| line |
true |
false |
branch |
|
66
|
0 |
0 |
unless $self->executable |
|
82
|
0 |
0 |
unless $infilename |
|
99
|
0 |
0 |
unless $infilename |
|
118
|
0 |
0 |
unless ($infilename1 and $infilename2) |
|
119
|
0 |
0 |
unless (-e $infilename1 and -e $infilename2) |
|
138
|
0 |
0 |
unless ($infilename1 and $infilename2) |
|
139
|
0 |
0 |
unless (-e $infilename1 and -e $infilename2) |
|
159
|
0 |
0 |
unless ($infilename) |
|
190
|
0 |
0 |
unless defined $tree |
|
193
|
0 |
0 |
$slice_length <= $threshold ? : |
|
194
|
0 |
0 |
if ($below) { } |
|
195
|
0 |
0 |
unless ($found_minima) |
|
196
|
0 |
0 |
if ($slice_length < do {
$minima
}->[0]) { } |
|
221
|
0 |
0 |
if ($command =~ /align|both/) |
|
222
|
0 |
0 |
if ($^O eq 'dec_osf') { } |
|
232
|
0 |
0 |
if ($command =~ /profile/) |
|
238
|
0 |
0 |
if ($command =~ /add_sequences/) |
|
244
|
0 |
0 |
if ($command =~ /tree/) |
|
245
|
0 |
0 |
if ($^O eq 'dec_osf') { } |
|
256
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
257
|
0 |
0 |
if $quiet |
|
261
|
0 |
0 |
unless ($status == 0) |
|
274
|
0 |
0 |
unless open my $pipe, "$commandstring |" |
|
277
|
0 |
0 |
unless $quiet |
|
280
|
0 |
0 |
if $_ =~ /Score:(\d+)/ |
|
283
|
0 |
0 |
if $_ =~ /Alignment Score (-?\d+)/ |
|
285
|
0 |
0 |
unless close $pipe |
|
290
|
0 |
0 |
$output =~ /gcg/i ? : |
|
291
|
0 |
0 |
if ($format =~ /clustal/i) |
|
299
|
0 |
0 |
if ($command eq 'both') |
|
305
|
0 |
0 |
unless ($self->save_tempfiles) |
|
308
|
0 |
0 |
if $f ne '' |
|
312
|
0 |
0 |
if ($command eq 'both') |
|
323
|
0 |
0 |
if ($param_string =~ /-bootstrap/) { } |
|
|
0 |
0 |
elsif ($param_string =~ /-tree/) { } |
|
337
|
0 |
0 |
unless ($self->save_tempfiles) |
|
339
|
0 |
0 |
if $f ne '' |
|
355
|
0 |
0 |
unless (ref $input) |
|
358
|
0 |
0 |
unless -e $input |
|
363
|
0 |
0 |
if (ref $input eq 'ARRAY') { } |
|
|
0 |
0 |
elsif (ref $input eq 'Bio::SimpleAlign') { } |
|
|
0 |
0 |
elsif (ref $input and $input->isa('Bio::PrimarySeqI') and $suffix == 2) { } |
|
369
|
0 |
0 |
unless scalar @$input > 1 |
|
372
|
0 |
0 |
unless defined $seq and $seq->isa('Bio::PrimarySeqI') and $seq->id |
|
417
|
0 |
0 |
unless ($param_string =~ /outfile/) |