| line |
true |
false |
branch |
|
151
|
1 |
0 |
unless (defined $Bio::Tools::Run::Vista::PROGRAMDIR) |
|
154
|
0 |
1 |
if (defined $Bio::Tools::Run::Vista::PROGRAMDIR) |
|
157
|
0 |
0 |
if (-e $f and -x $f) |
|
193
|
0 |
0 |
unless $Bio::Tools::Run::Vista::OK_FIELD{$attr} |
|
194
|
0 |
0 |
if @_ |
|
237
|
0 |
0 |
if $attr =~ /^-/ |
|
258
|
0 |
0 |
if (defined $exe) |
|
262
|
0 |
0 |
unless (defined $self->{'_pathtojava'}) |
|
263
|
0 |
0 |
if ($Bio::Tools::Run::Vista::PROGRAM and -e $Bio::Tools::Run::Vista::PROGRAM and -x $Bio::Tools::Run::Vista::PROGRAM) { } |
|
267
|
0 |
0 |
if ($exe = $self->io->exists_exe($Bio::Tools::Run::Vista::PROGRAMNAME) and -x $exe) { } |
|
271
|
0 |
0 |
if $warn |
|
322
|
0 |
0 |
unless open FASTA, $file |
|
327
|
0 |
0 |
if $line =~ /^$/ |
|
328
|
0 |
0 |
if (substr($line, 0, 1) eq '>') { } |
|
352
|
0 |
0 |
if (not ref $sim) { } |
|
356
|
0 |
0 |
unless $sim and $sim->isa('Bio::Align::AlignI') |
|
362
|
0 |
0 |
if (ref $ref eq 'ARRAY') { } |
|
|
0 |
0 |
elsif ($ref =~ /^\d+$/) { } |
|
385
|
0 |
0 |
if ($seq[$i]->id =~ /$ref/) |
|
406
|
0 |
0 |
unless ($ref[$index] eq '-' and $seq2[$index] eq '-') |
|
430
|
0 |
0 |
unless ($first[$index] eq '-' and $sec[$index] eq '-') |
|
456
|
0 |
0 |
if $self->diffs |
|
457
|
0 |
0 |
if ($self->region_file or $self->region_file_dir) |
|
459
|
0 |
0 |
if $self->region_file_dir |
|
463
|
0 |
0 |
if ($self->score_file or $self->score_file_dir) |
|
465
|
0 |
0 |
if $self->score_file_dir |
|
469
|
0 |
0 |
if ($self->alignment_file or $self->alignment_file_dir) |
|
471
|
0 |
0 |
if $self->alignment_file_dir |
|
476
|
0 |
0 |
if $self->contigs_file |
|
477
|
0 |
0 |
if $self->use_order |
|
481
|
0 |
0 |
if (ref $self->annotation eq 'ARRAY' and $self->annotation->[0]->isa('Bio::SeqFeatureI')) { } |
|
|
0 |
0 |
elsif ($self->annotation) { } |
|
488
|
0 |
0 |
if $self->annotation_format =~ /GFF/i |
|
489
|
0 |
0 |
if $annotation_file |
|
498
|
0 |
0 |
if $self->axis_label |
|
499
|
0 |
0 |
if $self->ticks_file |
|
500
|
0 |
0 |
if $self->snps_file |
|
501
|
0 |
0 |
if $self->gaps |
|
502
|
0 |
0 |
if $self->repeats_file |
|
503
|
0 |
0 |
if $self->filter_repeats |
|
504
|
0 |
0 |
if $self->num_pages |
|
505
|
0 |
0 |
if $self->start |
|
506
|
0 |
0 |
if $self->end |
|
508
|
0 |
0 |
if (ref $color eq 'HASH') |
|
516
|
0 |
0 |
if ($self->plotfile) { } |
|
544
|
0 |
0 |
if $self->quiet or $self->verbose < 0 |
|
545
|
0 |
0 |
if $self->debug |
|
550
|
0 |
0 |
if $status != 0 |
|
557
|
0 |
0 |
if ($val) |