| line |
true |
false |
branch |
|
458
|
0 |
39 |
unless exists $args_default{$_} |
|
462
|
0 |
9 |
unless $self->init |
|
481
|
20 |
0 |
if exists $$self{'abst'}{$key} |
|
505
|
17 |
2 |
unless $$rh_word{'WordAbstScore'} >= $$self{'WordAbstScoreMin'} |
|
508
|
24 |
0 |
if exists $$rh_word{$key} |
|
530
|
34 |
23 |
unless $$rh_word{'WordAbstScore'} >= $$self{'WordAbstScoreMin'} |
|
531
|
8 |
15 |
if $$rh_word{'WordSequence'} |
|
549
|
3 |
0 |
if (@_ == 2) |
|
567
|
9 |
0 |
unless (defined $$self{'print_colf'}) |
|
569
|
162 |
126 |
/^(Abst|Word|AbstWord)(Idx|Is|Num|Prop|Score)([A-Z]|$)/ ? : |
|
580
|
0 |
9 |
if ($$self{'verbose'} > 2) |
|
603
|
0 |
20 |
if ref $_[0] |
|
608
|
303664 |
0 |
$args{'lc'} ? : |
|
638
|
0 |
2 |
unless open $in_fh, $$self{'in_fname'} |
|
639
|
0 |
2 |
unless open $out_fh, ">$$self{'out_fname'}" |
|
645
|
0 |
3 |
if $$self{'verbose'} > 1 and not $. % 500 |
|
648
|
0 |
3 |
unless my $rh_pm_out = $self->parse_abstract($rh_pm_in) |
|
650
|
0 |
3 |
unless $$rh_pm_out{'abst'}{'AbstScore'} >= $$self{'AbstScoreMin'} |
|
655
|
0 |
593 |
if $$self{'WordNumPrintMax'} != -1 and $num_words > $$self{'WordNumPrintMax'} |
|
656
|
591 |
2 |
if ($$self{'WordNumPrintMin'} == -1 or $$self{'WordNumPrintMin'} == 1 and $num_words > $$self{'WordNumPrintMin'}) |
|
658
|
0 |
591 |
unless $$rh_word{'WordScore'} >= $$self{'WordScoreMin'} and $$rh_word{'WordAbstScore'} >= $$self{'WordAbstScoreMin'} |
|
660
|
15 |
576 |
if defined $$rh_word{'WordSequence'} and $seen{$$rh_word{'WordSequence'}}++ |
|
663
|
6398 |
538 |
defined $$rh_word{$_} ? : |
|
666
|
11560 |
0 |
defined $$rh_pm_out{'abst'}{$_} ? : |
|
673
|
0 |
2 |
unless close $out_fh |
|
674
|
0 |
2 |
unless close $in_fh |
|
692
|
0 |
2 |
if /^\#/ |
|
695
|
0 |
2 |
unless defined($_ = <$in_fh>) |
|
717
|
2 |
0 |
if defined $comment |
|
719
|
2 |
0 |
if defined $ra_colf |
|
737
|
0 |
12 |
unless $self->init_abstract($rh_pm_in) |
|
738
|
0 |
12 |
unless $self->AbstVars |
|
740
|
0 |
12 |
if $$self{'verbose'} > 2 |
|
792
|
40 |
44 |
if (defined $$rh_pm_in{$_}) { } |
|
|
0 |
44 |
elsif (defined $$rh_pm_in{"Abst$_"}) { } |
|
827
|
0 |
12 |
unless $self->AbstNumAb |
|
829
|
0 |
12 |
unless $self->AbstNumBind |
|
830
|
0 |
12 |
unless $self->AbstNumDigest |
|
831
|
0 |
12 |
unless $self->AbstNumMHC |
|
832
|
0 |
12 |
unless $self->AbstNumPeptide |
|
833
|
0 |
12 |
unless $self->AbstNumPhage |
|
834
|
0 |
12 |
unless $self->AbstNumProtease |
|
835
|
0 |
12 |
unless $self->AbstScore |
|
836
|
0 |
12 |
unless $self->Words |
|
837
|
0 |
12 |
unless $self->WordAbstScore |
|
838
|
0 |
12 |
unless $self->AbstMtext |
|
847
|
12 |
0 |
if ($$self{'verbose'} > 0) |
|
851
|
61 |
23 |
defined $$self{'abst'}{"ra_$_"} && ref $$self{'abst'}{"ra_$_"} eq 'ARRAY' ? : |
|
880
|
0 |
12 |
unless defined $$self{'abst'}{'AbstLcAllText'} |
|
930
|
0 |
12 |
unless defined $$self{'abst'}{'AbstLcAllText'} |
|
1005
|
0 |
12 |
