done?

Author: molpopgen

examples/haploid_wright_fisher.rs

@@ -163,7 +163,11 @@ fn stress_test_total_branch_length() {
                 if let Some(tree) = tree_iter.next() {
                     let b = tree.total_branch_length(false).unwrap();
                     let b2 = unsafe {
-                        tskit::bindings::tsk_tree_get_total_branch_length(tree.as_ll_ref(), -1, &mut x)
+                        tskit::bindings::tsk_tree_get_total_branch_length(
+                            tree.as_ll_ref(),
+                            -1,
+                            &mut x,
+                        )
                     };
                     assert!(b2 >= 0, "{}", b2);
                     assert!(f64::from(b) - x <= 1e-8);

src/edge_table.rs

@@ -253,7 +253,7 @@ impl EdgeTable {
     /// * `Some(position)` if `u` is valid.
     /// * `None` otherwise.
     pub fn right<E: Into<EdgeId> + Copy>(&self, row: E) -> Option<Position> {
-        self.table_.left(row.into())
+        self.table_.right(row.into())
     }
 
     /// Retrieve decoded metadata for a `row`.

src/mutation_table.rs

@@ -233,16 +233,7 @@ impl MutationTable {
     /// Will return [``IndexError``](crate::TskitError::IndexError)
     /// if ``row`` is out of range.
     pub fn site<M: Into<MutationId> + Copy>(&self, row: M) -> Option<SiteId> {
-        assert!(self.num_rows() == 0 || !self.as_ref().site.is_null());
-        // SAFETY: either the column is empty or the pointer is not null,
-        // in which case the correct lengths are from the low-level objects
-        unsafe {
-            sys::tsk_column_access::<SiteId, _, _, _>(
-                row.into(),
-                self.as_ref().site,
-                self.num_rows(),
-            )
-        }
+        self.table_.site(row.into())
     }
 
     /// Return the ``node`` value from row ``row`` of the table.
@@ -252,16 +243,7 @@ impl MutationTable {
     /// Will return [``IndexError``](crate::TskitError::IndexError)
     /// if ``row`` is out of range.
     pub fn node<M: Into<MutationId> + Copy>(&self, row: M) -> Option<NodeId> {
-        assert!(self.num_rows() == 0 || !self.as_ref().node.is_null());
-        // SAFETY: either the column is empty or the pointer is not null,
-        // in which case the correct lengths are from the low-level objects
-        unsafe {
-            sys::tsk_column_access::<NodeId, _, _, _>(
-                row.into(),
-                self.as_ref().node,
-                self.num_rows(),
-            )
-        }
+        self.table_.node(row.into())
     }
 
     /// Return the ``parent`` value from row ``row`` of the table.
@@ -271,16 +253,7 @@ impl MutationTable {
     /// Will return [``IndexError``](crate::TskitError::IndexError)
     /// if ``row`` is out of range.
     pub fn parent<M: Into<MutationId> + Copy>(&self, row: M) -> Option<MutationId> {
-        assert!(self.num_rows() == 0 || !self.as_ref().parent.is_null());
-        // SAFETY: either the column is empty or the pointer is not null,
-        // in which case the correct lengths are from the low-level objects
-        unsafe {
-            sys::tsk_column_access::<MutationId, _, _, _>(
-                row.into(),
-                self.as_ref().parent,
-                self.num_rows(),
-            )
-        }
+        self.table_.parent(row.into())
     }
 
     /// Return the ``time`` value from row ``row`` of the table.
@@ -290,12 +263,7 @@ impl MutationTable {
     /// Will return [``IndexError``](crate::TskitError::IndexError)
     /// if ``row`` is out of range.
     pub fn time<M: Into<MutationId> + Copy>(&self, row: M) -> Option<Time> {
-        assert!(self.num_rows() == 0 || !self.as_ref().time.is_null());
-        // SAFETY: either the column is empty or the pointer is not null,
-        // in which case the correct lengths are from the low-level objects
-        unsafe {
-            sys::tsk_column_access::<Time, _, _, _>(row.into(), self.as_ref().time, self.num_rows())
-        }
+        self.table_.time(row.into())
     }
 
     /// Get the ``derived_state`` value from row ``row`` of the table.

src/sys/mutation_table.rs

@@ -1,5 +1,10 @@
 use std::ptr::NonNull;
 
+use super::newtypes::MutationId;
+use super::newtypes::NodeId;
+use super::newtypes::SiteId;
+use super::newtypes::Time;
+
 use super::bindings::tsk_id_t;
 use super::bindings::tsk_mutation_table_add_row;
 use super::bindings::tsk_mutation_table_clear;
@@ -76,6 +81,22 @@ impl MutationTable {
             ))
         }
     }
+
+    pub fn time(&self, row: MutationId) -> Option<Time> {
+        safe_tsk_column_access!(self, row, Time, time)
+    }
+
+    pub fn site(&self, row: MutationId) -> Option<SiteId> {
+        safe_tsk_column_access!(self, row, SiteId, site)
+    }
+
+    pub fn node(&self, row: MutationId) -> Option<NodeId> {
+        safe_tsk_column_access!(self, row, NodeId, node)
+    }
+
+    pub fn parent(&self, row: MutationId) -> Option<MutationId> {
+        safe_tsk_column_access!(self, row, MutationId, parent)
+    }
 }
 
 impl Default for MutationTable {