From da606312a20690474297ccd3336e0ef8ea2d46e1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?L=C3=A9o=20Guignard?= <leo.guignard@univ-amu.fr>
Date: Fri, 27 Jun 2025 09:48:49 +0200
Subject: [PATCH] removing small typo in lineagetree manager and adding the
 number_of_nodes property

---
 src/LineageTree/lineageTree.py        |  4 +++
 src/LineageTree/lineageTreeManager.py | 46 ++++++++++++---------------
 2 files changed, 24 insertions(+), 26 deletions(-)

diff --git a/src/LineageTree/lineageTree.py b/src/LineageTree/lineageTree.py
index 9b71970..7742956 100644
--- a/src/LineageTree/lineageTree.py
+++ b/src/LineageTree/lineageTree.py
@@ -355,6 +355,10 @@ def nodes(self) -> frozenset[int]:
         """Nodes of the tree"""
         return frozenset(self._successor.keys())
 
+    @dynamic_property
+    def number_of_nodes(self) -> int:
+        return len(self.nodes)
+
     @dynamic_property
     def depth(self) -> dict[int, int]:
         """The depth of each node in the tree."""
diff --git a/src/LineageTree/lineageTreeManager.py b/src/LineageTree/lineageTreeManager.py
index 0f1564d..cf0fce8 100644
--- a/src/LineageTree/lineageTreeManager.py
+++ b/src/LineageTree/lineageTreeManager.py
@@ -412,12 +412,6 @@ def cross_lineage_edit_distance(
 
         Returns
         -------
-        Alignment
-            The alignment between the nodes by the subtrees spawned by the nodes n1,n2 and the normalization function.`
-        --
-        ΟΡ
-        --
-
         Alignment
             The alignment between the nodes by the subtrees spawned by the nodes n1,n2 and the normalization function.`
         tuple(tree,tree)
@@ -657,28 +651,28 @@ def plot_tree_distance_graphs(
                         matched_right.append(node_2)
                         l_node_2 = tree2.lT.get_chain_of_node(node_2)[-1]
                         matched_right.append(l_node_2)
-                        colors1[
-                            node_1
-                        ] = self.__calculate_distance_of_sub_tree(
-                            node_1,
-                            tree1.lT,
-                            node_2,
-                            tree2.lT,
-                            btrc,
-                            corres1,
-                            corres2,
-                            delta_tmp,
-                            self.norm_dict[norm],
-                            tree1.get_norm(node_1),
-                            tree2.get_norm(node_2),
+                        colors1[node_1] = (
+                            self.__calculate_distance_of_sub_tree(
+                                node_1,
+                                tree1.lT,
+                                node_2,
+                                tree2.lT,
+                                btrc,
+                                corres1,
+                                corres2,
+                                delta_tmp,
+                                self.norm_dict[norm],
+                                tree1.get_norm(node_1),
+                                tree2.get_norm(node_2),
+                            )
                         )
                         colors2[node_2] = colors1[node_1]
-                        colors1[
-                            tree1.lT.get_chain_of_node(node_1)[-1]
-                        ] = colors1[node_1]
-                        colors2[
-                            tree2.lT.get_chain_of_node(node_2)[-1]
-                        ] = colors2[node_2]
+                        colors1[tree1.lT.get_chain_of_node(node_1)[-1]] = (
+                            colors1[node_1]
+                        )
+                        colors2[tree2.lT.get_chain_of_node(node_2)[-1]] = (
+                            colors2[node_2]
+                        )
 
                         if tree1.lT.get_chain_of_node(node_1)[-1] != node_1:
                             matched_left.append(