| line |
true |
false |
branch |
|
219
|
0 |
5 |
unless defined $options{'sample_size'} |
|
222
|
4 |
1 |
unless defined $options{'threads'} |
|
225
|
0 |
5 |
if ($options{'threads'} > 1 and not $Bio::Phylo::EvolutionaryModels::Config{'useithreads'}) |
|
231
|
0 |
5 |
unless (defined $options{'algorithm'}) |
|
237
|
0 |
5 |
unless (defined $methods_require{$options{'algorithm'}}) |
|
244
|
0 |
8 |
unless (defined $options{'algorithm_options'}{$_}) |
|
252
|
0 |
0 |
if (defined $options{'incomplete_sampling'} and $options{'incomplete_sampling'} and not defined $options{'algorithm_options'}{'sampling_probability'}) |
|
262
|
0 |
5 |
unless (defined $options{'model'} or $options{'algorithm'} eq 'constant_rate_bd') |
|
275
|
0 |
5 |
if ($options{'threads'} > 1) { } |
|
300
|
0 |
0 |
if scalar @output < $index |
|
307
|
0 |
0 |
unless (defined $options{'output_format'} and $options{'output_format'} eq 'newick') |
|
326
|
0 |
5 |
if (defined $options{'output_format'} and $options{'output_format'} eq 'newick') { } |
|
|
4 |
2 |
elsif (defined $options{'output_format'} and $options{'output_format'} eq 'forest') { } |
|
425
|
0 |
16 |
unless ($candidate->is_ultrametric(1e-06)) |
|
443
|
5 |
11 |
if ($expected_samples > 1 or rand 1 < $expected_samples) |
|
455
|
0 |
5 |
if (defined $options{'counter'}) |
|
513
|
40 |
1148 |
if ($count->[$index] == $options{'tree_size'}) |
|
521
|
7 |
8 |
if $total_duration == 0 |
|
537
|
5 |
3 |
if ($expected_samples > 1 or rand 1 < $expected_samples) |
|
560
|
0 |
5 |
if (defined $options{'counter'}) |
|
616
|
0 |
1 |
if (ref $sampling_probability and scalar @{$sampling_probability;} != $mstar - $options{'tree_size'} + 1) |
|
627
|
0 |
1 |
unless (ref $sampling_probability) |
|
668
|
1091 |
605 |
if ($count->[$index] >= $options{'tree_size'}) |
|
684
|
1091 |
605 |
if ($count->[$index] >= $options{'tree_size'}) |
|
695
|
6 |
7 |
if $total_prob == 0 |
|
704
|
0 |
7 |
if $expected_samples > $options{'sample_size'} - scalar(@sample) |
|
712
|
5 |
3 |
if ($expected_samples > 1 or rand 1 < $expected_samples) |
|
738
|
0 |
5 |
if (defined $options{'counter'}) |
|
790
|
0 |
5 |
unless ($tree->is_ultrametric(1e-06)) |
|
810
|
0 |
5 |
if (defined $options{'counter'}) |
|
857
|
0 |
5 |
if ($br == $dr) { } |
|
871
|
0 |
45 |
if ($br == $dr) { } |
|
940
|
180 |
225 |
if $speciation_hash{$_} > $spec_index |
|
951
|
0 |
5 |
if (defined $options{'counter'}) |
|
1056
|
0 |
50 |
unless (defined $options{'tree_size'} or defined $options{'tree_age'}) |
|
1063
|
0 |
50 |
unless defined $options{'tree_size'} |
|
1064
|
50 |
0 |
unless defined $options{'tree_age'} |
|
1067
|
0 |
50 |
unless defined $options{'birth_rate'} |
|
1069
|
22 |
28 |
if defined $options{'death_rate'} and $options{'death_rate'} == 0 |
|
1086
|
0 |
50 |
if (defined $options{'root_edge'} and $options{'root_edge'}) { } |
|
1099
|
28 |
22 |
if (defined $options{'death_rate'}) { } |
|
1127
|
0 |
3096 |
if $time > $options{'tree_age'} |
|
1134
|
1843 |
1253 |
if ($next_speciation < $next_extinction or not defined $next_extinction) |
|
1165
|
14 |
3082 |
unless $tree_size |
|
1167
|
2884 |
198 |
if (defined $options{'death_rate'}) { } |
|
1209
|
0 |
0 |
unless (defined $options{'tree_size'} or defined $options{'tree_age'}) |
|
1215
|
0 |
0 |
unless (defined $options{'K_dash'}) |
|
1221
|
0 |
0 |
unless defined $options{'tree_size'} |
|
1222
|
0 |
0 |
unless defined $options{'tree_age'} |
|
1225
|
0 |
0 |
unless defined $options{'maximal_birth_rate'} |
|
1227
|
0 |
0 |
if defined $options{'death_rate'} and $options{'death_rate'} == 0 |
|
1248
|
0 |
0 |
if (defined $options{'root_edge'} and $options{'root_edge'}) { } |
|
1261
|
0 |
0 |
if (defined $options{'death_rate'}) { } |
|
1289
|
0 |
0 |
if $time > $options{'tree_age'} |
|
1296
|
0 |
0 |
if ($next_speciation < $next_extinction or not defined $next_extinction) |
|
1327
|
0 |
0 |
unless $tree_size |
|
1330
|
0 |
0 |
if ($options{'birth_rate'} == 0) { } |
|
1337
|
0 |
0 |
if (defined $options{'death_rate'}) { } |
|
1372
|
0 |
0 |
unless (defined $options{'tree_size'} or defined $options{'tree_age'}) |
|
1379
|
0 |
0 |
