| line |
true |
false |
branch |
|
89
|
0 |
0 |
if (not defined $s or ref $s and not $s->isa('Bio::PrimarySeqI'))
|
|
95
|
0 |
0 |
ref $s ? :
|
|
98
|
0 |
0 |
unless $pf->open("<$xfn")
|
|
148
|
0 |
0 |
unless my $in = 'IO::File'->new("<$xfn")
|
|
207
|
0 |
0 |
if /^:Protein/
|
|
211
|
0 |
0 |
if (scalar keys %retval == 0)
|
|
228
|
0 |
0 |
ref $s ? :
|
|
234
|
0 |
0 |
if (defined $cached and -e $cached)
|
|
235
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
247
|
0 |
0 |
if ($self->_hasSvmScore($xfn)) { }
|
|
248
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
252
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
290
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
291
|
0 |
0 |
if (eval {
do {
system "@cl"
}
})
|
|
293
|
0 |
0 |
if ($s & 127)
|
|
307
|
0 |
0 |
unless $fh->open("<$xfn")
|
|
311
|
0 |
0 |
if (/<scoreInfo>/)
|
|
354
|
0 |
0 |
unless my $in = 'IO::File'->new("$xmlFile")
|
|
358
|
0 |
0 |
if (/svmScore/)
|
|
387
|
0 |
0 |
unless my $in = 'IO::File'->new("$xmlFile")
|
|
388
|
0 |
0 |
unless my $out = 'IO::File'->new(">$outFile")
|
|
392
|
0 |
0 |
unless /threading/
|
|
395
|
0 |
0 |
if (not defined $svm{$t} or $svm{$t} eq '')
|
|
425
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
426
|
0 |
0 |
if (eval {
do {
system "$cmd"
}
})
|
|
429
|
0 |
0 |
if ($s & 127)
|
|
449
|
1 |
0 |
if (not -d $Bio::Prospect::Init::PROSPECT_PATH) { }
|
|
457
|
0 |
0 |
if (not -d $Bio::Prospect::Init::PDB_PATH) { }
|
|
472
|
0 |
0 |
unless ref $opts eq 'Bio::Prospect::Options'
|
|
477
|
0 |
0 |
if (exists $$opts{'phd'}) { }
|
|
|
0 |
0 |
elsif (exists $$opts{'ssp'}) { }
|
|
|
0 |
0 |
elsif (exists $$opts{'seq'}) { }
|
|
491
|
0 |
0 |
if exists $$opts{'freqfile'}
|
|
492
|
0 |
0 |
if $$opts{'zscore'}
|
|
493
|
0 |
0 |
if $$opts{'3d'}
|
|
494
|
0 |
0 |
$$opts{'global_local'} ? :
|
|
498
|
0 |
0 |
if ($$opts{'scop'}) { }
|
|
|
0 |
0 |
elsif (exists $$opts{'tfile'}) { }
|
|
|
0 |
0 |
elsif (exists $$opts{'templates'}) { }
|
|
511
|
0 |
0 |
unless defined $ENV{'DEBUG'} and $ENV{'DEBUG'} > 5
|
|
535
|
0 |
0 |
unless defined $seq
|