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"visit_8hpp_source.html":[10,0,0,0,0,0,2,0,6], "wrapper_8hpp_source.html":[10,0,0,0,0,4,0,5], -"zip__range_8hpp_source.html":[10,0,0,0,0,6,0,5], -"":[8,0,3], -"":[8,0,4,5,1], -"":[8,0,4,11,0], -"":[8,0,4,4,1,0], -"":[8,0,4,0,4,0], -"":[8,0,4,4,1,3], -"":[8,0,4,0,2,0], -"":[8,0,2,0], -"":[8,0,2,0,2], -"":[8,0,5], -"":[8,0,4,4,1,1], -"":[8,0,4,4,1,2,0], -"":[8,0,4,0,3], -"":[8,0,2,0,0], -"":[8,0,4,2], -"":[8,0,4,5,2,0], -"":[8,0,4,5,0,0], -"":[8,0,4,5,2], -"":[8,0,2,2] +"zip__range_8hpp_source.html":[10,0,0,0,0,6,0,5] }; diff --git a/newick_generator.html b/newick_generator.html index d26b9dc9..eb1ff630 100644 --- a/newick_generator.html +++ b/newick_generator.html @@ -217,9 +217,9 @@

quetzal::format::newick::TreeAlign
Set a root node branch length to zero. Remove all nested comments.
Definition: from_network.hpp:180

Since there are no comments stored in the labels of the generated random tree, the output of the different flavors are here quite similar:

Output

-
1 (,((,),(,))):0.0;
-
2 (,((,),(,)));
-
3 (,((,),(,)));
+
1 ((,),((,),)):0.0;
+
2 ((,),((,),));
+
3 ((,),((,),));

Custom properties

@@ -280,7 +280,7 @@

edge_info
Definition: newick_parser_2.cpp:12
vertex_info
Definition: coalescence_binary_tree_2.cpp:5

Output

-
1 ((O:2,(C:5,N:9)P:6)B:4,(I:4,U:0)S:3)O:0.0;
+
1 ((K:1,U:7)B:9,(W:0,(G:2,A:2)D:5)W:8)A:0.0;

From a Quetzal k-ary tree

@@ -320,9 +320,9 @@

quetzal::coalescence::get_random_k_ary_tree
std::pair< quetzal::coalescence::k_ary_tree< Vertex, Edge >, typename quetzal::coalescence::k_ary_tree< Vertex, Edge >::vertex_descriptor > get_random_k_ary_tree(int n_leaves, Generator &rng)
Generate a random k-ary tree.
Definition: k_ary_tree.hpp:761

Since there are no comments stored in the labels of the generated random tree, the output of the different flavors are here quite similar:

Output

-
1 (,((,),(,))):0.0;
-
2 (,((,),(,)));
-
3 (,((,),(,)));
+
1 ((,),(,(,))):0.0;
+
2 ((,),(,(,)));
+
3 ((,),(,(,)));

Custom properties

@@ -385,7 +385,7 @@

2 2
3 2
4 2
-
5 (E:0,(X:6,(I:8,(R:5,F:6)L:1)Q:6)E:8)P;
+
5 ((O:1,P:3)U:0,(D:0,(J:3,L:0)M:8)X:3)O;

Interfacing legacy code

diff --git a/spatial_graph_local_process.html b/spatial_graph_local_process.html index a45603c7..5b62ba5c 100644 --- a/spatial_graph_local_process.html +++ b/spatial_graph_local_process.html @@ -305,9 +305,9 @@

50 }

Output

1 Time series:
-
2 at vertex 0 : 1 1 1 1 3 5 6 10 17 25
-
3 at vertex 1 : 1 1 1 2 3 3 4 5 10 15
-
4 at vertex 2 : 1 1 2 4 5 9 14 23 37 57
+
2 at vertex 0 : 1 1 2 3 5 9 14 20 22 43
+
3 at vertex 1 : 1 1 2 4 8 9 10 20 34 40
+
4 at vertex 2 : 1 1 1 1 2 2 3 6 11 15
5 at vertex 3 : 0 0 0 0 0 0 0 0 0 0
6 at vertex 4 : 0 0 0 0 0 0 0 0 0 0
7 at vertex 5 : 0 0 0 0 0 0 0 0 0 0
@@ -375,9 +375,9 @@

52 }

Output

1 Time series:
-
2 at vertex 0 : 1 5 27 96 184 824 1426 590 1095 1468
-
3 at vertex 1 : 1 2 6 32 189 774 1672 0 0 0
-
4 at vertex 2 : 1 2 8 29 157 671 1154 768 1071 993
+
2 at vertex 0 : 1 2 8 32 101 519 1443 1051 1469 1005
+
3 at vertex 1 : 1 4 24 127 438 1098 1214 1079 1461 764
+
4 at vertex 2 : 1 3 21 103 445 909 1075 828 1334 591
5 at vertex 3 : 0 0 0 0 0 0 0 0 0 0
6 at vertex 4 : 0 0 0 0 0 0 0 0 0 0
7 at vertex 5 : 0 0 0 0 0 0 0 0 0 0
@@ -498,8 +498,8 @@

1 Time series:
2 at vertex 0 :
3  P1 : 200 0 0 0 0 0 0 0 0 0
-
4  P2 : 1 20.2366 5.5315 6.90286 8.5815 10.6186 13.0644 15.9632 19.3453 23.2178
-
5  P3 : 1 10.1322 0 0 0 0 0 0 0 0
+
4  P2 : 1 17.7013 21.627 23.2467 23.8997 24.6477 25.8431 27.8098 31.074 36.524
+
5  P3 : 1 6.81998 8.2145 8.61525 8.4973 8.19094 7.69996 6.94457 5.8236 4.2638
6 
7 at vertex 1 :
8  P1 : 0 0 0 0 0 0 0 0 0 0