add id field to table row types. Closes #76 (#77)

src/edge_table.rs

@@ -4,6 +4,7 @@ use crate::{tsk_id_t, tsk_size_t, TskitError};
 
 /// Row of an [`EdgeTable`]
 pub struct EdgeTableRow {
+    pub id: tsk_id_t,
     pub left: f64,
     pub right: f64,
     pub parent: tsk_id_t,
@@ -13,7 +14,8 @@ pub struct EdgeTableRow {
 
 impl PartialEq for EdgeTableRow {
     fn eq(&self, other: &Self) -> bool {
-        self.parent == other.parent
+        self.id == other.id
+            && self.parent == other.parent
             && self.child == other.child
             && crate::util::f64_partial_cmp_equal(&self.left, &other.left)
             && crate::util::f64_partial_cmp_equal(&self.right, &other.right)
@@ -28,6 +30,7 @@ fn make_edge_table_row(
 ) -> Option<EdgeTableRow> {
     if pos < table.num_rows() as tsk_id_t {
         let rv = EdgeTableRow {
+            id: pos,
             left: table.left(pos).unwrap(),
             right: table.right(pos).unwrap(),
             parent: table.parent(pos).unwrap(),

src/individual_table.rs

@@ -4,15 +4,17 @@ use crate::{tsk_flags_t, tsk_id_t, tsk_size_t, TskitError};
 
 /// Row of a [`IndividualTable`]
 pub struct IndividualTableRow {
-    pub flags: u32,
+    pub id: tsk_id_t,
+    pub flags: tsk_flags_t,
     pub location: Option<Vec<f64>>,
     pub parents: Option<Vec<tsk_id_t>>,
     pub metadata: Option<Vec<u8>>,
 }
 
 impl PartialEq for IndividualTableRow {
     fn eq(&self, other: &Self) -> bool {
-        self.flags == other.flags
+        self.id == other.id
+            && self.flags == other.flags
             && self.parents == other.parents
             && self.metadata == other.metadata
             && match &self.location {
@@ -52,6 +54,7 @@ fn make_individual_table_row(
 ) -> Option<IndividualTableRow> {
     if pos < table.num_rows() as tsk_id_t {
         let rv = IndividualTableRow {
+            id: pos,
             flags: table.flags(pos).unwrap(),
             location: table.location(pos).unwrap(),
             parents: table.parents(pos).unwrap(),

src/migration_table.rs

@@ -4,6 +4,7 @@ use crate::{tsk_id_t, TskitError};
 
 /// Row of a [`MigrationTable`]
 pub struct MigrationTableRow {
+    pub id: tsk_id_t,
     pub left: f64,
     pub right: f64,
     pub node: tsk_id_t,
@@ -15,7 +16,8 @@ pub struct MigrationTableRow {
 
 impl PartialEq for MigrationTableRow {
     fn eq(&self, other: &Self) -> bool {
-        self.node == other.node
+        self.id == other.id
+            && self.node == other.node
             && self.source == other.source
             && self.dest == other.dest
             && crate::util::f64_partial_cmp_equal(&self.left, &other.left)
@@ -32,6 +34,7 @@ fn make_migration_table_row(
 ) -> Option<MigrationTableRow> {
     if pos < table.num_rows() as tsk_id_t {
         Some(MigrationTableRow {
+            id: pos,
             left: table.left(pos).unwrap(),
             right: table.right(pos).unwrap(),
             node: table.node(pos).unwrap(),

src/mutation_table.rs

@@ -4,6 +4,7 @@ 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,
@@ -14,7 +15,8 @@ pub struct MutationTableRow {
 
 impl PartialEq for MutationTableRow {
     fn eq(&self, other: &Self) -> bool {
-        self.site == other.site
+        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)
@@ -30,6 +32,7 @@ fn make_mutation_table_row(
 ) -> 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(),

src/node_table.rs

@@ -4,6 +4,7 @@ use crate::{tsk_flags_t, tsk_id_t, TskitError};
 
