| line |
true |
false |
branch |
|
98
|
0 |
1 |
if (defined $ENV{'HYPHYDIR'}) |
|
99
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
143
|
0 |
3 |
if $ENV{'HYPHYDIR'} |
|
187
|
0 |
0 |
unless $tree |
|
188
|
0 |
0 |
unless $aln |
|
189
|
0 |
0 |
unless ($aln) |
|
195
|
0 |
0 |
if (not ref $aln and -e $aln) { } |
|
198
|
0 |
0 |
$self->save_tempfiles ? : |
|
210
|
0 |
0 |
if ($outfile eq '') |
|
215
|
0 |
0 |
if (not ref $tree and -e $tree) { } |
|
218
|
0 |
0 |
$self->save_tempfiles ? : |
|
255
|
0 |
0 |
unless open WRAPPER, '>', $wrapper |
|
261
|
0 |
0 |
if ($val eq '') |
|
268
|
0 |
0 |
if (ref($self) =~ /BatchFile/) { } |
|
275
|
0 |
0 |
if ($version >= 0.9920060501) { } |
|
303
|
0 |
0 |
unless (defined $self->{'_prepared'}) |
|
310
|
0 |
0 |
unless ($exe and -e $exe and -x _) |
|
316
|
0 |
0 |
unless my $pid = open(RUN, '-|', "$commandstring") |
|
320
|
0 |
0 |
if ($error != 0) |
|
330
|
0 |
0 |
if ($results =~ /error/i or $rc == 0) |
|
360
|
0 |
0 |
if (defined $value) |
|
382
|
0 |
0 |
if (defined $aln) |
|
383
|
0 |
0 |
if (-e $aln) { } |
|
|
0 |
0 |
elsif (not ref $aln && $aln->isa('Bio::Align::AlignI')) { } |
|
411
|
0 |
0 |
if (defined $tree) |
|
412
|
0 |
0 |
if (not ref $tree && $tree->isa('Bio::Tree::TreeI')) { } |
|
484
|
2 |
3 |
if (ref($val) =~ /ARRAY/i) |
|
485
|
0 |
2 |
if (ref($val->[0]) =~ /HASH/i) { } |
|
491
|
0 |
5 |
if (ref($val) =~ /HASH/i) { } |
|
|
3 |
2 |
elsif (not ref($val) =~ /HASH/i || ref($val) =~ /ARRAY/i) { } |
|
494
|
0 |
0 |
unless ref($val) =~ /HASH/i |
|
495
|
0 |
0 |
unless defined $param |
|
499
|
0 |
0 |
if defined $val |
|
525
|
0 |
0 |
if (exists $self->{'_params'}{$param}) { } |
|
547
|
0 |
0 |
if (@_) |
|
567
|
0 |
0 |
if (defined $self->{'_version'}) |
|
572
|
0 |
0 |
unless open WRAPPER, '>', $versionbf |
|
576
|
0 |
0 |
unless ($exe and -e $exe and -x _) |
|
580
|
0 |
0 |
unless open RUN, "$commandstring |" |
|
601
|
0 |
0 |
if (defined $self->{'_hyphylibdir'}) |
|
606
|
0 |
0 |
unless open WRAPPER, '>', $hyphylibdirbf |
|
610
|
0 |
0 |
unless ($exe and -e $exe and -x _) |
|
614
|
0 |
0 |
unless open RUN, "$commandstring |" |