| line |
true |
false |
branch |
|
218
|
0 |
5 |
unless defined $options{'sample_size'}
|
|
221
|
4 |
1 |
unless defined $options{'threads'}
|
|
224
|
0 |
5 |
if ($options{'threads'} > 1 and not $Bio::Phylo::EvolutionaryModels::Config{'useithreads'})
|
|
230
|
0 |
5 |
unless (defined $options{'algorithm'})
|
|
236
|
0 |
5 |
unless (defined $methods_require{$options{'algorithm'}})
|
|
243
|
0 |
8 |
unless (defined $options{'algorithm_options'}{$_})
|
|
251
|
0 |
0 |
if (defined $options{'incomplete_sampling'} and $options{'incomplete_sampling'} and not defined $options{'algorithm_options'}{'sampling_probability'})
|
|
261
|
0 |
5 |
unless (defined $options{'model'} or $options{'algorithm'} eq 'constant_rate_bd')
|
|
274
|
0 |
5 |
if ($options{'threads'} > 1) { }
|
|
299
|
0 |
0 |
if scalar @output < $index
|
|
306
|
0 |
0 |
unless (defined $options{'output_format'} and $options{'output_format'} eq 'newick')
|
|
325
|
0 |
5 |
if (defined $options{'output_format'} and $options{'output_format'} eq 'newick') { }
|
|
|
4 |
2 |
elsif (defined $options{'output_format'} and $options{'output_format'} eq 'forest') { }
|
|
424
|
0 |
14 |
unless ($candidate->is_ultrametric(1e-06))
|
|
442
|
5 |
11 |
if ($expected_samples > 1 or rand 1 < $expected_samples)
|
|
454
|
0 |
5 |
if (defined $options{'counter'})
|
|
512
|
95 |
3342 |
if ($count->[$index] == $options{'tree_size'})
|
|
520
|
35 |
20 |
if $total_duration == 0
|
|
536
|
5 |
16 |
if ($expected_samples > 1 or rand 1 < $expected_samples)
|
|
559
|
0 |
5 |
if (defined $options{'counter'})
|
|
615
|
0 |
1 |
if (ref $sampling_probability and scalar @{$sampling_probability;} != $mstar - $options{'tree_size'} + 1)
|
|
626
|
0 |
1 |
unless (ref $sampling_probability)
|
|
667
|
1141 |
617 |
if ($count->[$index] >= $options{'tree_size'})
|
|
683
|
1141 |
617 |
if ($count->[$index] >= $options{'tree_size'})
|
|
694
|
10 |
10 |
if $total_prob == 0
|
|
703
|
0 |
10 |
if $expected_samples > $options{'sample_size'} - scalar(@sample)
|
|
711
|
5 |
5 |
if ($expected_samples > 1 or rand 1 < $expected_samples)
|
|
737
|
0 |
5 |
if (defined $options{'counter'})
|
|
789
|
0 |
5 |
unless ($tree->is_ultrametric(1e-06))
|
|
809
|
0 |
5 |
if (defined $options{'counter'})
|
|
856
|
0 |
5 |
if ($br == $dr) { }
|
|
870
|
0 |
45 |
if ($br == $dr) { }
|
|
939
|
180 |
225 |
if $speciation_hash{$_} > $spec_index
|
|
950
|
0 |
5 |
if (defined $options{'counter'})
|
|
1055
|
0 |
95 |
unless (defined $options{'tree_size'} or defined $options{'tree_age'})
|
|
1062
|
0 |
95 |
unless defined $options{'tree_size'}
|
|
1063
|
95 |
0 |
unless defined $options{'tree_age'}
|
|
1066
|
0 |
95 |
unless defined $options{'birth_rate'}
|
|
1068
|
20 |
75 |
if defined $options{'death_rate'} and $options{'death_rate'} == 0
