| line |
true |
false |
branch |
|
212
|
0 |
1 |
unless ($key =~ /^-/) |
|
252
|
0 |
1 |
if $data_type |
|
253
|
0 |
1 |
if $data_format |
|
254
|
0 |
1 |
if $dataset_count |
|
255
|
0 |
1 |
if $model |
|
256
|
0 |
1 |
if $freq |
|
257
|
0 |
1 |
if $kappa |
|
258
|
0 |
1 |
if $invar |
|
259
|
0 |
1 |
if $category_number |
|
260
|
0 |
1 |
if $alpha |
|
261
|
0 |
1 |
if $tree |
|
262
|
0 |
1 |
if $opt_topology |
|
263
|
0 |
1 |
if $opt_lengths |
|
264
|
0 |
1 |
if $opt |
|
265
|
0 |
1 |
if $search |
|
266
|
0 |
1 |
if $rand_start |
|
267
|
0 |
1 |
if $rand_starts |
|
268
|
0 |
1 |
if $rand_seed |
|
269
|
0 |
1 |
if $no_memory_check |
|
270
|
0 |
1 |
if $bootstrap |
|
271
|
0 |
1 |
if $program_name |
|
289
|
0 |
7 |
if (defined $value) |
|
290
|
0 |
0 |
if ($value =~ /^${PROGRAM_NAME}[-a-z]*$/) { } |
|
334
|
0 |
0 |
if defined $self->{'_version'} |
|
338
|
0 |
0 |
unless ($version) |
|
342
|
0 |
0 |
if $1 and $1 >= 20080801 |
|
345
|
0 |
0 |
$version ? : |
|
364
|
0 |
0 |
if (ref $in and $in->isa('Bio::Align::AlignI')) { } |
|
|
0 |
0 |
elsif (not -e $in) { } |
|
|
0 |
0 |
elsif (-e $in) { } |
|
429
|
0 |
0 |
if ($self->version and $self->version >= 3) { } |
|
430
|
0 |
0 |
if (defined $value) |
|
431
|
0 |
0 |
if ($value eq 'nt') { } |
|
438
|
0 |
0 |
unless defined $self->{'_data_type'} |
|
441
|
0 |
0 |
if (defined $value) |
|
442
|
0 |
0 |
if ($value eq 'dna') { } |
|
449
|
0 |
0 |
unless defined $self->{'_data_type'} |
|
467
|
2 |
1 |
if (defined $value) |
|
468
|
0 |
2 |
unless $value eq 'i' or $value eq 's' |
|
488
|
1 |
1 |
if (defined $value) |
|
489
|
0 |
1 |
unless $value =~ /^[-+]?\d*$/ and $value > 0 |
|
519
|
0 |
0 |
if (defined $value) |
|
520
|
0 |
0 |
if ($self->version and $self->version >= 3) { } |
|
521
|
0 |
0 |
unless ($value =~ /\d{6}/) |
|
524
|
0 |
0 |
unless $$models3{$self->data_type}{$value} |
|
530
|
0 |
0 |
unless $$models{$self->data_type}{$value} |
|
535
|
0 |
0 |
if ($self->{'_model'}) |
|
539
|
0 |
0 |
if ($self->version and $self->version >= 3) { } |
|
540
|
0 |
0 |
if ($self->data_type eq 'aa') { } |
|
548
|
0 |
0 |
if ($self->data_type) { } |
|
569
|
1 |
1 |
if (defined $value) |
|
570
|
0 |
1 |
unless $value =~ /^[-+]?\d*\.?\d*$/ or $value eq 'e' |
|
575
|
1 |
1 |
unless defined $self->{'_kappa'} |
|
576
|
0 |
1 |
if $self->{'_kappa'} eq 'e' |
|
592
|
1 |
1 |
if (defined $value) |
|
593
|
0 |
1 |
unless $value =~ /^[-+]?\d*\.\d*$/ or $value eq 'e' |
|
598
|
1 |
1 |
unless defined $self->{'_invar'} |
|
599
|
0 |
1 |
if $self->{'_invar'} eq 'e' |
|
615
|
1 |
