| blib/lib/Bio/Phylo/Forest/TreeRole.pm | |||
|---|---|---|---|
| Criterion | Covered | Total | % |
| subroutine | 78 | 145 | 53.7 |
| pod | 77 | 92 | 83.7 |
| line | count | pod | subroutine |
|---|---|---|---|
| 2 | 31 | n/a | BEGIN |
| 3 | 31 | n/a | BEGIN |
| 4 | 31 | n/a | BEGIN |
| 5 | 31 | n/a | BEGIN |
| 6 | 31 | n/a | BEGIN |
| 7 | 31 | n/a | BEGIN |
| 8 | 31 | n/a | BEGIN |
| 9 | 31 | n/a | BEGIN |
| 10 | 31 | n/a | BEGIN |
| 11 | 31 | n/a | BEGIN |
| 12 | 31 | n/a | BEGIN |
| 84 | 225 | Yes | new |
| 89 | 0 | No | __ANON__ |
| 89 | 0 | No | _parse_newick |
| 89 | 0 | No | find_node |
| 89 | 0 | No | get_leaf_nodes |
| 89 | 0 | No | get_nodes |
| 89 | 0 | No | get_root_node |
| 89 | 0 | No | height |
| 89 | 0 | No | id |
| 89 | 0 | No | move_id_to_bootstrap |
| 89 | 0 | No | number_nodes |
| 89 | 0 | No | remove_Node |
| 89 | 0 | No | reroot |
| 89 | 0 | No | score |
| 89 | 0 | No | set_root |
| 89 | 0 | No | splice |
| 89 | 0 | n/a | total_branch_length |
| 89 | 0 | n/a | verbose |
| 96 | 31 | n/a | BEGIN |
| 116 | 0 | Yes | new_from_bioperl |
| 153 | 0 | n/a | _recurse |
| 185 | 9 | n/a | _analyze |
| 252 | 1 | Yes | get_midpoint |
| 302 | 151 | Yes | get_terminals |
| 307 | 4241 | n/a | __ANON__ |
| 317 | 0 | n/a | __ANON__ |
| 349 | 13 | Yes | get_internals |
| 368 | 1 | Yes | get_cherries |
| 402 | 0 | Yes | get_all_rootings |
| 410 | 0 | n/a | __ANON__ |
| 447 | 1716 | Yes | get_root |
| 494 | 0 | Yes | get_ntax |
| 515 | 3 | Yes | get_tallest_tip |
| 553 | 5 | Yes | get_nodes_for_taxa |
| 589 | 0 | Yes | get_mrca |
| 638 | 2 | Yes | is_binary |
| 641 | 33 | n/a | __ANON__ |
| 676 | 46 | Yes | is_ultrametric |
| 681 | 878 | n/a | __ANON__ |
| 725 | 2 | Yes | is_monophyletic |
| 760 | 0 | Yes | is_paraphyletic |
| 797 | 3 | Yes | is_clade |
| 840 | 1 | Yes | is_cladogram |
| 894 | 1 | Yes | calc_branch_length_distance |
| 915 | 2 | Yes | calc_branch_length_score |
| 948 | 23 | n/a | _calc_branch_diffs |
| 955 | 46 | n/a | __ANON__ |
| 1056 | 40 | Yes | calc_tree_length |
| 1059 | 628 | n/a | __ANON__ |
| 1087 | 3 | Yes | calc_tree_height |
| 1108 | 1 | Yes | calc_number_of_nodes |
| 1129 | 43 | Yes | calc_number_of_terminals |
| 1150 | 5 | Yes | calc_number_of_internals |
| 1172 | 1 | Yes | calc_number_of_cherries |
| 1204 | 4 | Yes | calc_total_paths |
| 1230 | 1 | Yes | calc_redundancy |
| 1256 | 6 | Yes | calc_imbalance |
| 1262 | 119 | n/a | __ANON__ |
| 1311 | 0 | Yes | calc_i2 |
