| line |
true |
false |
branch |
|
85
|
0 |
0 |
if $attr =~ /^-/ |
|
88
|
1 |
0 |
unless $self->matrix |
|
89
|
1 |
0 |
unless $self->output |
|
90
|
1 |
0 |
unless $self->methods |
|
102
|
0 |
7 |
if $attr eq 'OUTFILE_NAME' |
|
103
|
0 |
7 |
unless $Bio::Tools::Run::Alignment::TCoffee::OK_FIELD{$attr} |
|
105
|
3 |
4 |
if @_ |
|
112
|
0 |
0 |
if (defined $value) |
|
123
|
0 |
0 |
unless $exe = $self->executable |
|
137
|
0 |
0 |
if ($type =~ /align/i) { } |
|
|
0 |
0 |
elsif ($type =~ /profile/i) { } |
|
153
|
0 |
0 |
unless ($infilename) |
|
177
|
0 |
0 |
unless ($type1) |
|
180
|
0 |
0 |
unless ($type2) |
|
184
|
0 |
0 |
unless ($infilename1 and $infilename2) |
|
204
|
0 |
0 |
if ($command =~ /align/) |
|
211
|
0 |
0 |
if ($command =~ /profile/) |
|
220
|
0 |
0 |
if ($self->version and $self->version < 5) { } |
|
222
|
0 |
0 |
if ($self->matrix =~ /none/i or $self->matrix =~ /null/i) { } |
|
238
|
0 |
0 |
if ($type2 eq 'S') { } |
|
245
|
0 |
0 |
unless $self->matrix =~ /none/i or $self->matrix =~ /null/i |
|
246
|
0 |
0 |
if $self->methods |
|
262
|
0 |
0 |
if (not -e $outfile or -z $outfile) |
|
275
|
0 |
0 |
unless ($self->keepdnd) |
|
277
|
0 |
0 |
if not defined $f or $f eq '' |
|
280
|
0 |
0 |
if ($Bio::Root::IO::PATHSEP) { } |
|
286
|
0 |
0 |
if $f ne '' |
|
300
|
0 |
0 |
if (not ref $input) { } |
|
|
0 |
0 |
elsif (ref($input) =~ /ARRAY/i) { } |
|
|
0 |
0 |
elsif ($input->isa('Bio::Align::AlignI')) { } |
|
|
0 |
0 |
elsif ($input->isa('Bio::PrimarySeqI')) { } |
|
303
|
0 |
0 |
unless (-e $input) |
|
305
|
0 |
0 |
unless open my $IN, $infilename |
|
307
|
0 |
0 |
if ($header =~ /^\s+\d+\s+\d+/ or $header =~ /Pileup/i or $header =~ /clustal/i) |
|
324
|
0 |
0 |
if ($adjustedfilename ne $infilename) |
|
343
|
0 |
0 |
if (not ref $input->[0]) { } |
|
|
0 |
0 |
elsif ($input->[0]->isa('Bio::PrimarySeqI')) { } |
|
|
0 |
0 |
elsif ($input->[0]->isa('Bio::Align::AlignI')) { } |
|
351
|
0 |
0 |
unless ref $seq and $seq->isa('Bio::PrimarySeqI') |
|
353
|
0 |
0 |
if (not defined $seq->display_id or $seq->display_id =~ /^\s+$/) |
|
368
|
0 |
0 |
unless ref $aln and $aln->isa('Bio::Align::AlignI') |
|
423
|
0 |
0 |
unless defined $value |
|
425
|
0 |
0 |
if ($attr_key =~ /matrix/) { } |
|
434
|
0 |
0 |
unless $value |
|
441
|
0 |
0 |
unless ($self->outfile) |
|
449
|
0 |
0 |
if ($self->quiet or $self->verbose < 0) |
|
453
|
0 |
0 |
if ($self->version >= 4 and $self->version < 4.7) |
|
463
|
0 |
0 |
if @_ |
|
472
|
0 |
1 |
unless shift() |
|
|
1 |
1 |
if @_ |
|
473
|
1 |
1 |
unless $self->{'_methods'} |