| line |
true |
false |
branch |
|
156
|
1 |
5 |
if $attr =~ /^-/ or not $attr |
|
166
|
0 |
7 |
unless $Bio::Tools::Run::Alignment::StandAloneFasta::OK_FIELD{$attr} |
|
167
|
5 |
2 |
if @_ |
|
201
|
1 |
0 |
unless defined $exename |
|
203
|
0 |
1 |
if (defined $exe and -x $exe) |
|
206
|
1 |
0 |
unless (defined $self->{'_pathtoexe'}{$exename}) |
|
208
|
0 |
1 |
if -e $f and -x $f |
|
213
|
1 |
0 |
unless ($exe) |
|
214
|
0 |
1 |
if ($exe = $self->io->exists_exe($exename) and -x $exe) { } |
|
217
|
0 |
1 |
if $warn |
|
236
|
0 |
1 |
if $ENV{'FASTADIR'} |
|
269
|
0 |
0 |
unless $Bio::Tools::Run::Alignment::StandAloneFasta::library |
|
272
|
0 |
0 |
unless @seqs |
|
284
|
0 |
0 |
if (not $onfile) { } |
|
295
|
0 |
0 |
if ($outfile) |
|
312
|
0 |
0 |
if (not $outfile) { } |
|
313
|
0 |
0 |
unless open FASTARUN, "$para |" |
|
317
|
0 |
0 |
if ($self->verbose < 0) { } |
|
318
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
324
|
0 |
0 |
unless $status == 0 |
|
331
|
0 |
0 |
if ($outfile) |
|
332
|
0 |
0 |
unless open FILE, ">$outfile" |
|
344
|
0 |
0 |
if $outfile |
|
349
|
0 |
0 |
if (not $outfile) { } |
|
350
|
0 |
0 |
unless open FASTARUN, "$para |" |
|
354
|
0 |
0 |
if ($self->verbose < 0) { } |
|
355
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
361
|
0 |
0 |
unless $status == 0 |
|
369
|
0 |
0 |
if ($outfile) |
|
370
|
0 |
0 |
unless open FHOUT, $tempoutfile |
|
371
|
0 |
0 |
unless open FH, ">>$outfile" |
|
398
|
0 |
0 |
unless defined $lb |
|
400
|
0 |
0 |
if ($lb =~ /^%[a-zA-Z]+$/ or $lb =~ /^[a-zA-Z]$/) { } |
|
401
|
0 |
0 |
unless (defined $ENV{'FASTLIBS'}) |
|
405
|
0 |
0 |
unless (-e $lb) |
|
430
|
0 |
0 |
if @_ |
|
448
|
0 |
0 |
unless (defined $k) |
|
449
|
0 |
0 |
if ($k =~ /^[1-6]$/) { } |
|
473
|
0 |
0 |
unless (defined $input) |
|
478
|
0 |
0 |
if (not ref $input) { } |
|
|
0 |
0 |
elsif (ref($input) =~ /ARRAY/i) { } |
|
|
0 |
0 |
elsif ($input->isa('Bio::PrimarySeqI')) { } |
|
479
|
0 |
0 |
if (-e $input) { } |
|
489
|
0 |
0 |
if (ref $_ and $_->isa('Bio::PrimarySeqI')) { } |
|
495
|
0 |
0 |
unless (@seqs) |
|
520
|
0 |
0 |
unless $exe =~ /fast|ssearch/ |
|
522
|
0 |
0 |
if $^O =~ /mswin/i |
|
545
|
0 |
0 |
unless defined $value |