Merge pull request #46 from molpopgen/add_important_missing_functions

Add kc_distance and num_tracked_samples to Tree
tskit-dev · Apr 12, 2021 · f1887d5 · f1887d5
2 parents f559825 + fb85ba9
commit f1887d5
Showing 1 changed file with 146 additions and 1 deletion.
diff --git a/src/trees.rs b/src/trees.rs
@@ -51,7 +51,22 @@ impl Tree {
 
     fn new(ts: &TreeSequence, flags: TreeFlags) -> Result<Self, TskitError> {
         let mut tree = Self::wrap(ts.consumed.nodes().num_rows(), flags);
-        let rv = unsafe { ll_bindings::tsk_tree_init(tree.as_mut_ptr(), ts.as_ptr(), flags.bits) };
+        let mut rv =
+            unsafe { ll_bindings::tsk_tree_init(tree.as_mut_ptr(), ts.as_ptr(), flags.bits) };
+        if rv < 0 {
+            return Err(TskitError::ErrorCode { code: rv });
+        }
+        // Gotta ask Jerome about this one--why isn't this handled in tsk_tree_init??
+        if !flags.contains(TreeFlags::NO_SAMPLE_COUNTS) {
+            rv = unsafe {
+                ll_bindings::tsk_tree_set_tracked_samples(
+                    tree.as_mut_ptr(),
+                    ts.num_samples() as u64,
+                    tree.inner.samples,
+                )
+            };
+        }
+
         handle_tsk_return_value!(rv, tree)
     }
 
@@ -355,6 +370,39 @@ impl Tree {
             false => Ok(b),
         }
     }
+
+    /// Get the number of samples below node `u`.
+    ///
+    /// # Errors
+    ///
+    /// * [`TskitError`] if [`TreeFlags::NO_SAMPLE_COUNTS`].
+    pub fn num_tracked_samples(&self, u: tsk_id_t) -> Result<u64, TskitError> {
+        let mut n = u64::MAX;
+        let np: *mut u64 = &mut n;
+        let code = unsafe { ll_bindings::tsk_tree_get_num_tracked_samples(self.as_ptr(), u, np) };
+        handle_tsk_return_value!(code, n)
+    }
+
+    /// Calculate the average Kendall-Colijn (`K-C`) distance between
+    /// pairs of trees whose intervals overlap.
+    ///
+    /// # Note
+    ///
+    /// * [Citation](https://doi.org/10.1093/molbev/msw124)
+    ///
+    /// # Parameters
+    ///
+    /// * `lambda` specifies the relative weight of topology and branch length.
+    ///   If `lambda` is 0, we only consider topology.
+    ///   If `lambda` is 1, we only consider branch lengths.
+    pub fn kc_distance(&self, other: &Tree, lambda: f64) -> Result<f64, TskitError> {
+        let mut kc = f64::NAN;
+        let kcp: *mut f64 = &mut kc;
+        let code = unsafe {
+            ll_bindings::tsk_tree_kc_distance(self.as_ptr(), other.as_ptr(), lambda, kcp)
+        };
+        handle_tsk_return_value!(code, kc)
+    }
 }
 
 impl streaming_iterator::StreamingIterator for Tree {
@@ -763,6 +811,7 @@ impl TreeSequence {
     /// # Parameters
     ///
     /// * `lambda` specifies the relative weight of topology and branch length.
+    ///    See [`Tree::kc_distance`] for more details.
     pub fn kc_distance(&self, other: &TreeSequence, lambda: f64) -> Result<f64, TskitError> {
         let mut kc: f64 = f64::NAN;
         let kcp: *mut f64 = &mut kc;
@@ -771,6 +820,11 @@ impl TreeSequence {
         };
         handle_tsk_return_value!(code, kc)
     }
+
+    // FIXME: document
+    pub fn num_samples(&self) -> tsk_size_t {
+        unsafe { ll_bindings::tsk_treeseq_get_num_samples(self.as_ptr()) }
+    }
 }
 
 #[cfg(test)]
@@ -799,6 +853,51 @@ mod test_trees {
         tables.tree_sequence().unwrap()
     }
 
