| line |
true |
false |
branch |
|
156
|
0 |
1 |
if ($class ne $pkg) |
|
162
|
0 |
1 |
unless defined $cutoff |
|
187
|
1 |
1 |
if (defined $new_cutoff) |
|
206
|
1 |
0 |
if (defined $new_verbose) |
|
248
|
1 |
0 |
if (defined $new_universe) |
|
250
|
1 |
0 |
if ($new_universe =~ /^(user|union|genes|intersection)$/) { } |
|
285
|
1338 |
7 |
if (exists $$self{'PATHWAYS'}{$arg{'dbacc'}} and exists $$self{'PATHWAYS'}{$arg{'dbacc'}}{'DESC'}) { } |
|
287
|
0 |
1338 |
if ($arg{'desc'} ne $$self{'PATHWAYS'}{$arg{'dbacc'}}{'DESC'}) |
|
320
|
0 |
11349 |
if (exists $$self{'GENES'}{$arg{'gene'}}{'PVAL'} and $$self{'GENES'}{$arg{'gene'}}{'PVAL'} != $arg{'pval'}) |
|
357
|
1 |
0 |
if (lc $order ne 'sorted') { } |
|
394
|
0 |
0 |
unless defined $all_option |
|
398
|
0 |
0 |
unless (exists $$self{'PATHWAYS'}{$pathway}) |
|
401
|
0 |
0 |
if ($all_option eq 'ALL') { } |
|
402
|
0 |
0 |
if ($name eq 'FDR') |
|
405
|
0 |
0 |
unless (exists $$self{'PATHWAYS'}{$pathway}{'ALL_RESULTS'}{$name}) |
|
411
|
0 |
0 |
unless (exists $$self{'PATHWAYS'}{$pathway}{'BEST_RESULTS'}{$name}) |
|
453
|
0 |
0 |
if ($fdr < 1 or $fdr > $$self{'FDR_CUTOFF'} or int $fdr != $fdr) |
|
474
|
0 |
0 |
if (defined $_[0]) |
|
475
|
0 |
0 |
if ($$self{'UNIVERSE'} eq 'user') { } |
|
494
|
0 |
1 |
if $$self{'STATE'} eq 'calculated' |
|
495
|
0 |
1 |
if $$self{'VERBOSE'} |
|
507
|
2 |
0 |
if ($cutoff > 0 and $cutoff <= 100 and $cutoff == int $cutoff) { } |
|
523
|
0 |
12694 |
if (scalar(@{$arg_ref;}) % 2 == 1) |
|
529
|
0 |
26733 |
unless (exists $args{$arg}) |
|
533
|
0 |
12694 |
if (scalar @missing) |
|
543
|
0 |
0 |
unless (exists $$self{'PATHWAYS'}{$pathway}) |
|
551
|
314 |
461 |
defined $$self{'GENES'}{$b}{'PVAL'} ? : |
|
|
391 |
775 |
defined $$self{'GENES'}{$a}{'PVAL'} ? : |
|
|
145173 |
1166 |
defined $$self{'GENES'}{$a}{'PVAL'} && defined $$self{'GENES'}{$b}{'PVAL'} ? : |
|
570
|
0 |
35 |
if $$self{'VERBOSE'} |
|
579
|
7055 |
18110 |
if defined $_ and $_ <= $qlevel * $i++ / $$self{'GENE_COUNT'} |
|
586
|
1 |
0 |
unless (defined $$self{'GENE_COUNT'}) |
|
589
|
0 |
1 |
if ($$self{'UNIVERSE'} eq 'genes') { } |
|
|
0 |
1 |
elsif ($$self{'UNIVERSE'} eq 'user') { } |
|
|
0 |
1 |
elsif ($$self{'UNIVERSE'} eq 'union') { } |
|
|
1 |
0 |
elsif ($$self{'UNIVERSE'} eq 'intersection') { } |
|
598
|
0 |
0 |
unless ($$self{'GENE_COUNT'} >= scalar keys %{$$self{'GENES'};} and $$self{'GENE_COUNT'} >= $sum) |
|
615
|
10715 |
719 |
unless ($exists_pathway and $exists_pval) |
|
616
|
0 |
10715 |
if $$self{'VERBOSE'} |
|
625
|
0 |
1 |
if $$self{'VERBOSE'} |
|
632
|
719 |
0 |
if (defined $$self{'GENES'}{$gene}{'PVAL'}) |
|
640
|
1205 |
140 |
if (exists $seen{$pgene}) |
|
646
|
0 |
7 |
if ($$self{'VERBOSE'}) |
|
647
|
0 |
0 |
if ($old_size != $new_size) { } |
|
676
|
0 |
1 |
if $fdr_gene_cutoff == 0 |
|
687
|
24 |
336 |
if defined $seen{$g} |
|
697
|
0 |
0 |
if ($$self{'VERBOSE'}) |
|
701
|
0 |
0 |
if ($pval == 0) { } |
|
716
|
0 |
0 |
if ($pval < $bestpval) |
|
735
|
0 |
0 |
if ($$self{'VERBOSE'}) |
|
762
|
0 |
0 |
unless defined $$array_ref[$i] |