| blib/lib/Bio/Phylo/Forest/TreeRole.pm | |||
|---|---|---|---|
| Criterion | Covered | Total | % |
| subroutine | 79 | 146 | 54.1 |
| 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 |
| 13 | 31 | n/a | BEGIN |
| 85 | 196 | Yes | new |
| 90 | 0 | No | __ANON__ |
| 90 | 0 | No | _parse_newick |
| 90 | 0 | No | find_node |
| 90 | 0 | No | get_leaf_nodes |
| 90 | 0 | No | get_nodes |
| 90 | 0 | No | get_root_node |
| 90 | 0 | No | height |
| 90 | 0 | No | id |
| 90 | 0 | No | move_id_to_bootstrap |
| 90 | 0 | No | number_nodes |
| 90 | 0 | No | remove_Node |
| 90 | 0 | No | reroot |
| 90 | 0 | No | score |
| 90 | 0 | No | set_root |
| 90 | 0 | No | splice |
| 90 | 0 | n/a | total_branch_length |
| 90 | 0 | n/a | verbose |
| 97 | 31 | n/a | BEGIN |
| 117 | 0 | Yes | new_from_bioperl |
| 154 | 0 | n/a | _recurse |
| 186 | 9 | n/a | _analyze |
| 253 | 1 | Yes | get_midpoint |
| 303 | 151 | Yes | get_terminals |
| 308 | 4483 | n/a | __ANON__ |
| 318 | 0 | n/a | __ANON__ |
| 350 | 13 | Yes | get_internals |
| 369 | 1 | Yes | get_cherries |
| 403 | 0 | Yes | get_all_rootings |
| 411 | 0 | n/a | __ANON__ |
| 448 | 1804 | Yes | get_root |
| 495 | 0 | Yes | get_ntax |
| 516 | 3 | Yes | get_tallest_tip |
| 554 | 5 | Yes | get_nodes_for_taxa |
| 590 | 0 | Yes | get_mrca |
| 639 | 2 | Yes | is_binary |
| 642 | 33 | n/a | __ANON__ |
| 677 | 44 | Yes | is_ultrametric |
| 682 | 840 | n/a | __ANON__ |
| 726 | 2 | Yes | is_monophyletic |
| 761 | 0 | Yes | is_paraphyletic |
| 798 | 3 | Yes | is_clade |
| 841 | 1 | Yes | is_cladogram |
| 895 | 1 | Yes | calc_branch_length_distance |
| 916 | 2 | Yes | calc_branch_length_score |
| 949 | 23 | n/a | _calc_branch_diffs |
| 956 | 46 | n/a | __ANON__ |
| 1057 | 40 | Yes | calc_tree_length |
| 1060 | 628 | n/a | __ANON__ |
| 1088 | 3 | Yes | calc_tree_height |
| 1109 | 1 | Yes | calc_number_of_nodes |
| 1130 | 43 | Yes | calc_number_of_terminals |
| 1151 | 5 | Yes | calc_number_of_internals |
| 1173 | 1 | Yes | calc_number_of_cherries |
| 1205 | 4 | Yes | calc_total_paths |
| 1231 | 1 | Yes | calc_redundancy |
| 1257 | 6 | Yes | calc_imbalance |
| 1263 | 119 | n/a | __ANON__ |
| 1312 | 0 | Yes | calc_i2 |
| 1385 | 0 | Yes | calc_gamma |
| 1475 | 1 | Yes | calc_fiala_stemminess |
| 1522 | 3 | Yes | calc_rohlf_stemminess |
| 1588 | 4 | Yes | calc_resolution |
| 1617 | 6 | Yes | calc_branching_times |
| 1628 | 125 | n/a | __ANON__ |
| 1670 | 3 | Yes | calc_waiting_times |
| 1699 | 1 | Yes | calc_node_ages |
| 1702 | 5 | n/a | __ANON__ |
| 1737 | 2 | Yes | calc_ltt |
| 1774 | 21 | Yes | calc_symdiff |
| 1803 | 0 | Yes | calc_avtd |
| 1830 | 0 | Yes | calc_fp |
| 1869 | 0 | Yes | calc_fp_mean |
| 1890 | 0 | Yes | calc_es |
| 1924 | 0 | Yes | calc_es_mean |
| 1945 | 0 | Yes | calc_pe |
| 1966 | 0 | Yes | calc_pe_mean |
| 1987 | 0 | Yes | calc_shapley |
| 2037 | 0 | n/a | _calc_shapley_traverse |
| 2091 | 0 | Yes | calc_shapley_mean |
| 2159 | 141 | Yes | visit_depth_first |
| 2207 | 0 | Yes | visit_breadth_first |
| 2228 | 3 | Yes | visit_level_order |
| 2261 | 1 | Yes | chronompl |
| 2264 | 7 | n/a | __ANON__ |
| 2304 | 0 | Yes | grafenbl |
| 2308 | 0 | n/a | __ANON__ |
| 2327 | 0 | n/a | __ANON__ |
| 2357 | 2 | Yes | agetobl |
| 2392 | 0 | Yes | rankprobbl |
| 2437 | 1 | Yes | ultrametricize |
| 2475 | 1 | Yes | scale |
| 2505 | 2 | Yes | resolve |
| 2559 | 0 | Yes | replicate |
| 2587 | 0 | n/a | __ANON__ |
| 2602 | 0 | n/a | __ANON__ |
| 2603 | 0 | n/a | __ANON__ |
| 2617 | 0 | n/a | __ANON__ |
| 2639 | 0 | n/a | __ANON__ |
| 2698 | 0 | n/a | _make_taxon_name |
| 2741 | 0 | Yes | generize |
| 2820 | 10 | Yes | prune_tips |
| 2846 | 24 | n/a | _get_tip_objects |
| 2890 | 14 | Yes | keep_tips |
| 2915 | 262 | n/a | __ANON__ |
| 2962 | 3 | Yes | negative_to_zero |
| 2987 | 2 | Yes | ladderize |
| 2991 | 18 | n/a | __ANON__ |
| 3065 | 4 | Yes | sort_tips |
| 3076 | 34 | n/a | __ANON__ |
| 3112 | 0 | Yes | exponentiate |
| 3139 | 0 | Yes | multiply |
| 3144 | 0 | n/a | __ANON__ |
| 3167 | 0 | Yes | log_transform |
| 3204 | 6 | Yes | remove_unbranched_internals |
| 3208 | 1141 | n/a | __ANON__ |
| 3286 | 0 | Yes | remove_orphans |
| 3292 | 0 | n/a | __ANON__ |
| 3299 | 0 | n/a | __ANON__ |
| 3327 | 0 | Yes | deroot |
| 3390 | 2 | Yes | clone |
| 3395 | 0 | n/a | __ANON__ |
| 3396 | 0 | n/a | __ANON__ |
| 3400 | 0 | n/a | __ANON__ |
| 3439 | 0 | Yes | to_nexus |
| 3460 | 25 | Yes | to_newick |
| 3480 | 0 | Yes | to_xml |
| 3513 | 0 | Yes | to_svg |
| 3532 | 0 | Yes | to_dom |
| 3568 | 0 | n/a | _consolidate |
| 3570 | 0 | n/a | __ANON__ |
| 3588 | 451 | n/a | _container |
| 3603 | 29342 | n/a | _type |
| 3604 | 2 | n/a | _tag |