| line |
l |
!l |
condition |
|
458
|
0 |
0 |
carp("not ok: arg=$_ is not allowed in new()") and return |
|
638
|
0 |
0 |
carp("not ok: open $$self{'in_fname'}: $!") and return |
|
639
|
0 |
0 |
carp("not ok: open $$self{'out_fname'}: $!") and return |
|
648
|
0 |
0 |
carp('not ok: parse_abstract') and return |
|
673
|
0 |
0 |
carp("not ok: close $$self{'out_fname'}: $!") and return |
|
674
|
0 |
0 |
carp("not ok: close $$self{'in_fname'}: $!") and return |
|
692
|
0 |
0 |
$comment .= $_ and next |
|
1870
|
0 |
0 |
carp("not ok: expected WordScore arg[1] = hash ref, got $rh_word") and return |
|
1934
|
0 |
0 |
carp("not ok: expected WordScoreForMatch arg[1]: hash ref, got: $rh_word") and return |
|
2006
|
0 |
0 |
carp("not ok: expected WordIsGeneOrDict arg[1]: hash ref, got: $rh_word") and return |
| line |
!l |
l&&!r |
l&&r |
condition |
|
645
|
3 |
0 |
0 |
$$self{'verbose'} > 1 and not $. % 500 |
|
655
|
591 |
2 |
0 |
$$self{'WordNumPrintMax'} != -1 and $num_words > $$self{'WordNumPrintMax'} |
|
656
|
0 |
2 |
0 |
$$self{'WordNumPrintMin'} == 1 and $num_words > $$self{'WordNumPrintMin'} |
|
658
|
0 |
0 |
591 |
$$rh_word{'WordScore'} >= $$self{'WordScoreMin'} and $$rh_word{'WordAbstScore'} >= $$self{'WordAbstScoreMin'} |
|
660
|
532 |
44 |
15 |
defined $$rh_word{'WordSequence'} and $seen{$$rh_word{'WordSequence'}}++ |
|
851
|
23 |
0 |
61 |
defined $$self{'abst'}{"ra_$_"} && ref $$self{'abst'}{"ra_$_"} eq 'ARRAY' |
|
1047
|
0 |
7 |
5 |
defined $_ and /\b((19|20)\d\d)\b/ |
|
|
7 |
0 |
5 |
defined $_ and /\b((19|20)\d\d)\b/ and $AbstNumDigestScoreForYear{$1} |
|
1375
|
7 |
0 |
5 |
$$self{'WordNumPrintMin'} == 1 and $$self{'WordNumPrintMax'} == 1 |
|
1404
|
7 |
0 |
0 |
$$self{'WordNumPrintMin'} == 1 and not @words |
|
1566
|
0 |
558 |
47 |
$_ = $str and s/($aa3_to_aa1_re)/_BeginTag_$aa3_to_aa1{$1}_EndTag_/g > 1 |
|
|
0 |
556 |
2 |
$_ = $str and s/\b($aa3_to_aa1_lc_re)\b/_BeginTag_$aa3_to_aa1_lc{$1}_EndTag_/g > 1 |
|
1762
|
0 |
0 |
78 |
$rh_word and ref $rh_word eq 'HASH' |
|
1873
|
1043 |
0 |
78 |
$$rh_word{'WordSequence'} and $$rh_word{'WordOrig'} |
|
1888
|
69 |
6 |
2 |
$$rh_word{'WordNumNotDegen'} <= 2 and $$rh_word{'WordSeqLen'} >= 6 |
|
|
69 |
5 |
1 |
$$rh_word{'WordNumNotDegen'} <= 2 and $$rh_word{'WordSeqLen'} >= 5 |
|
1972
|
1 |
3 |
1 |
$$rh_word{'WordSubLenMax'} and $$rh_word{'WordSubLenMax'} <= 4 |
|
2019
|
22 |
0 |
30 |
$length > 2 and $length / $$rh_word{'WordSeqLen'} > 0.25 |
|
2110
|
0 |
0 |
12 |
$$self{'words'} and ref $$self{'words'} eq 'ARRAY' |
|
2116
|
524 |
0 |
597 |
$$_{'WordScore'} >= $$self{'WordScoreMin'} and $$_{'WordAbstScore'} >= $$self{'WordAbstScoreMin'} |
|
2168
|
0 |
16922 |
40 |
defined $$_{$key} and $$_{$key} eq $val |
| line |
l |
!l&&r |
!l&&!r |
condition |
|
334
|
0 |
0 |
4 |
$VERBOSE ||= $ENV{'VERBOSE'} || $ENV{'TEST_VERBOSE'} || 0 |
|
461
|
0 |
9 |
0 |
ref $class || $class |
|
656
|
591 |
0 |
2 |
$$self{'WordNumPrintMin'} == -1 or $$self{'WordNumPrintMin'} == 1 and $num_words > $$self{'WordNumPrintMin'} |
|
1322
|
0 |
2 |
10 |
$$rh_abst{'AbstPropAllCap'} > 0.3 or $$rh_abst{'AbstNumAllCap'} > 30 |
|
1566
|
47 |
0 |
558 |
$_ = $str and s/($aa3_to_aa1_re)/_BeginTag_$aa3_to_aa1{$1}_EndTag_/g > 1 or $_ = $str and s/\b($aa3_to_aa1_lc_re)\b/_BeginTag_$aa3_to_aa1_lc{$1}_EndTag_/g > 1 |
|
1716
|
1 |
2 |
12 |
m[/X|X/] or has_repeats_at_slashes($_) |
|
1806
|
64 |
2 |
0 |
$re ||= qr/(?=(.{$$self{'kmer_length'}}))/ |
|
1888
|
0 |
0 |
77 |
$$rh_word{'WordPropDegen'} > 0.95 or $$rh_word{'WordNumNotDegen'} <= 1 |
|
|
0 |
0 |
77 |
$$rh_word{'WordPropDegen'} > 0.95 or $$rh_word{'WordNumNotDegen'} <= 1 or $$rh_word{'WordNumNotDegen'} <= 2 and $$rh_word{'WordSeqLen'} >= 6 |
|
|
0 |
0 |
75 |
$$rh_word{'WordPropDegen'} > 0.7 or $$rh_word{'WordNumNotDegen'} <= 2 and $$rh_word{'WordSeqLen'} >= 5 |
|
1959
|
80 |
15 |
0 |
$WordScoreForMatchLen{$$rh_word{"${_}Len"}} || $WordScoreForMatchLenMin |
|
1965
|
35 |
14 |
21 |
$$rh_word{'WordIsGene'} or $$rh_word{'WordIsDict'} |
|
1981
|
5 |
49 |
16 |
$$rh_word{'WordIsDNA'} or $$rh_word{'WordIsDict'} |
|
|
54 |
0 |
16 |
$$rh_word{'WordIsDNA'} or $$rh_word{'WordIsDict'} or $$rh_word{'WordIsGene'} |
|
|
49 |
3 |
13 |
$$rh_word{'WordIsDNA'} or $$rh_word{'WordIsDict'} or $$rh_word{'WordIsGene'} or $$rh_word{'WordIsRoman'} |