| line |
true |
false |
branch |
|
617
|
0 |
0 |
if $attr =~ /^-/ |
|
620
|
1 |
0 |
unless $self->matrix |
|
621
|
1 |
0 |
unless $self->output |
|
622
|
1 |
0 |
unless $self->methods |
|
634
|
0 |
7 |
if $attr eq 'OUTFILE_NAME' |
|
635
|
0 |
7 |
unless $Bio::Tools::Run::Alignment::TCoffee::OK_FIELD{$attr} |
|
637
|
3 |
4 |
if @_ |
|
654
|
0 |
0 |
if (defined $value) |
|
675
|
0 |
0 |
unless $exe = $self->executable |
|
708
|
0 |
0 |
if ($type =~ /align/i) { } |
|
|
0 |
0 |
elsif ($type =~ /profile/i) { } |
|
747
|
0 |
0 |
unless ($infilename) |
|
787
|
0 |
0 |
unless ($type1) |
|
790
|
0 |
0 |
unless ($type2) |
|
794
|
0 |
0 |
unless ($infilename1 and $infilename2) |
|
826
|
0 |
0 |
if ($command =~ /align/) |
|
833
|
0 |
0 |
if ($command =~ /profile/) |
|
842
|
0 |
0 |
if ($self->version and $self->version < 5) { } |
|
844
|
0 |
0 |
if (not $self->matrix =~ /none/i || $self->matrix =~ /null/i) { } |
|
860
|
0 |
0 |
if ($type2 eq 'S') { } |
|
867
|
0 |
0 |
unless $self->matrix =~ /none/i or $self->matrix =~ /null/i |
|
868
|
0 |
0 |
if $self->methods |
|
884
|
0 |
0 |
if (not -e $outfile or -z $outfile) |
|
897
|
0 |
0 |
unless ($self->keepdnd) |
|
899
|
0 |
0 |
if not defined $f or $f eq '' |
|
902
|
0 |
0 |
if ($Bio::Root::IO::PATHSEP) { } |
|
908
|
0 |
0 |
if $f ne '' |
|
935
|
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')) { } |
|
938
|
0 |
0 |
unless (-e $input) |
|
940
|
0 |
0 |
unless open my $IN, $infilename |
|
942
|
0 |
0 |
if ($header =~ /^\s+\d+\s+\d+/ or $header =~ /Pileup/i or $header =~ /clustal/i) |
|
959
|
0 |
0 |
if ($adjustedfilename ne $infilename) |
|
978
|
0 |
0 |
if (not ref $input->[0]) { } |
|
|
0 |
0 |
elsif ($input->[0]->isa('Bio::PrimarySeqI')) { } |
|
|
0 |
0 |
elsif ($input->[0]->isa('Bio::Align::AlignI')) { } |
|
986
|
0 |
0 |
unless ref $seq and $seq->isa('Bio::PrimarySeqI') |
|
988
|
0 |
0 |
if (not defined $seq->display_id or $seq->display_id =~ /^\s+$/) |
|
1003
|
0 |
0 |
unless ref $aln and $aln->isa('Bio::Align::AlignI') |
|
1069
|
0 |
0 |
unless defined $value |
|
1071
|
0 |
0 |
if ($attr_key =~ /matrix/) { } |
|
1080
|
0 |
0 |
unless $value |
|
1087
|
0 |
0 |
unless ($self->outfile) |
|
1095
|
0 |
0 |
if ($self->quiet or $self->verbose < 0) |
|
1099
|
0 |
0 |
if ($self->version >= 4 and $self->version < 4.7) |
|
1119
|
0 |
0 |
if @_ |
|
1138
|
0 |
1 |
unless shift() |
|
|
1 |
1 |
if @_ |
|
1139
|
1 |
1 |
unless $self->{'_methods'} |