Skip to content

refactor: Reduce code duplication adding individual table rows #458

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Jan 27, 2023
Merged

refactor: Reduce code duplication adding individual table rows #458

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
75 changes: 0 additions & 75 deletions src/_macros.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -380,81 +380,6 @@ macro_rules! handle_metadata_return {
};
}

macro_rules! individual_table_add_row_details {
($flags: ident,
$location: ident,
$parents: ident,
$metadata: expr,
$metadata_len: expr,
$table: expr) => {{
let rv = unsafe {
$crate::bindings::tsk_individual_table_add_row(
$table,
$flags.into().bits(),
$location.get_slice().as_ptr().cast::<f64>(),
$location.get_slice().len() as $crate::bindings::tsk_size_t,
$parents
.get_slice()
.as_ptr()
.cast::<$crate::bindings::tsk_id_t>(),
$parents.get_slice().len() as $crate::bindings::tsk_size_t,
$metadata,
$metadata_len,
)
};
handle_tsk_return_value!(rv, rv.into())
}};
}

macro_rules! individual_table_add_row {
($(#[$attr:meta])* => $name: ident, $self: ident, $table: expr) => {
$(#[$attr])*
pub fn $name<F,L,P>(&mut $self,
flags: F,
location: L,
parents: P,
) -> Result<$crate::IndividualId, $crate::TskitError>
where
F: Into<$crate::IndividualFlags>,
L: $crate::IndividualLocation,
P: $crate::IndividualParents,
{
individual_table_add_row_details!(flags,
location,
parents,
std::ptr::null(),
0,
$table)
}
};
}

macro_rules! individual_table_add_row_with_metadata {
($(#[$attr:meta])* => $name: ident, $self: ident, $table: expr) => {
$(#[$attr])*
pub fn $name<F,L,P,M>(&mut $self,
flags: F,
location: L,
parents: P,
metadata: &M,
) -> Result<$crate::IndividualId, $crate::TskitError>
where
F: Into<$crate::IndividualFlags>,
L: $crate::IndividualLocation,
P: $crate::IndividualParents,
M: $crate::metadata::IndividualMetadata
{
let md = $crate::metadata::EncodedMetadata::new(metadata)?;
individual_table_add_row_details!(flags,
location,
parents,
md.as_ptr(),
md.len()?.into(),
$table)
}
};
}

macro_rules! mutation_table_add_row_details {
($site: ident, $node: ident, $parent: ident,
$time: ident, $derived_state: ident,
Expand Down
64 changes: 62 additions & 2 deletions src/individual_table.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -491,8 +491,68 @@ match tables.individuals().metadata::<MutationMetadata>(0.into())
self.table_.clear().map_err(|e| e.into())
}

individual_table_add_row!(=> add_row, self, self.as_mut_ptr());
individual_table_add_row_with_metadata!(=> add_row_with_metadata, self, self.as_mut_ptr());
fn add_row_details<F, L, P>(
&mut self,
flags: F,
location: L,
parents: P,
metadata: *const i8,
metadata_length: u64,
) -> Result<crate::IndividualId, crate::TskitError>
where
F: Into<crate::IndividualFlags>,
L: crate::IndividualLocation,
P: crate::IndividualParents,
{
let rv = unsafe {
crate::bindings::tsk_individual_table_add_row(
self.as_mut_ptr(),
flags.into().bits(),
location.get_slice().as_ptr().cast::<f64>(),
location.get_slice().len() as crate::bindings::tsk_size_t,
parents
.get_slice()
.as_ptr()
.cast::<crate::bindings::tsk_id_t>(),
parents.get_slice().len() as crate::bindings::tsk_size_t,
metadata,
metadata_length,
)
};
handle_tsk_return_value!(rv, rv.into())
}

pub fn add_row<F, L, P>(
&mut self,
flags: F,
location: L,
parents: P,
) -> Result<crate::IndividualId, crate::TskitError>
where
F: Into<crate::IndividualFlags>,
L: crate::IndividualLocation,
P: crate::IndividualParents,
{
self.add_row_details(flags, location, parents, std::ptr::null(), 0)
}

