Add tree_pos to tsk_tree_t struct

Author: duncanMR

c/tskit/trees.c

@@ -4565,6 +4565,11 @@ tsk_tree_init(tsk_tree_t *self, const tsk_treeseq_t *tree_sequence, tsk_flags_t
             goto out;
         }
     }
+
+    ret = tsk_tree_position_init(&self->tree_pos, tree_sequence, 0);
+    if (ret != 0) {
+        goto out;
+    }
     ret = tsk_tree_clear(self);
 out:
     return ret;
@@ -4613,6 +4618,7 @@ tsk_tree_free(tsk_tree_t *self)
     tsk_safe_free(self->next_sample);
     tsk_safe_free(self->num_children);
     tsk_safe_free(self->edge);
+    tsk_tree_position_free(&self->tree_pos);
     return 0;
 }
 

c/tskit/trees.h

@@ -111,6 +111,28 @@ typedef struct {
     tsk_table_collection_t *tables;
 } tsk_treeseq_t;
 
+typedef struct {
+    tsk_id_t index;
+    struct {
+        double left;
+        double right;
+    } interval;
+    struct {
+        tsk_id_t start;
+        tsk_id_t stop;
+        const tsk_id_t *order;
+    } in;
+    struct {
+        tsk_id_t start;
+        tsk_id_t stop;
+        const tsk_id_t *order;
+    } out;
+    tsk_id_t left_current_index;
+    tsk_id_t right_current_index;
+    int direction;
+    const tsk_treeseq_t *tree_sequence;
+} tsk_tree_position_t;
+
 /**
 @brief A single tree in a tree sequence.
 
@@ -256,6 +278,7 @@ typedef struct {
     int direction;
     tsk_id_t left_index;
     tsk_id_t right_index;
+    tsk_tree_position_t tree_pos;
 } tsk_tree_t;
 
 /****************************************************************************/
@@ -1823,31 +1846,6 @@ bool tsk_tree_equals(const tsk_tree_t *self, const tsk_tree_t *other);
 int tsk_diff_iter_init_from_ts(
     tsk_diff_iter_t *self, const tsk_treeseq_t *tree_sequence, tsk_flags_t options);
 
-/* Temporarily putting this here to avoid problems with doxygen. Will need to
- * move up the file later when it gets incorporated into the tsk_tree_t object.
- */
-typedef struct {
-    tsk_id_t index;
-    struct {
-        double left;
-        double right;
-    } interval;
-    struct {
-        tsk_id_t start;
-        tsk_id_t stop;
-        const tsk_id_t *order;
-    } in;
-    struct {
-        tsk_id_t start;
-        tsk_id_t stop;
-        const tsk_id_t *order;
-    } out;
-    tsk_id_t left_current_index;
-    tsk_id_t right_current_index;
-    int direction;
-    const tsk_treeseq_t *tree_sequence;
-} tsk_tree_position_t;
-
 int tsk_tree_position_init(
     tsk_tree_position_t *self, const tsk_treeseq_t *tree_sequence, tsk_flags_t options);
 int tsk_tree_position_free(tsk_tree_position_t *self);

docs/_config.yml

@@ -77,7 +77,7 @@ sphinx:
           ["c:identifier", "FILE"],
           ["c:identifier", "bool"],
           # This is for the anonymous interval struct embedded in the tsk_tree_t.
-          ["c:identifier", "tsk_tree_t.@1"],
+          ["c:identifier", "tsk_tree_t.@4"],
           ["c:type", "int32_t"],
           ["c:type", "uint32_t"],
           ["c:type", "uint64_t"],