unless defined $$self{'abst'}{'AbstLcAllText'} |
|
1047
|
5 |
7 |
if defined $_ and /\b((19|20)\d\d)\b/ and $AbstNumDigestScoreForYear{$1} |
|
1067
|
0 |
12 |
unless defined $$self{'abst'}{'AbstLcAllText'} |
|
1114
|
0 |
12 |
unless defined $$self{'abst'}{'AbstLcAllText'} |
|
1127
|
6 |
6 |
unless @matches |
|
1133
|
0 |
6 |
unless scalar(@matches) - scalar(@matches_neg) > 0 |
|
1180
|
0 |
12 |
unless defined $$self{'abst'}{'AbstLcAllText'} |
|
1202
|
7 |
5 |
unless @matches |
|
1207
|
0 |
5 |
unless scalar(@matches) - scalar(@matches_neg) > 0 |
|
1242
|
0 |
12 |
unless defined $$self{'abst'}{'AbstLcAllText'} |
|
1260
|
10 |
2 |
unless @matches |
|
1301
|
219 |
1941 |
if /[A-Z]/ |
|
1308
|
0 |
12 |
if $$self{'verbose'} > 2 |
|
1317
|
0 |
12 |
if $$self{'verbose'} > 2 |
|
1322
|
2 |
10 |
if ($$rh_abst{'AbstPropAllCap'} > 0.3 or $$rh_abst{'AbstNumAllCap'} > 30) { } |
|
1327
|
0 |
12 |
if $$self{'verbose'} > 2 |
|
1329
|
0 |
12 |
if $$rh_abst{'AbstScore'} < 0 |
|
1332
|
0 |
12 |
if $$self{'verbose'} > 2 |
|
1333
|
0 |
12 |
if $$self{'verbose'} > 2 |
|
1375
|
5 |
7 |
if ($$self{'WordNumPrintMin'} == 1 and $$self{'WordNumPrintMax'} == 1) |
|
1387
|
559 |
562 |
if (not /\S/) { } |
|
|
6 |
556 |
elsif ($_ = $self->aa3_to_aa1($$rh_word{'WordOrig'})) { } |
|
|
72 |
484 |
elsif ($_ = $self->to_aa1($$rh_word{'WordOrig'})) { } |
|
1393
|
0 |
6 |
unless $self->WordVars($rh_word) |
|
1398
|
0 |
72 |
unless $self->WordVars($rh_word) |
|
1401
|
0 |
1121 |
unless $self->WordScore($rh_word) |
|
1404
|
0 |
7 |
if ($$self{'WordNumPrintMin'} == 1 and not @words) |
|
1566
|
556 |
2 |
unless $_ = $str and s/($aa3_to_aa1_re)/_BeginTag_$aa3_to_aa1{$1}_EndTag_/g > 1 or $_ = $str and s/\b($aa3_to_aa1_lc_re)\b/_BeginTag_$aa3_to_aa1_lc{$1}_EndTag_/g > 1 |
|
1623
|
91 |
485 |
if (/$aa1_re/) |
|
1688
|
13 |
1890 |
if ($num_parens == 1) |
|
1691
|
264 |
1639 |
unless $num_changes |
|
1715
|
125 |
15 |
unless m[/] |
|
1716
|
3 |
12 |
if (m[/X|X/] or has_repeats_at_slashes($_)) { } |
|
1719
|
6 |
0 |
if length $str < length $_ |
|
1744
|
2 |
37 |
if $seen{$_}++ |
|
1762
|
0 |
78 |
unless $rh_word and ref $rh_word eq 'HASH' |
|
1768
|
78 |
0 |
if ($$rh_word{'WordSequence'}) |
|
1776
|
72 |
6 |
if ($$rh_word{'WordAaSymbols'} == 1) |
|
1782
|
72 |
0 |
if $$rh_word{'WordSeqLen'} |
|
1785
|
5 |
67 |
if $$rh_word{'WordPropDNA'} >= 0.9 |
|
1805
|
6 |
66 |
if length $str < $$self{'kmer_length'} |
|
1808
|
0 |
218 |
unless (defined $log_prop_sequence{$_}) |
|
1812
|
0 |
218 |
unless (defined $log_prop_nonsequence{$_}) |
|
1870
|
0 |
1121 |
unless ref $rh_word eq 'HASH' |
|
1873
|
1043 |
78 |
unless ($$rh_word{'WordSequence'} and $$rh_word{'WordOrig'}) |
|
1876
|
0 |
1121 |
if $$self{'verbose'} > 2 |
|
1877
|
1043 |
78 |
unless $$rh_word{'WordScore'} |
|
1879
|
0 |
78 |
if $$self{'verbose'} > 2 |
|
1880
|
78 |
0 |
if (exists $WordScoreForSeqLen{$$rh_word{'WordSeqLen'}}) { } |
|
1885
