blib/lib/Peptide/Pubmed.pm | |||
---|---|---|---|
Criterion | Covered | Total | % |
condition | 75 | 140 | 53.5 |
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 $$_{$key} eq $val |
line | l | !l | condition |
---|---|---|---|
334 | 0 | 4 | $ENV{'VERBOSE'} || $ENV{'TEST_VERBOSE'} || 0 |
700 | 0 | 2 | $comment || '' |
804 | 12 | 0 | join(';; ', map("${_}: $$self{'abst'}{$_}", ('AbstTitle', 'AbstAbstract', 'AbstMesh', 'AbstChemical'))) || '' |
1321 | 8 | 4 | $$rh_abst{'AbstNumWords'} || 1 |
1772 | 78 | 0 | $$rh_word{'WordSeqLen'} || 1 |
2127 | 0 | 0 | $$self{'abst'}{'AbstAbstract'} || '' |
line | l | !l&&r | !l&&!r | condition |
---|---|---|---|---|
334 | 0 | 0 | 4 | $VERBOSE ||= $ENV{'VERBOSE'} || $ENV{'TEST_VERBOSE'} || 0 |
461 | 0 | 9 | 0 | ref $class || $class |
656 | 591 | 0 | 2 | $$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'} |