 /// Row of a [`NodeTable`]
 pub struct NodeTableRow {
+    pub id: tsk_id_t,
     pub time: f64,
     pub flags: tsk_flags_t,
     pub population: tsk_id_t,
@@ -13,7 +14,8 @@ pub struct NodeTableRow {
 
 impl PartialEq for NodeTableRow {
     fn eq(&self, other: &Self) -> bool {
-        self.flags == other.flags
+        self.id == other.id
+            && self.flags == other.flags
             && self.population == other.population
             && self.individual == other.individual
             && crate::util::f64_partial_cmp_equal(&self.time, &other.time)
@@ -28,6 +30,7 @@ fn make_node_table_row(
 ) -> Option<NodeTableRow> {
     if pos < table.num_rows() as tsk_id_t {
         Some(NodeTableRow {
+            id: pos,
             time: table.time(pos).unwrap(),
             flags: table.flags(pos).unwrap(),
             population: table.population(pos).unwrap(),

src/population_table.rs

@@ -6,12 +6,13 @@ use crate::{tsk_id_t, tsk_size_t};
 /// Row of a [`PopulationTable`]
 #[derive(Eq)]
 pub struct PopulationTableRow {
+    pub id: tsk_id_t,
     pub metadata: Option<Vec<u8>>,
 }
 
 impl PartialEq for PopulationTableRow {
     fn eq(&self, other: &Self) -> bool {
-        self.metadata == other.metadata
+        self.id == other.id && self.metadata == other.metadata
     }
 }
 
@@ -22,6 +23,7 @@ fn make_population_table_row(
 ) -> Option<PopulationTableRow> {
     if pos < table.num_rows() as tsk_id_t {
         let rv = PopulationTableRow {
+            id: pos,
             metadata: match decode_metadata {
                 true => match metadata_to_vector!(table, pos).unwrap() {
                     Some(x) => Some(x),

src/site_table.rs

@@ -5,14 +5,16 @@ use crate::{tsk_id_t, tsk_size_t};
 
 /// Row of a [`SiteTable`]
 pub struct SiteTableRow {
+    pub id: tsk_id_t,
     pub position: f64,
     pub ancestral_state: Option<Vec<u8>>,
     pub metadata: Option<Vec<u8>>,
 }
 
 impl PartialEq for SiteTableRow {
     fn eq(&self, other: &Self) -> bool {
-        crate::util::f64_partial_cmp_equal(&self.position, &other.position)
+        self.id == other.id
+            && crate::util::f64_partial_cmp_equal(&self.position, &other.position)
             && self.ancestral_state == other.ancestral_state
             && self.metadata == other.metadata
     }
@@ -25,6 +27,7 @@ fn make_site_table_row(
 ) -> Option<SiteTableRow> {
     if pos < table.num_rows() as tsk_id_t {
         let rv = SiteTableRow {
+            id: pos,
             position: table.position(pos).unwrap(),
             ancestral_state: table.ancestral_state(pos).unwrap(),
             metadata: match decode_metadata {

src/table_collection.rs

@@ -631,20 +631,11 @@ mod test {
             assert!(row.metadata.is_none());
         }
 
