| line |
true |
false |
branch |
|
441
|
0 |
0 |
unless $self->executable |
|
470
|
0 |
0 |
unless $infilename |
|
508
|
0 |
0 |
unless $infilename |
|
542
|
0 |
0 |
unless ($infilename1 and $infilename2) |
|
543
|
0 |
0 |
unless (-e $infilename1 and -e $infilename2) |
|
577
|
0 |
0 |
unless ($infilename1 and $infilename2) |
|
578
|
0 |
0 |
unless (-e $infilename1 and -e $infilename2) |
|
616
|
0 |
0 |
unless ($infilename) |
|
662
|
0 |
0 |
unless defined $tree |
|
665
|
0 |
0 |
$slice_length <= $threshold ? : |
|
666
|
0 |
0 |
if ($below) { } |
|
667
|
0 |
0 |
unless ($found_minima) |
|
668
|
0 |
0 |
if ($slice_length < do {
$minima
}->[0]) { } |
|
704
|
0 |
0 |
if ($command =~ /align|both/) |
|
705
|
0 |
0 |
if ($^O eq 'dec_osf') { } |
|
715
|
0 |
0 |
if ($command =~ /profile/) |
|
721
|
0 |
0 |
if ($command =~ /add_sequences/) |
|
727
|
0 |
0 |
if ($command =~ /tree/) |
|
728
|
0 |
0 |
if ($^O eq 'dec_osf') { } |
|
739
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
740
|
0 |
0 |
if $quiet |
|
744
|
0 |
0 |
unless ($status == 0) |
|
757
|
0 |
0 |
unless open my $pipe, "$commandstring |" |
|
760
|
0 |
0 |
unless $quiet |
|
763
|
0 |
0 |
if $_ =~ /Score:(\d+)/ |
|
766
|
0 |
0 |
if $_ =~ /Alignment Score (-?\d+)/ |
|
768
|
0 |
0 |
unless close $pipe |
|
773
|
0 |
0 |
$output =~ /gcg/i ? : |
|
774
|
0 |
0 |
if ($format =~ /clustal/i) |
|
782
|
0 |
0 |
if ($command eq 'both') |
|
788
|
0 |
0 |
unless ($self->save_tempfiles) |
|
791
|
0 |
0 |
if $f ne '' |
|
795
|
0 |
0 |
if ($command eq 'both') |
|
806
|
0 |
0 |
if ($param_string =~ /-bootstrap/) { } |
|
|
0 |
0 |
elsif ($param_string =~ /-tree/) { } |
|
820
|
0 |
0 |
unless ($self->save_tempfiles) |
|
822
|
0 |
0 |
if $f ne '' |
|
847
|
0 |
0 |
unless (ref $input) |
|
850
|
0 |
0 |
unless -e $input |
|
855
|
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 $suffix == 2) { } |
|
861
|
0 |
0 |
unless scalar @$input > 1 |
|
864
|
0 |
0 |
unless defined $seq and $seq->isa('Bio::PrimarySeqI') and $seq->id |
|
919
|
0 |
0 |
unless ($param_string =~ /outfile/) |