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 |