-        for (i, row) in tables.nodes_iter(true).enumerate() {
-            assert!(close_enough(
-                tables.nodes().time(i as tsk_id_t).unwrap(),
-                row.time
-            ));
-            assert_eq!(tables.nodes().flags(i as tsk_id_t).unwrap(), row.flags);
-            assert_eq!(
-                tables.nodes().population(i as tsk_id_t).unwrap(),
-                row.population
-            );
-            assert_eq!(
-                tables.nodes().individual(i as tsk_id_t).unwrap(),
-                row.individual
-            );
+        for row in tables.nodes_iter(true) {
+            assert!(close_enough(tables.nodes().time(row.id).unwrap(), row.time));
+            assert_eq!(tables.nodes().flags(row.id).unwrap(), row.flags);
+            assert_eq!(tables.nodes().population(row.id).unwrap(), row.population);
+            assert_eq!(tables.nodes().individual(row.id).unwrap(), row.individual);
             assert!(row.metadata.is_none());
         }
     }
@@ -665,17 +656,14 @@ mod test {
             assert_eq!(tables.edges().child(i as tsk_id_t).unwrap(), row.child);
             assert!(row.metadata.is_none());
         }
-        for (i, row) in tables.edges_iter(true).enumerate() {
+        for row in tables.edges_iter(true) {
+            assert!(close_enough(tables.edges().left(row.id).unwrap(), row.left));
             assert!(close_enough(
-                tables.edges().left(i as tsk_id_t).unwrap(),
-                row.left
-            ));
-            assert!(close_enough(
-                tables.edges().right(i as tsk_id_t).unwrap(),
+                tables.edges().right(row.id).unwrap(),
                 row.right
             ));
-            assert_eq!(tables.edges().parent(i as tsk_id_t).unwrap(), row.parent);
-            assert_eq!(tables.edges().child(i as tsk_id_t).unwrap(), row.child);
+            assert_eq!(tables.edges().parent(row.id).unwrap(), row.parent);
+            assert_eq!(tables.edges().child(row.id).unwrap(), row.child);
             assert!(row.metadata.is_none());
         }
     }
@@ -728,15 +716,12 @@ mod test {
         }
         assert_eq!(no_anc_state, 1);
         no_anc_state = 0;
-        for (i, row) in tables.sites_iter(true).enumerate() {
-            assert!(close_enough(
-                sites.position(i as tsk_id_t).unwrap(),
-                row.position
-            ));
+        for row in tables.sites_iter(true) {
+            assert!(close_enough(sites.position(row.id).unwrap(), row.position));
             if row.ancestral_state.is_some() {
-                if i == 0 {
+                if row.id == 0 {
                     assert_eq!(row.ancestral_state.unwrap(), b"Eggnog");
-                } else if i == 2 {
+                } else if row.id == 2 {
                     assert_eq!(row.ancestral_state.unwrap(), longer_metadata.as_bytes());
                 }
             } else {
@@ -803,16 +788,13 @@ mod test {
         assert_eq!(nmuts, 3);
 
         nmuts = 0;
-        for (i, row) in tables.mutations_iter(true).enumerate() {
-            assert_eq!(row.site, tables.mutations().site(i as tsk_id_t).unwrap());
-            assert_eq!(row.node, tables.mutations().node(i as tsk_id_t).unwrap());
-            assert_eq!(
-                row.parent,
-                tables.mutations().parent(i as tsk_id_t).unwrap()
-            );
+        for row in tables.mutations_iter(true) {
+            assert_eq!(row.site, tables.mutations().site(row.id).unwrap());
+            assert_eq!(row.node, tables.mutations().node(row.id).unwrap());
+            assert_eq!(row.parent, tables.mutations().parent(row.id).unwrap());
             assert!(close_enough(
                 row.time,
-                tables.mutations().time(i as tsk_id_t).unwrap()
+                tables.mutations().time(row.id).unwrap()
             ));
             assert!(row.metadata.is_none());
             nmuts += 1;
@@ -981,6 +963,7 @@ mod test {
     fn test_edge_table_row_equality() {
         let tables = make_small_table_collection();
         for (i, row) in tables.edges_iter(true).enumerate() {
+            assert!(row.id == i as tsk_id_t);
             assert!(row == tables.edges().row(i as tsk_id_t, true).unwrap());
             assert!(!(row != tables.edges().row(i as tsk_id_t, true).unwrap()));
             if i > 0 {
@@ -993,11 +976,12 @@ mod test {
     fn test_node_table_row_equality() {
         let tables = make_small_table_collection();
         for (i, row) in tables.nodes_iter(true).enumerate() {
+            assert!(row.id == i as tsk_id_t);
             assert!(row == tables.nodes().row(i as tsk_id_t, true).unwrap());
             assert!(!(row != tables.nodes().row(i as tsk_id_t, true).unwrap()));
         }
         assert!(tables.nodes().row(0, true) != tables.nodes().row(1, true));
-        assert!(tables.nodes().row(1, true) == tables.nodes().row(2, true));
+        assert!(tables.nodes().row(1, true) != tables.nodes().row(2, true));
     }
 
     #[test]