| 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 $options{'output_format'} eq 'forest') { }
|
|
425
|
0 |
12 |
unless ($candidate->is_ultrametric(1e-06))
|
|
443
|
5 |
7 |
if ($expected_samples > 1 or rand 1 < $expected_samples)
|
|
455
|
0 |
5 |
if (defined $options{'counter'})
|
|
513
|
79 |
1936 |
if ($count->[$index] == $options{'tree_size'})
|
|
521
|
21 |
10 |
if $total_duration == 0
|
|
537
|
5 |
7 |
if ($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 $sampling_probability)
|
|
668
|
1115 |
616 |
if ($count->[$index] >= $options{'tree_size'})
|
|
684
|
1115 |
616 |
if ($count->[$index] >= $options{'tree_size'})
|
|
695
|
8 |
9 |
if $total_prob == 0
|
|
704
|
1 |
8 |
if $expected_samples > $options{'sample_size'} - scalar(@sample)
|
|
712
|
5 |
4 |
if ($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 |
66 |
unless (defined $options{'tree_size'} or defined $options{'tree_age'})
|
|
1063
|
0 |
66 |
unless defined $options{'tree_size'}
|
|
1064
|
66 |
0 |
unless defined $options{'tree_age'}
|
|
1067
|
0 |
66 |
unless defined $options{'birth_rate'}
|
|
1069
|
18 |
48 |
if defined $options{'death_rate'} and $options{'death_rate'} == 0
|
|
1086
|
0 |
66 |
if (defined $options{'root_edge'} and $options{'root_edge'}) { }
|
|
1099
|
48 |
18 |
if (defined $options{'death_rate'}) { }
|
|
1127
|
0 |
3938 |
if $time > $options{'tree_age'}
|
|
1134
|
2296 |
1642 |
if ($next_speciation < $next_extinction or not defined $next_extinction)
|
|
1165
|
30 |
3908 |
unless $tree_size
|
|
1167
|
3746 |
162 |
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 |
1112 |
unless defined $node
|
|
2129
|
15 |
1112 |
unless defined $time
|
|
2132
|
257 |
870 |
if ($time + $node->get_branch_length >= $age)
|
|
2135
|
110 |
147 |
unless $node->is_terminal
|
|
2143
|
366 |
504 |
if $node->is_terminal
|
|
2180
|
147 |
484 |
if (abs(($_->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) / $height) < 1e-06)
|
|
2286
|
631 |
565 |
if ($node->is_terminal) { }
|
|
2287
|
97 |
534 |
if (not $keep{$node->get_name})
|
|
2295
|
9665 |
2276 |
if $keep{$tip->get_name}
|
|
2297
|
29 |
536 |
if (not $seen_tip_to_keep)
|
|
2331
|
0 |
60 |
if $end_time == 0
|
|
2340
|
2242 |
1612 |
if (scalar @extinction == 0 or scalar @speciation and $speciation[0] < $extinction[0]) { }
|
|
2372
|
60 |
4484 |
unless defined $node
|
|
2373
|
60 |
4484 |
unless defined $time
|
|
2377
|
2302 |
2242 |
if $node->is_terminal
|
|
2408
|
1191 |
5 |
if (scalar @_) { }
|
|
2420
|
126 |
1070 |
if ($root_distance > $root->get_generic('tree_height'))
|
|
2425
|
1196 |
0 |
if (defined $children)
|
|
2449
|
0 |
0 |
if $k > $n or $k < 0
|