more

Author: molpopgen

src/migration_table.rs

@@ -44,7 +44,7 @@ fn make_migration_table_row(table: &MigrationTable, pos: tsk_id_t) -> Option<Mig
         source: table.source(pos)?,
         dest: table.dest(pos)?,
         time: table.time(pos)?,
-        metadata: table.raw_metadata(pos).map(|m| m.to_vec()),
+        metadata: table.table_.raw_metadata(pos).map(|m| m.to_vec()),
     })
 }
 
@@ -155,7 +155,7 @@ impl streaming_iterator::StreamingIterator for MigrationTableRowView<'_> {
         self.source = self.table.source(self.id).unwrap_or(PopulationId::NULL);
         self.dest = self.table.dest(self.id).unwrap_or(PopulationId::NULL);
         self.time = self.table.time(self.id).unwrap_or_else(|| f64::NAN.into());
-        self.metadata = self.table.raw_metadata(self.id);
+        self.metadata = self.table.table_.raw_metadata(self.id);
     }
 }
 
@@ -308,7 +308,7 @@ impl MigrationTable {
         &self,
         row: impl Into<MigrationId>,
     ) -> Option<Result<T, TskitError>> {
-        let buffer = self.raw_metadata(row)?;
+        let buffer = self.table_.raw_metadata(row)?;
         Some(decode_metadata_row!(T, buffer).map_err(|e| e.into()))
     }
 
@@ -357,7 +357,7 @@ impl MigrationTable {
             source: self.source(r)?,
             dest: self.dest(r)?,
             time: self.time(r)?,
-            metadata: self.raw_metadata(r.into()),
+            metadata: self.table_.raw_metadata(r.into()),
         };
         Some(view)
     }

src/mutation_table.rs

@@ -275,22 +275,7 @@ impl MutationTable {
     /// Will return [``IndexError``](crate::TskitError::IndexError)
     /// if ``row`` is out of range.
     pub fn derived_state<M: Into<MutationId>>(&self, row: M) -> Option<&[u8]> {
-        assert!(
-            (self.num_rows() == 0 && self.as_ref().derived_state_length == 0)
-                || (!self.as_ref().derived_state.is_null()
-                    && !self.as_ref().derived_state_offset.is_null())
-        );
-        // SAFETY: either both columns are empty or both pointers at not NULL,
-        // in which case the correct lengths are from the low-level objects
-        unsafe {
-            sys::tsk_ragged_column_access(
-                row.into(),
-                self.as_ref().derived_state,
-                self.num_rows(),
-                self.as_ref().derived_state_offset,
-                self.as_ref().derived_state_length,
-            )
-        }
+        self.table_.derived_state(row.into())
     }
 
     /// Retrieve decoded metadata for a `row`.

src/site_table.rs

@@ -32,7 +32,7 @@ fn make_site_table_row(table: &SiteTable, pos: tsk_id_t) -> Option<SiteTableRow>
         id: pos.into(),
         position: table.position(pos)?,
         ancestral_state,
-        metadata: table.raw_metadata(pos).map(|m| m.to_vec()),
+        metadata: table.table_.raw_metadata(pos).map(|m| m.to_vec()),
     })
 }
 
@@ -121,7 +121,7 @@ impl streaming_iterator::StreamingIterator for SiteTableRowView<'_> {
             .position(self.id)
             .unwrap_or_else(|| f64::NAN.into());
         self.ancestral_state = self.table.ancestral_state(self.id);
-        self.metadata = self.table.raw_metadata(self.id);
+        self.metadata = self.table.table_.raw_metadata(self.id);
     }
 }
 
@@ -246,7 +246,7 @@ impl SiteTable {
         &self,
         row: impl Into<SiteId>,
     ) -> Option<Result<T, TskitError>> {
-        let buffer = self.raw_metadata(row)?;
+        let buffer = self.table_.raw_metadata(row)?;
         Some(decode_metadata_row!(T, buffer).map_err(TskitError::from))
     }
 
@@ -291,7 +291,7 @@ impl SiteTable {
             id: r.into(),
             position: self.position(r)?,
             ancestral_state: self.ancestral_state(r),
-            metadata: self.raw_metadata(r.into()),
+            metadata: self.table_.raw_metadata(r.into()),
         };
         Some(view)
     }

src/sys/migration_table.rs

@@ -100,6 +100,8 @@ impl MigrationTable {
     pub fn right(&self, row: MigrationId) -> Option<Position> {
         safe_tsk_column_access!(self, row, Position, right)
     }
+
+    raw_metadata_getter_for_tables!(MigrationId);
 }
 
 impl Default for MigrationTable {

src/sys/mutation_table.rs

@@ -99,6 +99,25 @@ impl MutationTable {
     }
 
     raw_metadata_getter_for_tables!(MutationId);
+
+    pub fn derived_state(&self, row: MutationId) -> Option<&[u8]> {
+        assert!(
+            (self.as_ref().num_rows == 0 && self.as_ref().derived_state_length == 0)
+                || (!self.as_ref().derived_state.is_null()
+                    && !self.as_ref().derived_state_offset.is_null())
+        );
+        // SAFETY: either both columns are empty or both pointers at not NULL,
+        // in which case the correct lengths are from the low-level objects
+        unsafe {
+super::tsk_ragged_column_access(
+                row,
+                self.as_ref().derived_state,
+                self.as_ref().num_rows,
+                self.as_ref().derived_state_offset,
+                self.as_ref().derived_state_length,
+            )
+        }
+    }
 }
 
 impl Default for MutationTable {