1 |
if (defined $value) |
|
616
|
0 |
1 |
unless $value =~ /^[+]?\d*$/ and $value > 0 |
|
635
|
2 |
1 |
if (defined $value) |
|
636
|
0 |
2 |
unless $value =~ /^[-+]?\d*\.?\d*$/ or $value eq 'e' |
|
641
|
1 |
2 |
unless defined $self->{'_alpha'} |
|
642
|
1 |
1 |
if $self->{'_alpha'} eq 'e' |
|
658
|
2 |
1 |
if (defined $value) |
|
659
|
0 |
2 |
unless -e $value or $value eq 'BIONJ' |
|
684
|
0 |
0 |
if $self->version and $self->version >= 3 |
|
686
|
0 |
0 |
if (defined $value) |
|
687
|
0 |
0 |
if ($value) { } |
|
712
|
0 |
0 |
if $self->version and $self->version >= 3 |
|
714
|
0 |
0 |
if (defined $value) |
|
715
|
0 |
0 |
if ($value) { } |
|
744
|
0 |
0 |
if $self->version < 3 |
|
746
|
0 |
0 |
if (defined $value) |
|
747
|
0 |
0 |
unless $value =~ /^[\d\. ]$/ or $value eq 'e' or $value eq 'd' |
|
770
|
0 |
0 |
if $self->version < 3 |
|
772
|
0 |
0 |
if (defined $value) |
|
773
|
0 |
0 |
if $value =~ /tlr|tl|tr|l|n/ |
|
792
|
0 |
0 |
if $self->version < 3 |
|
794
|
0 |
0 |
if (defined $value) |
|
795
|
0 |
0 |
if $value =~ /NNI|SPR|BEST/ |
|
814
|
0 |
0 |
if $self->version < 3 |
|
816
|
0 |
0 |
if (defined $value) |
|
817
|
0 |
0 |
if ($value) { } |
|
841
|
0 |
0 |
if $self->version < 3 |
|
843
|
0 |
0 |
if (defined $value) |
|
844
|
0 |
0 |
unless $value =~ /^[-+]?\d+$/ |
|
867
|
0 |
0 |
if $self->version < 3 |
|
869
|
0 |
0 |
if (defined $value) |
|
870
|
0 |
0 |
unless $value =~ /^[-+]?\d+$/ |
|
889
|
0 |
0 |
if $self->version < 3 |
|
891
|
0 |
0 |
if (defined $value) |
|
892
|
0 |
0 |
if ($value) { } |
|
914
|
0 |
0 |
if $self->version < 3 |
|
916
|
0 |
0 |
if (defined $value) |
|
917
|
0 |
0 |
unless $value =~ /^\d+$/ |
|
935
|
0 |
0 |
if (defined $value) |
|
936
|
0 |
0 |
if ($value =~ /$PROGRAM_NAME/) { } |
|
959
|
0 |
0 |
if ($self->version >= 3) { } |
|
975
|
0 |
0 |
unless open my $FH_STAT, '<', $stat_file |
|
987
|
0 |
0 |
unless open my $FH_TREE, '<', $tree_file |
|
993
|
0 |
0 |
unless open my $FH_TREE, '<', $tree_file |
|
1018
|
0 |
0 |
if ($self->version >= 3) { } |
|
1023
|
0 |
0 |
if $self->data_format eq 's' |
|
1024
|
0 |
0 |
if $self->dataset_count > 1 |
|
1026
|
0 |
0 |
if $self->bootstrap |
|
1030
|
0 |
0 |
if $self->freq |
|
1032
|
0 |
0 |
if ($self->data_type eq 'dna') |
|
1039
|
0 |
0 |
if $self->tree ne 'BIONJ' |
|
1040
|
0 |
0 |
if $self->opt |
|
1043
|
0 |
0 |
if ($self->search eq 'SPR') |
|
1044
|
0 |
0 |
if $self->rand_start |
|
1045
|
0 |
0 |
if $self->rand_starts |
|
1050
|
0 |
0 |
if $self->no_memory_check |
|
1063
|
0 |
0 |
unless ($self->data_type) |