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use crate::bindings as ll_bindings;
use crate::metadata;
use crate::{tsk_id_t, tsk_size_t, TskitError};
/// Row of a [`MutationTable`]
pub struct MutationTableRow {
pub id: tsk_id_t,
pub site: tsk_id_t,
pub node: tsk_id_t,
pub parent: tsk_id_t,
pub time: f64,
pub derived_state: Option<Vec<u8>>,
pub metadata: Option<Vec<u8>>,
}
impl PartialEq for MutationTableRow {
fn eq(&self, other: &Self) -> bool {
self.id == other.id
&& self.site == other.site
&& self.node == other.node
&& self.parent == other.parent
&& crate::util::f64_partial_cmp_equal(&self.time, &other.time)
&& self.derived_state == other.derived_state
&& self.metadata == other.metadata
}
}
fn make_mutation_table_row(
table: &MutationTable,
pos: tsk_id_t,
decode_metadata: bool,
) -> Option<MutationTableRow> {
if pos < table.num_rows() as tsk_id_t {
let rv = MutationTableRow {
id: pos,
site: table.site(pos).unwrap(),
node: table.node(pos).unwrap(),
parent: table.parent(pos).unwrap(),
time: table.time(pos).unwrap(),
derived_state: table.derived_state(pos).unwrap(),
metadata: match decode_metadata {
true => match metadata_to_vector!(table, pos).unwrap() {
Some(x) => Some(x),
None => None,
},
false => None,
},
};
Some(rv)
} else {
None
}
}
pub type MutationTableRefIterator<'a> = crate::table_iterator::TableIterator<&'a MutationTable<'a>>;
pub type MutationTableIterator<'a> = crate::table_iterator::TableIterator<MutationTable<'a>>;
impl<'a> Iterator for MutationTableRefIterator<'a> {
type Item = MutationTableRow;
fn next(&mut self) -> Option<Self::Item> {
let rv = make_mutation_table_row(&self.table, self.pos, self.decode_metadata);
self.pos += 1;
rv
}
}
impl<'a> Iterator for MutationTableIterator<'a> {
type Item = MutationTableRow;
fn next(&mut self) -> Option<Self::Item> {
let rv = make_mutation_table_row(&self.table, self.pos, self.decode_metadata);
self.pos += 1;
rv
}
}
/// An immutable view of site table.
///
/// These are not created directly.
/// Instead, use [`TableCollection::mutations`](crate::TableCollection::mutations)
/// to get a reference to an existing mutation table;
pub struct MutationTable<'a> {
table_: &'a ll_bindings::tsk_mutation_table_t,
}
impl<'a> MutationTable<'a> {
pub(crate) fn new_from_table(mutations: &'a ll_bindings::tsk_mutation_table_t) -> Self {
MutationTable { table_: mutations }
}
/// Return the number of rows.
pub fn num_rows(&'a self) -> tsk_size_t {
self.table_.num_rows
}
/// Return the ``site`` value from row ``row`` of the table.
///
/// # Errors
///
/// Will return [``IndexError``](crate::TskitError::IndexError)
/// if ``row`` is out of range.
pub fn site(&'a self, row: tsk_id_t) -> Result<tsk_id_t, TskitError> {
unsafe_tsk_column_access!(row, 0, self.num_rows(), self.table_.site)
}
/// Return the ``node`` value from row ``row`` of the table.
///
/// # Errors
///
/// Will return [``IndexError``](crate::TskitError::IndexError)
/// if ``row`` is out of range.
pub fn node(&'a self, row: tsk_id_t) -> Result<tsk_id_t, TskitError> {
unsafe_tsk_column_access!(row, 0, self.num_rows(), self.table_.node)
}
/// Return the ``parent`` value from row ``row`` of the table.
///
/// # Errors
///
/// Will return [``IndexError``](crate::TskitError::IndexError)
/// if ``row`` is out of range.
pub fn parent(&'a self, row: tsk_id_t) -> Result<tsk_id_t, TskitError> {
unsafe_tsk_column_access!(row, 0, self.num_rows(), self.table_.parent)
}
/// Return the ``time`` value from row ``row`` of the table.
///
/// # Errors
///
/// Will return [``IndexError``](crate::TskitError::IndexError)
/// if ``row`` is out of range.
pub fn time(&'a self, row: tsk_id_t) -> Result<f64, TskitError> {
unsafe_tsk_column_access!(row, 0, self.num_rows(), self.table_.time)
}
/// Get the ``derived_state`` value from row ``row`` of the table.
///
/// # Return
///
/// Will return `None` if there is no derived state.
///
/// # Errors
///
/// Will return [``IndexError``](crate::TskitError::IndexError)
/// if ``row`` is out of range.
pub fn derived_state(&'a self, row: tsk_id_t) -> Result<Option<Vec<u8>>, TskitError> {
metadata::char_column_to_vector(
self.table_.derived_state,
self.table_.derived_state_offset,
row,
self.table_.num_rows,
self.table_.derived_state_length,
)
}
pub fn metadata<T: metadata::MetadataRoundtrip>(
&'a self,
row: tsk_id_t,
) -> Result<Option<T>, TskitError> {
let buffer = metadata_to_vector!(self, row)?;
decode_metadata_row!(T, buffer)
}
/// Return an iterator over rows of the table.
/// The value of the iterator is [`MutationTableRow`].
///
/// # Parameters
///
/// * `decode_metadata`: if `true`, then a *copy* of row metadata
/// will be provided in [`MutationTableRow::metadata`].
/// The meta data are *not* decoded.
/// Rows with no metadata will contain the value `None`.
///
pub fn iter(&self, decode_metadata: bool) -> MutationTableRefIterator {
crate::table_iterator::make_table_iterator::<&MutationTable<'a>>(&self, decode_metadata)
}
/// Return row `r` of the table.
///
/// # Parameters
///
/// * `r`: the row id.
/// * `decode_metadata`: if `true`, then a *copy* of row metadata
/// will be provided in [`MutationTableRow::metadata`].
/// The meta data are *not* decoded.
/// Rows with no metadata will contain the value `None`.
///
/// # Errors
///
/// [`TskitError::IndexError`] if `r` is out of range.
pub fn row(&self, r: tsk_id_t, decode_metadata: bool) -> Result<MutationTableRow, TskitError> {
table_row_access!(r, decode_metadata, self, make_mutation_table_row)
}
}