| line |
true |
false |
branch |
|
219
|
0 |
0 |
if ($tree and ref $tree and $tree->isa('Bio::Tree::TreeI')) |
|
224
|
0 |
0 |
$node->node_name ? : |
|
|
0 |
0 |
$seq_id ? : |
|
283
|
0 |
0 |
if ($thing) |
|
284
|
0 |
0 |
if (-e $thing) { } |
|
|
0 |
0 |
elsif (ref $thing and $thing->isa('Bio::Matrix::Mlagan')) { } |
|
299
|
0 |
0 |
unless (defined $self->{'_nuc_matrix'}) |
|
306
|
0 |
0 |
if defined wantarray |
|
327
|
0 |
0 |
if (ref($input1) =~ /ARRAY/i) { } |
|
|
0 |
0 |
elsif ($input1->isa('Bio::PrimarySeqI')) { } |
|
336
|
0 |
0 |
unless ($seq1->isa('Bio::PrimarySeqI')) |
|
366
|
0 |
0 |
if (ref $input2) { } |
|
367
|
0 |
0 |
if ($input2->isa('Bio::PrimarySeqI')) |
|
424
|
0 |
0 |
if ($executable eq 'lagan.pl') { } |
|
|
0 |
0 |
elsif ($executable eq 'mlagan') { } |
|
430
|
0 |
0 |
if ($self->{'_nuc_matrix_set'}) |
|
444
|
0 |
0 |
if $nucmatrixfile |
|
462
|
0 |
0 |
unless ($exe = $self->executable($executable)) |
|
469
|
0 |
0 |
if ($executable eq 'lagan.pl') |
|
472
|
0 |
0 |
if ($executable eq 'mlagan') |
|
477
|
0 |
0 |
if (defined $input2) |
|
483
|
0 |
0 |
if ($version <= 3 and $matrix_file) |
|
486
|
0 |
0 |
unless -e $orig |
|
487
|
0 |
0 |
if system "cp $orig $orig.bk" |
|
488
|
0 |
0 |
if system "cp $matrix_file $orig" |
|
492
|
0 |
0 |
if ($self->silent || $self->quiet and not $^O =~ /os2|dos|MSWin32|amigaos/) |
|
494
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
501
|
0 |
0 |
unless opendir my $cwd_dir, $cwd |
|
504
|
0 |
0 |
if ($thing =~ /anch/) |
|
511
|
0 |
0 |
$version <= 3 ? : |
|
513
|
0 |
0 |
if ($version <= 1 and $self->{'_nucmatrixfile'}) |
|
515
|
0 |
0 |
if system "mv $orig.bk $orig" |
|
518
|
0 |
0 |
unless opendir $cwd_dir, $cwd |
|
520
|
0 |
0 |
if ($thing =~ /anch/) |
|
521
|
0 |
0 |
unless $ok_files{$thing} |
|
549
|
1 |
0 |
unless defined $exename |
|
551
|
0 |
1 |
if (defined $exe and -x $exe) |
|
554
|
1 |
0 |
unless (defined $self->{'_pathtoexe'}{$exename}) |
|
556
|
0 |
1 |
if -e $f and -x $f |
|
558
|
1 |
0 |
unless ($exe) |
|
559
|
0 |
1 |
if ($exe = $self->io->exists_exe($exename) and -x $exe) { } |
|
562
|
0 |
1 |
if $warn |
|
570
|
1 |
0 |
unless ($PROGRAM_DIR) |
|
592
|
0 |
1 |
if $self->program_dir |
|
593
|
0 |
1 |
$^O =~ /mswin/i ? : |
|
629
|
0 |
0 |
unless open my $VER, "$exe -version 2>&1 |" |
|
634
|
0 |
0 |
unless close $VER |