unless defined $options{'tree_size'} |
|
1380
|
0 |
0 |
unless defined $options{'tree_age'} |
|
1406
|
0 |
0 |
if (defined $options{'root_edge'} and $options{'root_edge'}) { } |
|
1446
|
0 |
0 |
if $time > $options{'tree_age'} |
|
1449
|
0 |
0 |
if ($next_rate_change - $time_last < &min($next_extinction, $next_speciation)) { } |
|
1464
|
0 |
0 |
if ($next_speciation < $next_extinction or not defined $next_extinction) |
|
1496
|
0 |
0 |
unless $tree_size |
|
1500
|
0 |
0 |
if (scalar(@terminals) % 100 == 0) |
|
1535
|
0 |
0 |
unless (defined $options{'tree_size'} or defined $options{'tree_age'}) |
|
1542
|
0 |
0 |
unless defined $options{'tree_size'} |
|
1543
|
0 |
0 |
unless defined $options{'tree_age'} |
|
1546
|
0 |
0 |
unless defined $options{'birth_rate'} |
|
1547
|
0 |
0 |
unless defined $options{'evolving_std'} |
|
1566
|
0 |
0 |
if (defined $options{'root_edge'} and $options{'root_edge'}) { } |
|
1590
|
0 |
0 |
if $time > $options{'tree_age'} |
|
1634
|
0 |
0 |
if ($new_speciation_rate < 0) |
|
1647
|
0 |
0 |
if ($net_rate == 0) |
|
1651
|
0 |
0 |
unless $tree_size |
|
1685
|
0 |
0 |
unless (defined $options{'tree_size'} or defined $options{'tree_age'}) |
|
1692
|
0 |
0 |
unless defined $options{'tree_size'} |
|
1693
|
0 |
0 |
unless defined $options{'tree_age'} |
|
1710
|
0 |
0 |
if ($rate_times_in[0] != 0) |
|
1715
|
0 |
0 |
if (scalar @birth_rates_in != scalar @death_rates_in) |
|
1720
|
0 |
0 |
if (scalar @birth_rates_in != scalar @rate_times_in) |
|
1741
|
0 |
0 |
if (defined $options{'root_edge'} and $options{'root_edge'}) { } |
|
1744
|
0 |
0 |
if ($birth_rates[0] > 0) { } |
|
1759
|
0 |
0 |
if ($death_rates[0] > 0) { } |
|
1799
|
0 |
0 |
if $time > $options{'tree_age'} |
|
1802
|
0 |
0 |
if ($next_rate_change - $time_last < &min($next_extinction, $next_speciation)) { } |
|
1816
|
0 |
0 |
if (scalar @rate_times_in) { } |
|
1828
|
0 |
0 |
if ($next_speciation < $next_extinction) { } |
|
1853
|
0 |
0 |
if ($net_birth_rate == 0) |
|
1867
|
0 |
0 |
if ($next_speciation < $next_extinction or not defined $next_extinction) |
|
1909
|
0 |
0 |
unless $tree_size |
|
1911
|
0 |
0 |
if ($net_birth_rate > 0) { } |
|
1919
|
0 |
0 |
if ($net_death_rate > 0) { } |
|
1954
|
0 |
0 |
unless (defined $options{'tree_size'} or defined $options{'tree_age'}) |
|
1961
|
0 |
0 |
unless defined $options{'tree_size'} |
|
1962
|
0 |
0 |
unless defined $options{'tree_age'} |
|
1965
|
0 |
0 |
unless defined $options{'birth_rate'} |
|
1966
|
0 |
0 |
unless defined $options{'model_param'} |
|
1985
|
0 |
0 |
if (defined $options{'root_edge'} and $options{'root_edge'}) { } |
|
2009
|
0 |
0 |
if $time > $options{'tree_age'} |
|
2052
|
0 |
0 |
if ($new_speciation_rate < 0) |
|
2062
|
0 |
0 |
if ($net_rate == 0) |
|
2066
|
0 |
0 |
unless $tree_size |
|
2128
|
15 |
972 |
unless defined $node |
|
2129
|
15 |
972 |
unless defined $time |
|
2132
|
249 |
738 |
if ($time + $node->get_branch_length >= $age) |
|
2135
|
114 |
135 |
unless $node->is_terminal |
|
2143
|
303 |
435 |
if $node->is_terminal |
|
2180
|
144 |
638 |
if (abs(($_->get_generic('root_distance') - $tree_height) / $tree_height) < 1e-06) |
|
2190
|
0 |
5 |
if (@names < $size) |
|
2206
|
0 |
0 |
if (abs(($_->get_generic('root_distance') - $tree_height) / $tree_height) < 1e-06) |
|
2243
|
0 |
0 |
unless $height > 0 |
|
2245
|
0 |
0 |
unless $leaves |
|
2249
|
0 |
0 |
unless (abs(($_->get_generic('root_distance') - $height) / $height) < 1e-06) |
|
2286
|
782 |
729 |
if ($node->is_terminal) { } |
|
2287
|
94 |
688 |
if (not $keep{$node->get_name}) |
|
2295
|
13787 |
2718 |
if $keep{$tip->get_name} |
|
2297
|
25 |
704 |
if (not $seen_tip_to_keep) |
|
2331
|
0 |
44 |
if $end_time == 0 |
|
2340
|
1789 |
1239 |
if (scalar @extinction == 0 or scalar @speciation and $speciation[0] < $extinction[0]) { } |
|
2372
|
44 |
3578 |
unless defined $node |
|
2373
|
44 |
3578 |
unless defined $time |
|
2377
|
1833 |
1789 |
if $node->is_terminal |
|
2408
|
1506 |
5 |
if (scalar @_) { } |
|
2420
|
166 |
1345 |
if ($root_distance > $root->get_generic('tree_height')) |
|
2425
|
1511 |
0 |
if (defined $children) |
|
2449
|
0 |
0 |
if $k > $n or $k < 0 |