| line |
true |
false |
branch |
|
165
|
0 |
3 |
if $ENV{'KALIGNDIR'} |
|
183
|
0 |
0 |
if ($arg =~ /^-/) { } |
|
201
|
0 |
0 |
if $attr =~ /^-/ |
|
205
|
0 |
1 |
if (defined $self->out) |
|
217
|
0 |
1 |
unless $Bio::Tools::Run::Alignment::Kalign::OK_FIELD{$attr} |
|
219
|
0 |
1 |
if @_ |
|
236
|
0 |
0 |
if (defined $value) |
|
258
|
0 |
0 |
unless $exe = $self->executable |
|
309
|
0 |
0 |
if (defined $input) { } |
|
|
0 |
0 |
elsif (defined $self->in) { } |
|
316
|
0 |
0 |
unless ($infilename) |
|
348
|
0 |
0 |
if (not -e $outfile or -z $outfile) |
|
375
|
0 |
0 |
if (not ref $input) { } |
|
|
0 |
0 |
elsif (ref($input) =~ /ARRAY/i) { } |
|
378
|
0 |
0 |
unless (-e $input) |
|
380
|
0 |
0 |
unless open IN, $infilename |
|
383
|
0 |
0 |
unless $header =~ /^\s+$/ |
|
386
|
0 |
0 |
unless ($header =~ /^>\s*\S+/) |
|
394
|
0 |
0 |
if (not ref $input->[0]) { } |
|
|
0 |
0 |
elsif ($input->[0]->isa('Bio::PrimarySeqI')) { } |
|
402
|
0 |
0 |
unless ref $seq and $seq->isa('Bio::PrimarySeqI') |
|
404
|
0 |
0 |
if (not defined $seq->display_id or $seq->display_id =~ /^\s+$/) |
|
446
|
0 |
0 |
unless defined $value |
|
454
|
0 |
0 |
unless $value |
|
461
|
0 |
0 |
unless ($self->outfile_name) |
|
469
|
0 |
0 |
if ($self->quiet or $self->verbose < 0) |
|
470
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
489
|
1 |
0 |
if @_ |