|
|
1085
|
0 |
95 |
if (defined $options{'root_edge'} and $options{'root_edge'}) { }
|
|
1098
|
75 |
20 |
if (defined $options{'death_rate'}) { }
|
|
1126
|
0 |
5423 |
if $time > $options{'tree_age'}
|
|
1133
|
3169 |
2254 |
if ($next_speciation < $next_extinction or not defined $next_extinction)
|
|
1164
|
48 |
5375 |
unless $tree_size
|
|
1166
|
5195 |
180 |
if (defined $options{'death_rate'}) { }
|
|
1208
|
0 |
0 |
unless (defined $options{'tree_size'} or defined $options{'tree_age'})
|
|
1214
|
0 |
0 |
unless (defined $options{'K_dash'})
|
|
1220
|
0 |
0 |
unless defined $options{'tree_size'}
|
|
1221
|
0 |
0 |
unless defined $options{'tree_age'}
|
|
1224
|
0 |
0 |
unless defined $options{'maximal_birth_rate'}
|
|
1226
|
0 |
0 |
if defined $options{'death_rate'} and $options{'death_rate'} == 0
|
|
1247
|
0 |
0 |
if (defined $options{'root_edge'} and $options{'root_edge'}) { }
|
|
1260
|
0 |
0 |
if (defined $options{'death_rate'}) { }
|
|
1288
|
0 |
0 |
if $time > $options{'tree_age'}
|
|
1295
|
0 |
0 |
if ($next_speciation < $next_extinction or not defined $next_extinction)
|
|
1326
|
0 |
0 |
unless $tree_size
|
|
1329
|
0 |
0 |
if ($options{'birth_rate'} == 0) { }
|
|
1336
|
0 |
0 |
if (defined $options{'death_rate'}) { }
|
|
1371
|
0 |
0 |
unless (defined $options{'tree_size'} or defined $options{'tree_age'})
|
|
1378
|
0 |
0 |
unless defined $options{'tree_size'}
|
|
1379
|
0 |
0 |
unless defined $options{'tree_age'}
|
|
1405
|
0 |
0 |
if (defined $options{'root_edge'} and $options{'root_edge'}) { }
|
|
1445
|
0 |
0 |
if $time > $options{'tree_age'}
|
|
1448
|
0 |
0 |
if ($next_rate_change - $time_last < &min($next_extinction, $next_speciation)) { }
|
|
1463
|
0 |
0 |
if ($next_speciation < $next_extinction or not defined $next_extinction)
|
|
1495
|
0 |
0 |
unless $tree_size
|
|
1499
|
0 |
0 |
if (scalar(@terminals) % 100 == 0)
|
|
1534
|
0 |
0 |
unless (defined $options{'tree_size'} or defined $options{'tree_age'})
|
|
1541
|
0 |
0 |
unless defined $options{'tree_size'}
|
|
1542
|
0 |
0 |
unless defined $options{'tree_age'}
|
|
1545
|
0 |
0 |
unless defined $options{'birth_rate'}
|
|
1546
|
0 |
0 |
unless defined $options{'evolving_std'}
|
|
1565
|
0 |
0 |
if (defined $options{'root_edge'} and $options{'root_edge'}) { }
|
|
1589
|
0 |
0 |
if $time > $options{'tree_age'}
|
|
1633
|
0 |
0 |
if ($new_speciation_rate < 0)
|
|
1646
|
0 |
0 |
if ($net_rate == 0)
|
|
1650
|
0 |
0 |
unless $tree_size
|
|
1684
|
0 |
0 |
unless (defined $options{'tree_size'} or defined $options{'tree_age'})
|
|
1691
|
0 |
0 |
unless defined $options{'tree_size'}
|
|
1692
|
0 |
0 |
unless defined $options{'tree_age'}
|
|
1709
|
0 |
0 |
if ($rate_times_in[0] != 0)
|
|
1714
|
0 |
0 |
if (scalar @birth_rates_in != scalar @death_rates_in)