| 1384 | 0 | Yes | calc_gamma |
| 1474 | 1 | Yes | calc_fiala_stemminess |
| 1521 | 3 | Yes | calc_rohlf_stemminess |
| 1587 | 4 | Yes | calc_resolution |
| 1616 | 6 | Yes | calc_branching_times |
| 1627 | 125 | n/a | __ANON__ |
| 1669 | 3 | Yes | calc_waiting_times |
| 1698 | 1 | Yes | calc_node_ages |
| 1701 | 5 | n/a | __ANON__ |
| 1736 | 2 | Yes | calc_ltt |
| 1773 | 21 | Yes | calc_symdiff |
| 1802 | 0 | Yes | calc_avtd |
| 1829 | 0 | Yes | calc_fp |
| 1868 | 0 | Yes | calc_fp_mean |
| 1889 | 0 | Yes | calc_es |
| 1923 | 0 | Yes | calc_es_mean |
| 1944 | 0 | Yes | calc_pe |
| 1965 | 0 | Yes | calc_pe_mean |
| 1986 | 0 | Yes | calc_shapley |
| 2036 | 0 | n/a | _calc_shapley_traverse |
| 2090 | 0 | Yes | calc_shapley_mean |
| 2158 | 143 | Yes | visit_depth_first |
| 2206 | 0 | Yes | visit_breadth_first |
| 2227 | 3 | Yes | visit_level_order |
| 2260 | 1 | Yes | chronompl |
| 2263 | 7 | n/a | __ANON__ |
| 2303 | 0 | Yes | grafenbl |
| 2307 | 0 | n/a | __ANON__ |
| 2326 | 0 | n/a | __ANON__ |
| 2356 | 2 | Yes | agetobl |
| 2391 | 0 | Yes | rankprobbl |
| 2436 | 1 | Yes | ultrametricize |
| 2474 | 1 | Yes | scale |
| 2504 | 2 | Yes | resolve |
| 2558 | 0 | Yes | replicate |
| 2586 | 0 | n/a | __ANON__ |
| 2601 | 0 | n/a | __ANON__ |
| 2602 | 0 | n/a | __ANON__ |
| 2616 | 0 | n/a | __ANON__ |
| 2638 | 0 | n/a | __ANON__ |
| 2697 | 0 | n/a | _make_taxon_name |
| 2740 | 0 | Yes | generize |
| 2819 | 10 | Yes | prune_tips |
| 2845 | 24 | n/a | _get_tip_objects |
| 2889 | 14 | Yes | keep_tips |
| 2914 | 258 | n/a | __ANON__ |
| 2961 | 3 | Yes | negative_to_zero |
| 2986 | 2 | Yes | ladderize |
| 2990 | 18 | n/a | __ANON__ |
| 3064 | 4 | Yes | sort_tips |
| 3075 | 34 | n/a | __ANON__ |
| 3111 | 0 | Yes | exponentiate |
| 3138 | 0 | Yes | multiply |
| 3143 | 0 | n/a | __ANON__ |
| 3166 | 0 | Yes | log_transform |
| 3203 | 6 | Yes | remove_unbranched_internals |
| 3207 | 989 | n/a | __ANON__ |
| 3285 | 0 | Yes | remove_orphans |
| 3291 | 0 | n/a | __ANON__ |
| 3298 | 0 | n/a | __ANON__ |
| 3326 | 0 | Yes | deroot |
| 3389 | 2 | Yes | clone |
| 3394 | 0 | n/a | __ANON__ |
| 3395 | 0 | n/a | __ANON__ |
| 3399 | 0 | n/a | __ANON__ |
| 3438 | 0 | Yes | to_nexus |
| 3459 | 25 | Yes | to_newick |
| 3479 | 0 | Yes | to_xml |
| 3512 | 0 | Yes | to_svg |
| 3531 | 0 | Yes | to_dom |
| 3567 | 0 | n/a | _consolidate |
| 3569 | 0 | n/a | __ANON__ |
| 3587 | 451 | n/a | _container |
| 3602 | 33007 | n/a | _type |
| 3603 | 2 | n/a | _tag |