| line |
true |
false |
branch |
|
246
|
0 |
12 |
if (not exists $args{$arg}) { } |
|
|
0 |
12 |
elsif (not defined $args{$arg}) { } |
|
263
|
2 |
2 |
if (exists $args{'population'}) |
|
279
|
1 |
3 |
if (exists $args{'totalNumGenes'}) |
|
287
|
0 |
4 |
if (exists $args{'population'} and exists $args{'totalNumGenes'}) |
|
308
|
2 |
2 |
if ($self->__isUsingPopulation) { } |
|
329
|
3 |
1 |
if (not defined $self->totalNumGenes) { } |
|
|
0 |
1 |
elsif ($populationSize > $self->totalNumGenes) { } |
|
341
|
0 |
0 |
if ($GO::TermFinder::WARNINGS) |
|
360
|
1 |
3 |
if ($populationSize < $self->totalNumGenes) |
|
658
|
14 |
2101 |
unless $self->__correctionMethod eq 'none' |
|
662
|
2 |
2113 |
if $self->__shouldCalculateFDR |
|
678
|
0 |
2116 |
if (not exists $args{'genes'}) { } |
|
|
0 |
2116 |
elsif (not defined $args{'genes'}) { } |
|
693
|
0 |
2116 |
unless (exists $kAllowedCorrectionMethods{$self->__correctionMethod}) |
|
703
|
2 |
2114 |
if (exists $args{'calculateFDR'} and $args{'calculateFDR'} != 0) { } |
|
729
|
1058 |
1058 |
if ($self->__isUsingPopulation) |
|
745
|
16 |
20087 |
if ($databaseId =~ /^$kFakeIdPrefix/o and not $self->__origNameInPopulation($$databaseId2OrigNameRef{$databaseId}) or not $self->__databaseIdIsInBackground($databaseId)) |
|
766
|
1 |
1057 |
if (@missingIds == @{$databaseIdsRef;}) |
|
776
|
3 |
1054 |
if (@missingIds) |
|
778
|
0 |
3 |
if ($GO::TermFinder::WARNINGS) |
|
838
|
0 |
2115 |
if (scalar $self->genesDatabaseIds > $self->totalNumGenes) |
|
840
|
0 |
0 |
if ($GO::TermFinder::WARNINGS) |
|
1077
|
0 |
53129 |
if $gene eq '' |
|
1081
|
0 |
53129 |
if (exists $genes{$gene}) |
|
1083
|
0 |
0 |
if ($GO::TermFinder::WARNINGS and not exists $warned{$gene}) |
|
1098
|
0 |
53129 |
if ($self->__annotationProvider->nameIsAmbiguous($gene)) { } |
|
1100
|
0 |
0 |
if $GO::TermFinder::WARNINGS |
|
1102
|
0 |
0 |
if ($self->__annotationProvider->nameIsStandardName($gene)) { } |
|
1104
|
0 |
0 |
if ($GO::TermFinder::WARNINGS) |
|
1116
|
0 |
0 |
if ($GO::TermFinder::WARNINGS) |
|
1138
|
19 |
53110 |
unless (defined $databaseId) |
|
1147
|
0 |
16 |
if (defined $self->__totalNumAnnotatedGenes and $self->__totalNumAnnotatedGenes == $self->totalNumGenes and $GO::TermFinder::WARNINGS and not $self->__isUsingPopulation) |
|
1173
|
0 |
53129 |
if (defined $databaseId and exists $databaseIds{$databaseId}) |
|
1189
|
53129 |
0 |
if defined $databaseId |
|
1195
|
0 |
0 |
if (%duplicates and $GO::TermFinder::WARNINGS) |
|
1252
|
66050 |
3 |
unless ($databaseId =~ /^$kFakeIdPrefix/o) |
|
1258
|
534 |
65519 |
unless (defined $goidsRef and @{$goidsRef;}) |
|
1285
|
15361 |
50692 |
if (exists $$self{$kDirectAnnotationToAspect}{$databaseId}) |
|
1328
|
19429 |
93245 |
unless (exists $$self{$kGOIDsForDatabaseIds}{$databaseId}) |
|
1339
|
0 |
32710 |
unless ($self->__ontologyProvider->nodeFromId($goid)) |
|
1341
|
0 |
0 |
if ($GO::TermFinder::WARNINGS) |
|
1365
|
4516 |
28194 |
if ($goid eq $aspectId) |
|
1409
|
2115 |
347210 |
if $goid eq $rootGoid |
|
1416
|
242073 |
105137 |
if $self->__numAnnotationsToGoId($goid) <= 1 |
|
1427
|
0 |
457821 |
unless $$a{'PVALUE'} <=> $$b{'PVALUE'} |
|
1454
|
0 |
105137 |
if ($N - $M < $n - $x) |
|
1468
|
0 |
105137 |
if ($M == $N) { } |
|
1578
|
10 |
2 |
if ($correctionFactor > 1) |
|
1590
|
1676 |
235 |
if $$hypothesis{'CORRECTED_PVALUE'} > 1 |
|
1647
|
0 |
2000 |
unless @pvals |
|
1665
|
2000 |
15269 |
if $pvals[0]{'PVALUE'} > $$realHypothesis{'PVALUE'} |
|
1682
|
34 |
40 |
if (exists $$realHypothesis{'NUM_OBSERVATIONS'}) { } |
|
1772
|
2 |
2 |
if ($self->__isUsingPopulation) { } |
|
1788
|
0 |
4 |
if (not defined $self->totalNumGenes) { } |
|
1932
|
0 |
100 |
unless @pvals |
|
1957
|
3700 |
14324 |
if $$pval{'PVALUE'} > $$realHypothesis{'PVALUE'} |
|
1979
|
32 |
42 |
if (exists $realHypotheses[$i]{'FDR_OBSERVATIONS'}) { } |
|
1989
|
6 |
26 |
if ($realHypotheses[$i]{'FDR_RATE'} > 1) |
|
2059
|
290499 |
554230 |
unless exists $nodeToIndex{$goid} |