| line |
true |
false |
branch |
|
383
|
0 |
1 |
if ($o1 and $o2) |
|
388
|
0 |
1 |
if $q |
|
389
|
1 |
0 |
if $program |
|
390
|
0 |
1 |
if $model |
|
427
|
1 |
7 |
if (@_) |
|
430
|
0 |
1 |
unless exists $INFERNAL_PROGRAM{lc $p} |
|
435
|
54 |
136 |
if exists $in_exe{$self->{'_program'}} |
|
453
|
0 |
0 |
if @_ |
|
469
|
0 |
3 |
if ($dir) |
|
488
|
0 |
0 |
unless $self->executable |
|
492
|
0 |
0 |
if ($string =~ /Infernal\s([\d.]+)/) |
|
494
|
0 |
0 |
if $v < 1 |
|
513
|
0 |
0 |
if (ref $seq[0] and $seq[0]->isa('Bio::PrimarySeqI')) { } |
|
|
0 |
0 |
elsif (ref $seq[0] and $seq[0]->isa('Bio::Align::AlignI')) { } |
|
539
|
0 |
0 |
if (ref $seq[0] and $seq[0]->isa('Bio::PrimarySeqI')) { } |
|
560
|
0 |
0 |
if (ref $seq[0]) { } |
|
561
|
0 |
0 |
if ($seq[0]->isa('Bio::PrimarySeqI')) { } |
|
|
0 |
0 |
elsif ($seq[0]->isa('Bio::Align::AlignI')) { } |
|
565
|
0 |
0 |
if (scalar @seq != 2) |
|
575
|
0 |
0 |
$params{'merge'} ? : |
|
611
|
0 |
0 |
if (ref $seq[0] and $seq[0]->isa('Bio::Align::AlignI')) { } |
|
688
|
0 |
1 |
ref $_[0] eq 'ARRAY' ? : |
|
|
0 |
1 |
ref $_[0] eq 'HASH' ? : |
|
700
|
0 |
1 |
if (exists $INFERNAL_PARAMS{$key}) { } |
|
703
|
0 |
0 |
$type eq 'switch' && $val ? : |
|
|
0 |
0 |
$type eq 'param' ? : |
|
706
|
0 |
0 |
if ($validate) |
|
708
|
0 |
0 |
unless exists $in_exe{$key} |
|
711
|
0 |
1 |
if $validate |
|
729
|
0 |
0 |
if (@_) |
|
749
|
1 |
1 |
if (@_) |
|
750
|
0 |
1 |
defined $_[0] ? : |
|
782
|
0 |
0 |
if ($exec) { } |
|
783
|
0 |
0 |
unless exists $INFERNAL_PROGRAM{$exec} |
|
785
|
0 |
0 |
if (grep {$exec eq $_;} @{$INFERNAL_PARAMS{$p};}[2 .. $#{$INFERNAL_PARAMS{$p};}]) |
|
816
|
0 |
0 |
if (exists $self->{'parameters'}) { } |
|
825
|
0 |
0 |
lc $option eq 'valid' ? : |
|
|
0 |
0 |
lc $option eq 'full' ? : |
|
|
0 |
0 |
ref $option eq 'ARRAY' ? : |
|
851
|
0 |
0 |
if ($seqs or $aligns) |
|
852
|
0 |
0 |
unless $seqs and ref $seqs eq 'ARRAY' or $aligns and ref $aligns eq 'ARRAY' |
|
864
|
0 |
0 |
unless defined $exe |
|
866
|
0 |
0 |
if exists $params{'o'} |
|
868
|
0 |
0 |
if (not defined $model and $prog ne 'cmbuild') |
|
875
|
0 |
0 |
if ($params{$p}[0]) |
|
876
|
0 |
0 |
$params{$p}[1] eq 'param' ? : |
|
883
|
0 |
0 |
if ($prog eq 'cmscore' or $prog eq 'cmstat' or $prog eq 'cmcalibrate') { } |
|
|
0 |
0 |
elsif ($prog eq 'cmsearch') { } |
|
|
0 |
0 |
elsif ($prog eq 'cmalign') { } |
|
|
0 |
0 |
elsif ($prog eq 'cmbuild') { } |
|
|
0 |
0 |
elsif ($prog eq 'cmemit') { } |
|
884
|
0 |
0 |
if $outfile |
|
887
|
0 |
0 |
unless (defined $seqs) |
|
890
|
0 |
0 |
if $outfile |
|
893
|
0 |
0 |
if ($params{'merge'}) { } |
|
894
|
0 |
0 |
if not defined $aligns or @$aligns < 2 |
|
898
|
0 |
0 |
unless defined $seqs |
|
902
|
0 |
0 |
if $outfile |
|
904
|
0 |
0 |
unless defined $aligns |
|
906
|
0 |
0 |
if ($model) { } |
|
908
|
0 |
0 |
if $outfile |
|
913
|
0 |
0 |
if (not $outfile) { } |
|
921
|
0 |
0 |
if ($self->quiet and $prog ne 'cmsearch') |
|
922
|
0 |
0 |
if ($prog eq 'cmalign') { } |
|
923
|
0 |
0 |
unless exists $params{'q'} |
|
925
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
962
|
0 |
0 |
if (my $caller = (&CORE::GLOBAL::caller(1))[3]) { } |
|
964
|
0 |
0 |
unless exists $ALLOWED{$caller} |
|
983
|
0 |
0 |
$prog eq 'cmemit' ? : |
|
|
0 |
0 |
$prog eq 'cmemit' && $has{'a'} ? : |
|
|
0 |
0 |
$prog eq 'cmalign' ? : |
|
|
0 |
0 |
$prog eq 'cmsearch' ? : |
|
988
|
0 |
0 |
if ($out) { } |
|
990
|
0 |
0 |
if ($status or not -e $out or -z $out) |
|
991
|
0 |
0 |
$! ? : |
|
995
|
0 |
0 |
if ($obj and ref $obj) |
|
1001
|
0 |
0 |
unless open my $fh, "$str |" |
|
1002
|
0 |
0 |
if ($obj and ref $obj) { } |
|
1010
|
0 |
0 |
if $io |
|
1014
|
0 |
0 |
if $obj and ref $obj |
|
1079
|
0 |
0 |
if ($?) |
|
1085
|
0 |
0 |
if $line =~ /^#/ |
|
1086
|
0 |
0 |
if ($line =~ /^\s*(-{1,2})(\S+)\s+(<\S+>)?/) { } |
|
|
0 |
0 |
elsif ($line =~ /Usage:\s*(.+)$/) { } |
|
1088
|
0 |
0 |
$3 ? : |
|
1089
|
0 |
0 |
if (exists $params{$p}) |
|
1090
|
0 |
0 |
if ($data{'prefix'} ne $params{$p}{'prefix'}) |
|
1093
|
0 |
0 |
if ($data{'arg'} ne $params{$p}{'arg'}) |
|
1117
|
0 |
0 |
ref $params{$k}{$sub} eq 'ARRAY' ? : |