|
|
1719
|
0 |
0 |
if (scalar @birth_rates_in != scalar @rate_times_in)
|
|
1740
|
0 |
0 |
if (defined $options{'root_edge'} and $options{'root_edge'}) { }
|
|
1743
|
0 |
0 |
if ($birth_rates[0] > 0) { }
|
|
1758
|
0 |
0 |
if ($death_rates[0] > 0) { }
|
|
1798
|
0 |
0 |
if $time > $options{'tree_age'}
|
|
1801
|
0 |
0 |
if ($next_rate_change - $time_last < &min($next_extinction, $next_speciation)) { }
|
|
1815
|
0 |
0 |
if (scalar @rate_times_in) { }
|
|
1827
|
0 |
0 |
if ($next_speciation < $next_extinction) { }
|
|
1852
|
0 |
0 |
if ($net_birth_rate == 0)
|
|
1866
|
0 |
0 |
if ($next_speciation < $next_extinction or not defined $next_extinction)
|
|
1908
|
0 |
0 |
unless $tree_size
|
|
1910
|
0 |
0 |
if ($net_birth_rate > 0) { }
|
|
1918
|
0 |
0 |
if ($net_death_rate > 0) { }
|
|
1953
|
0 |
0 |
unless (defined $options{'tree_size'} or defined $options{'tree_age'})
|
|
1960
|
0 |
0 |
unless defined $options{'tree_size'}
|
|
1961
|
0 |
0 |
unless defined $options{'tree_age'}
|
|
1964
|
0 |
0 |
unless defined $options{'birth_rate'}
|
|
1965
|
0 |
0 |
unless defined $options{'model_param'}
|
|
1984
|
0 |
0 |
if (defined $options{'root_edge'} and $options{'root_edge'}) { }
|
|
2008
|
0 |
0 |
if $time > $options{'tree_age'}
|
|
2051
|
0 |
0 |
if ($new_speciation_rate < 0)
|
|
2061
|
0 |
0 |
if ($net_rate == 0)
|
|
2065
|
0 |
0 |
unless $tree_size
|
|
2127
|
15 |
828 |
unless defined $node
|
|
2128
|
15 |
828 |
unless defined $time
|
|
2131
|
252 |
591 |
if ($time + $node->get_branch_length >= $age)
|
|
2134
|
116 |
136 |
unless $node->is_terminal
|
|
2142
|
230 |
361 |
if $node->is_terminal
|
|
2179
|
145 |
422 |
if (abs(($_->get_generic('root_distance') - $tree_height) / $tree_height) < 1e-06)
|
|
2189
|
0 |
5 |
if (@names < $size)
|
|
2205
|
0 |
0 |
if (abs(($_->get_generic('root_distance') - $tree_height) / $tree_height) < 1e-06)
|
|
2242
|
0 |
0 |
unless $height > 0
|
|
2244
|
0 |
0 |
unless $leaves
|
|
2248
|
0 |
0 |
unless (abs(($_->get_generic('root_distance') - $height) / $height) < 1e-06)
|
|
2285
|
567 |
510 |
if ($node->is_terminal) { }
|
|
2286
|
95 |
472 |
if (not $keep{$node->get_name})
|
|
2294
|
7344 |
1904 |
if $keep{$tip->get_name}
|
|
2296
|
26 |
484 |
if (not $seen_tip_to_keep)
|
|
2330
|
0 |
89 |
if $end_time == 0
|
|
2339
|
3115 |
2206 |
if (scalar @extinction == 0 or scalar @speciation and $speciation[0] < $extinction[0]) { }
|
|
2371
|
89 |
6230 |
unless defined $node
|
|
2372
|
89 |
6230 |
unless defined $time
|
|
2376
|
3204 |
3115 |
if $node->is_terminal
|
|
2407
|
1072 |
5 |
if (scalar @_) { }
|
|
2419
|
105 |
972 |
if ($root_distance > $root->get_generic('tree_height'))
|
|
2424
|
1077 |
0 |
if (defined $children)
|
|
2448
|
0 |
0 |
if $k > $n or $k < 0
|