+    fn make_small_table_collection_two_trees() -> TableCollection {
+        // The two trees are:
+        //  0
+        // +++
+        // | |  1
+        // | | +++
+        // 2 3 4 5
+
+        //     0
+        //   +-+-+
+        //   1   |
+        // +-+-+ |
+        // 2 4 5 3
+
+        let mut tables = TableCollection::new(1000.).unwrap();
+        tables.add_node(0, 2.0, TSK_NULL, TSK_NULL).unwrap();
+        tables.add_node(0, 1.0, TSK_NULL, TSK_NULL).unwrap();
+        tables
+            .add_node(TSK_NODE_IS_SAMPLE, 0.0, TSK_NULL, TSK_NULL)
+            .unwrap();
+        tables
+            .add_node(TSK_NODE_IS_SAMPLE, 0.0, TSK_NULL, TSK_NULL)
+            .unwrap();
+        tables
+            .add_node(TSK_NODE_IS_SAMPLE, 0.0, TSK_NULL, TSK_NULL)
+            .unwrap();
+        tables
+            .add_node(TSK_NODE_IS_SAMPLE, 0.0, TSK_NULL, TSK_NULL)
+            .unwrap();
+        tables.add_edge(500., 1000., 0, 1).unwrap();
+        tables.add_edge(0., 500., 0, 2).unwrap();
+        tables.add_edge(0., 1000., 0, 3).unwrap();
+        tables.add_edge(500., 1000., 1, 2).unwrap();
+        tables.add_edge(0., 1000., 1, 4).unwrap();
+        tables.add_edge(0., 1000., 1, 5).unwrap();
+        tables.full_sort().unwrap();
+        tables.build_index(0).unwrap();
+        tables
+    }
+
+    fn treeseq_from_small_table_collection_two_trees() -> TreeSequence {
+        let tables = make_small_table_collection_two_trees();
+        tables.tree_sequence().unwrap()
+    }
+
     #[test]
     fn test_create_treeseq_new_from_tables() {
         let tables = make_small_table_collection();
@@ -877,18 +976,46 @@ mod test_trees {
         }
     }
 
+    #[test]
+    fn test_num_tracked_samples() {
+        let treeseq = treeseq_from_small_table_collection();
+        assert_eq!(treeseq.inner.num_samples, 2);
+        let mut tree_iter = treeseq.tree_iterator(TreeFlags::default()).unwrap();
+        if let Some(tree) = tree_iter.next() {
+            assert_eq!(tree.num_tracked_samples(2).unwrap(), 1);
+            assert_eq!(tree.num_tracked_samples(1).unwrap(), 1);
+            assert_eq!(tree.num_tracked_samples(0).unwrap(), 2);
+        }
+    }
+
+    #[should_panic]
+    #[test]
+    fn test_num_tracked_samples_not_tracking_samples() {
+        let treeseq = treeseq_from_small_table_collection();
+        assert_eq!(treeseq.inner.num_samples, 2);
+        let mut tree_iter = treeseq.tree_iterator(TreeFlags::NO_SAMPLE_COUNTS).unwrap();
+        if let Some(tree) = tree_iter.next() {
+            assert_eq!(tree.num_tracked_samples(2).unwrap(), 0);
+            assert_eq!(tree.num_tracked_samples(1).unwrap(), 0);
+            assert_eq!(tree.num_tracked_samples(0).unwrap(), 0);
+        }
+    }
+
     #[test]
     fn test_iterate_samples() {
         let tables = make_small_table_collection();
         let treeseq = tables.tree_sequence().unwrap();
 
         let mut tree_iter = treeseq.tree_iterator(TreeFlags::SAMPLE_LISTS).unwrap();
         if let Some(tree) = tree_iter.next() {
+            assert!(!tree.flags.contains(TreeFlags::NO_SAMPLE_COUNTS));
+            assert!(tree.flags.contains(TreeFlags::SAMPLE_LISTS));
             let mut s = vec![];
             for i in tree.samples(0).unwrap() {
                 s.push(i);
             }
             assert_eq!(s.len(), 2);
+            assert_eq!(s.len(), tree.num_tracked_samples(0).unwrap() as usize);
             assert_eq!(s[0], 1);
             assert_eq!(s[1], 2);
 
@@ -899,12 +1026,30 @@ mod test_trees {
                 }
                 assert_eq!(s.len(), 1);
                 assert_eq!(s[0], u);
+                assert_eq!(s.len(), tree.num_tracked_samples(u).unwrap() as usize);
             }
         } else {
             panic!("Expected a tree");
         }
     }
 
+    #[test]
+    fn test_iterate_samples_two_trees() {
+        let treeseq = treeseq_from_small_table_collection_two_trees();
+        assert_eq!(treeseq.inner.num_trees, 2);
+        let mut tree_iter = treeseq.tree_iterator(TreeFlags::SAMPLE_LISTS).unwrap();
+        while let Some(tree) = tree_iter.next() {
+            for n in tree.nodes(NodeTraversalOrder::Preorder) {
+                let mut nsamples = 0;
+                for _ in tree.samples(n).unwrap() {
+                    nsamples += 1;
+                }
+                assert!(nsamples > 0);
+                assert_eq!(nsamples, tree.num_tracked_samples(n).unwrap());
+            }
+        }
+    }
+
     #[test]
     fn test_kc_distance_naive_test() {
         let ts1 = treeseq_from_small_table_collection();