Debug, Eq, PartialEq, Ord, PartialOrd, std::hash::Hash)]
pub struct SizeType(tsk_size_t);
impl std::fmt::Display for SizeType {
fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
write!(f, "{}", self.0)
}
}
impl From<tsk_size_t> for SizeType {
fn from(value: tsk_size_t) -> Self {
Self(value)
}
}
impl From<SizeType> for tsk_size_t {
fn from(value: SizeType) -> Self {
value.0
}
}
impl TryFrom<SizeType> for usize {
type Error = TskitError;
fn try_from(value: SizeType) -> Result<Self, Self::Error> {
match usize::try_from(value.0) {
Ok(x) => Ok(x),
Err(_) => Err(TskitError::RangeError(format!(
"could not convert {} to usize",
value
))),
}
}
}
impl From<usize> for SizeType {
fn from(value: usize) -> Self {
Self(value as tsk_size_t)
}
}
impl TryFrom<tsk_id_t> for SizeType {
type Error = crate::TskitError;
fn try_from(value: tsk_id_t) -> Result<Self, Self::Error> {
match tsk_size_t::try_from(value) {
Ok(v) => Ok(Self(v)),
Err(_) => Err(crate::TskitError::RangeError(
stringify!(value.0).to_string(),
)),
}
}
}
impl TryFrom<SizeType> for tsk_id_t {
type Error = crate::TskitError;
fn try_from(value: SizeType) -> Result<Self, Self::Error> {
match tsk_id_t::try_from(value.0) {
Ok(v) => Ok(v),
Err(_) => Err(TskitError::RangeError(stringify!(value.0).to_string())),
}
}
}
impl PartialEq<SizeType> for tsk_size_t {
fn eq(&self, other: &SizeType) -> bool {
*self == other.0
}
}
impl PartialEq<tsk_size_t> for SizeType {
fn eq(&self, other: &tsk_size_t) -> bool {
self.0 == *other
}
}
impl PartialOrd<tsk_size_t> for SizeType {
fn partial_cmp(&self, other: &tsk_size_t) -> Option<std::cmp::Ordering> {
self.0.partial_cmp(other)
}
}
impl PartialOrd<SizeType> for tsk_size_t {
fn partial_cmp(&self, other: &SizeType) -> Option<std::cmp::Ordering> {
self.partial_cmp(&other.0)
}
}
#[repr(transparent)]
#[derive(Copy, Clone, Debug, PartialEq, PartialOrd)]
pub struct Time(f64);
#[repr(transparent)]
#[derive(Copy, Clone, Debug, PartialEq, PartialOrd)]
pub struct Position(f64);
#[repr(transparent)]
#[derive(Copy, Clone, Debug, PartialEq, PartialOrd)]
pub struct Location(f64);
impl_f64_newtypes!(Time);
impl_f64_newtypes!(Position);
impl_f64_newtypes!(Location);
impl_time_position_arithmetic!(Time, Position);
impl_time_position_arithmetic!(Position, Time);
pub(crate) const TSK_NULL: tsk_id_t = -1;
pub use edge_table::{EdgeTable, EdgeTableRow, OwnedEdgeTable};
pub use error::TskitError;
pub use flags::*;
pub use individual_table::{IndividualTable, IndividualTableRow, OwnedIndividualTable};
pub use migration_table::{MigrationTable, MigrationTableRow, OwnedMigrationTable};
pub use mutation_table::{MutationTable, MutationTableRow, OwnedMutationTable};
pub use node_table::{NodeTable, NodeTableRow, OwnedNodeTable};
pub use population_table::{OwnedPopulationTable, PopulationTable, PopulationTableRow};
pub use site_table::{OwnedSiteTable, SiteTable, SiteTableRow};
pub use table_collection::TableCollection;
pub use traits::IndividualLocation;
pub use traits::IndividualParents;
pub use traits::TskitTypeAccess;
pub use tree_interface::{NodeTraversalOrder, TreeInterface};
pub use trees::{Tree, TreeSequence};
#[cfg(feature = "provenance")]
#[cfg_attr(doc_cfg, doc(cfg(feature = "provenance")))]
pub mod provenance;
#[cfg(feature = "provenance")]
#[cfg_attr(doc_cfg, doc(cfg(feature = "provenance")))]
#[repr(transparent)]
#[derive(Copy, Clone, Debug, Eq, PartialEq, Ord, PartialOrd, std::hash::Hash)]
pub struct ProvenanceId(tsk_id_t);
#[cfg(feature = "provenance")]
impl_id_traits!(ProvenanceId);
pub type TskReturnValue = Result<i32, TskitError>;
pub type RawFlags = crate::bindings::tsk_flags_t;
pub fn version() -> &'static str {
env!("CARGO_PKG_VERSION")
}
pub fn c_api_major_version() -> u32 {
bindings::TSK_VERSION_MAJOR
}
pub fn c_api_minor_version() -> u32 {
bindings::TSK_VERSION_MINOR
}
pub fn c_api_patch_version() -> u32 {
bindings::TSK_VERSION_PATCH
}
pub fn c_api_version() -> String {
format!(
"{}.{}.{}",
c_api_major_version(),
c_api_minor_version(),
c_api_patch_version()
)
}
#[cfg(test)]
mod tests {
use super::c_api_version;
use super::Location;
use super::Position;
use super::Time;
#[test]
fn test_c_api_version() {
let _ = c_api_version();
}
#[test]
fn test_f64_newtype_Display() {
let x = Position::from(1.0);
let mut output = String::new();
std::fmt::write(&mut output, format_args!("{}", x))
.expect("Error occurred while trying to write in String");
assert_eq!(output, "1".to_string());
let x = Time::from(1.0);
let mut output = String::new();
std::fmt::write(&mut output, format_args!("{}", x))
.expect("Error occurred while trying to write in String");
assert_eq!(output, "1".to_string());
let x = Location::from(1.0);
let mut output = String::new();
std::fmt::write(&mut output, format_args!("{}", x))
.expect("Error occurred while trying to write in String");
assert_eq!(output, "1".to_string());
}
}
mod test_fixtures;
mod test_simplification;
mod test_tsk_variables;