|
0 |
78 |
if $$self{'verbose'} > 2 |
|
1886
|
1 |
77 |
unless $$rh_word{'WordScore'} |
|
1888
|
2 |
75 |
if ($$rh_word{'WordPropDegen'} > 0.95 or $$rh_word{'WordNumNotDegen'} <= 1 or $$rh_word{'WordNumNotDegen'} <= 2 and $$rh_word{'WordSeqLen'} >= 6) { } |
|
|
1 |
74 |
elsif ($$rh_word{'WordPropDegen'} > 0.7 or $$rh_word{'WordNumNotDegen'} <= 2 and $$rh_word{'WordSeqLen'} >= 5) { } |
|
|
0 |
74 |
elsif ($$rh_word{'WordPropDegen'} > 0.6) { } |
|
1904
|
0 |
77 |
if $$self{'verbose'} > 2 |
|
1905
|
2 |
75 |
unless $$rh_word{'WordScore'} |
|
1907
|
0 |
75 |
unless $self->WordScoreForMatch($rh_word) |
|
1908
|
0 |
75 |
if $$self{'verbose'} > 2 |
|
1909
|
0 |
75 |
unless $$rh_word{'WordScore'} |
|
1914
|
0 |
75 |
if $$self{'verbose'} > 2 |
|
1917
|
0 |
75 |
if $$self{'verbose'} > 2 |
|
1934
|
0 |
75 |
unless ref $rh_word eq 'HASH' |
|
1938
|
5 |
70 |
unless $$rh_word{'WordAaSymbols'} == 1 |
|
1939
|
0 |
70 |
unless $self->WordIsGeneOrDict($rh_word) |
|
1940
|
0 |
70 |
if $$self{'verbose'} > 2 |
|
1946
|
71 |
190 |
$3 ? : |
|
1947
|
247 |
14 |
unless $next_roman_len > 0 |
|
1949
|
6 |
8 |
if $$rh_word{'WordIsRomanLen'} >= 2 |
|
1953
|
185 |
95 |
unless $$rh_word{$_} |
|
1957
|
17 |
78 |
if $$rh_word{"${_}Len"} > $$rh_word{'WordSeqLen'} |
|
1962
|
0 |
95 |
if $$self{'verbose'} > 2 |
|
1965
|
21 |
49 |
unless ($$rh_word{'WordIsGene'} or $$rh_word{'WordIsDict'}) |
|
1969
|
0 |
5 |
if $$self{'verbose'} > 2 |
|
1972
|
1 |
4 |
if $$rh_word{'WordSubLenMax'} and $$rh_word{'WordSubLenMax'} <= 4 |
|
1975
|
0 |
5 |
if $$self{'verbose'} > 2 |
|
1981
|
13 |
3 |
unless ($$rh_word{'WordIsDNA'} or $$rh_word{'WordIsDict'} or $$rh_word{'WordIsGene'} or $$rh_word{'WordIsRoman'}) |
|
1988
|
0 |
70 |
if $$self{'verbose'} > 2 |
|
1989
|
0 |
70 |
if $$self{'verbose'} > 2 |
|
2006
|
0 |
70 |
unless ref $rh_word eq 'HASH' |
|
2013
|
20 |
50 |
if (@subwords != 1) |
|
2019
|
30 |
22 |
if $length > 2 and $length / $$rh_word{'WordSeqLen'} > 0.25 |
|
2022
|
29 |
23 |
if $$rh_word{'WordSubLenMax'} < $length |
|
2025
|
39 |
31 |
$$rh_word{'WordLcOrig'} eq $$rh_word{'WordLcSequence'} ? : |
|
2033
|
131 |
131 |
if ($bad eq 'Dict') { } |
|
|
131 |
0 |
elsif ($bad eq 'Gene') { } |
|
2036
|
109 |
153 |
if ($is_bad) |
|
2078
|
11 |
1115 |
if $$rh_abst{'AbstMaxWordScore'} < $$rh_word{'WordScore'} |
|
2083
|
75 |
1051 |
$$rh_word{'WordScore'} > 0 ? : |
|
2088
|
12 |
0 |
if ($$self{'verbose'} > 0) |
|
2092
|
0 |
12 |
if $$self{'verbose'} > 2 |
|
2110
|
12 |
0 |
if ($$self{'words'} and ref $$self{'words'} eq 'ARRAY') { } |
|
2116
|
5 |
1121 |
if (not defined $$_{'WordOrig'}) { } |
|
|
597 |
524 |
elsif ($$_{'WordScore'} >= $$self{'WordScoreMin'} and $$_{'WordAbstScore'} >= $$self{'WordAbstScoreMin'}) { } |
|
2144
|
0 |
4540 |
unless defined $number |
|
2148
|
0 |
4540 |
if $number < 0 |
|
2149
|
0 |
4540 |
if $number > 1 |
|
2168
|
40 |
16922 |
if defined $$_{$key} and $$_{$key} eq $val |