| line |
true |
false |
branch |
|
347
|
0 |
1 |
if ($^O =~ /darwin/i) { } |
|
|
0 |
1 |
elsif ($^O =~ /mswin/i) { } |
|
352
|
0 |
1 |
if (defined $ENV{'SLRDIR'}) |
|
353
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
407
|
0 |
3 |
if $ENV{'SLRDIR'} |
|
436
|
0 |
1 |
if defined $aln |
|
437
|
0 |
1 |
if defined $tree |
|
438
|
0 |
1 |
if defined $st |
|
439
|
0 |
1 |
if defined $exe |
|
442
|
0 |
1 |
if (defined $params) |
|
443
|
0 |
0 |
if (not ref($params) =~ /HASH/i) { } |
|
467
|
0 |
0 |
unless ($self->save_tempfiles) |
|
471
|
0 |
0 |
unless $tree |
|
472
|
0 |
0 |
unless $aln |
|
473
|
0 |
0 |
unless ($aln) |
|
477
|
0 |
0 |
unless ($tree) |
|
508
|
0 |
0 |
$self->save_tempfiles ? : |
|
511
|
0 |
0 |
$Bio::Tools::Run::Phylo::SLR::MINNAMELEN > $aln->maxdisplayname_length ? : |
|
523
|
0 |
0 |
$self->save_tempfiles ? : |
|
544
|
0 |
0 |
unless open SLR, ">$slr_ctl" |
|
552
|
0 |
0 |
if $param eq 'outfile' |
|
586
|
0 |
0 |
unless $slrexe and -e $slrexe and -x _ |
|
588
|
0 |
0 |
unless open $run, "$slrexe |" |
|
592
|
0 |
0 |
if (grep {/\berr(or)?: /io;} @output or not $exit_status) |
|
597
|
0 |
0 |
unless open RESULTS, "$tmpdir/$outfile" |
|
603
|
0 |
0 |
if (/^\#/) |
|
604
|
0 |
0 |
if (/\!/) { } |
|
|
0 |
0 |
elsif (/\+/) { } |
|
|
0 |
0 |
elsif (/\-\s+/) { } |
|
|
0 |
0 |
elsif (/Constant/) { } |
|
|
0 |
0 |
elsif (/All gaps/) { } |
|
|
0 |
0 |
elsif (/Single character/) { } |
|
|
0 |
0 |
elsif (/Synonymous/) { } |
|
612
|
0 |
0 |
if (/^\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)/) { } |
|
624
|
0 |
0 |
if ($@) |
|
646
|
0 |
0 |
if (defined $value) |
|
669
|
0 |
0 |
if (defined $aln) |
|
670
|
0 |
0 |
if (-e $aln) { } |
|
|
0 |
0 |
elsif (not ref $aln && $aln->isa('Bio::Align::AlignI')) { } |
|
698
|
0 |
0 |
if (defined $tree) |
|
699
|
0 |
0 |
unless (ref $tree and $tree->isa('Bio::Tree::TreeI')) |
|
743
|
0 |
0 |
unless (defined $self->{'no_param_checks'} and $self->{'no_param_checks'} == 1) |
|
744
|
0 |
0 |
unless (defined $Bio::Tools::Run::Phylo::SLR::VALIDVALUES{$param}) |
|
748
|
0 |
0 |
if (ref($Bio::Tools::Run::Phylo::SLR::VALIDVALUES{$param}) =~ /ARRAY/i and scalar @{$Bio::Tools::Run::Phylo::SLR::VALIDVALUES{$param};} > 0) |
|
751
|
0 |
0 |
unless (grep {$value eq $_;} @{$Bio::Tools::Run::Phylo::SLR::VALIDVALUES{$param};}) |
|
776
|
1 |
0 |
unless defined $keepold |
|
780
|
0 |
19 |
if defined $self->{'_slrparams'}{$param} and $keepold |
|
781
|
12 |
7 |
if (ref($val) =~ /ARRAY/i) { } |
|
808
|
0 |
0 |
if (defined $value) |
|
840
|
0 |
0 |
if (@_) |
|
843
|
0 |
0 |
unless (defined $self->{'_slrparams'}{'outfile'}) |
|
884
|
1 |
0 |
unless ($self->save_tempfiles) |