pub fn add_row_with_metadata<F, L, P, M>(
&mut self,
flags: F,
location: L,
parents: P,
metadata: &M,
) -> Result<crate::IndividualId, crate::TskitError>
where
F: Into<crate::IndividualFlags>,
L: crate::IndividualLocation,
P: crate::IndividualParents,
M: crate::metadata::IndividualMetadata,
{
let md = crate::metadata::EncodedMetadata::new(metadata)?;
let mdlen = md.len()?;
self.add_row_details(flags, location, parents, md.as_ptr(), mdlen.into())
}

build_table_column_slice_getter!(
/// Get the flags column as a slice
Expand Down
41 changes: 33 additions & 8 deletions src/table_collection.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -313,15 +313,14 @@ impl TableCollection {
.add_row_with_metadata(left, right, parent, child, metadata)
}

individual_table_add_row!(
/// Add a row to the individual table
///
/// # Examples
///
/// ## No flags, location, nor parents
///
/// ```
/// #
/// #
/// # let mut tables = tskit::TableCollection::new(1.0).unwrap();
/// tables.add_individual(0, None, None).unwrap();
/// # assert!(tables.individuals().location(0).is_none());
Expand All @@ -331,7 +330,7 @@ impl TableCollection {
/// ## No flags, a 3d location, no parents
///
/// ```
/// #
/// #
/// # let mut tables = tskit::TableCollection::new(1.0).unwrap();
/// tables.add_individual(0, &[-0.5, 0.3, 10.0], None).unwrap();
/// # match tables.individuals().location(0) {
Expand All @@ -343,16 +342,27 @@ impl TableCollection {
/// ## No flags, no location, two parents
/// ```
/// # let mut tables = tskit::TableCollection::new(1.0).unwrap();
/// #
/// #
/// tables.add_individual(0, None, &[1, 11]);
/// # match tables.individuals().parents(0) {
/// # Some(parents) => parents.iter().zip([1, 11].iter()).for_each(|(a,b)| assert_eq!(a, b)),
/// # None => panic!("expected parents"),
/// # }
/// ```
=> add_individual, self, &mut (*self.as_mut_ptr()).individuals);
pub fn add_individual<F, L, P>(
&mut self,
flags: F,
location: L,
parents: P,
) -> Result<crate::IndividualId, crate::TskitError>
where
F: Into<crate::IndividualFlags>,
L: crate::IndividualLocation,
P: crate::IndividualParents,
{
self.individuals_mut().add_row(flags, location, parents)
}

individual_table_add_row_with_metadata!(
/// Add a row with metadata to the individual table
///
/// # Examples
Expand All @@ -363,7 +373,7 @@ impl TableCollection {
///
/// ```
/// # #[cfg(feature = "derive")] {
///
///
/// # let mut tables = tskit::TableCollection::new(100.).unwrap();
/// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::IndividualMetadata)]
/// # #[serializer("serde_json")]
Expand All @@ -376,7 +386,22 @@ impl TableCollection {
/// # let decoded = tables.individuals().metadata::<IndividualMetadata>(0.into()).unwrap().unwrap();
/// # assert_eq!(decoded.x, 1);
/// # }
=> add_individual_with_metadata, self, &mut (*self.as_mut_ptr()).individuals);
pub fn add_individual_with_metadata<F, L, P, M>(
&mut self,
flags: F,
location: L,
parents: P,
metadata: &M,
) -> Result<crate::IndividualId, crate::TskitError>
where
F: Into<crate::IndividualFlags>,
L: crate::IndividualLocation,
P: crate::IndividualParents,
M: crate::metadata::IndividualMetadata,
{
self.individuals_mut()
.add_row_with_metadata(flags, location, parents, metadata)
}

migration_table_add_row!(
/// Add a row to the migration table
Expand Down