| line |
true |
false |
branch |
|
419
|
1 |
91 |
if defined $rpttype |
|
462
|
5339 |
15331 |
if /^\s+$/ |
|
463
|
2 |
15329 |
if /CPU time:/ |
|
464
|
0 |
15329 |
if /^>\s*$/ |
|
465
|
4 |
15325 |
if /[*]+\s+No hits found\s+[*]+/ |
|
466
|
85 |
15240 |
if (/^((?:\S+?)?BLAST[NPX]?)\s+(.+)$/i or /^(P?GENEWISE|HFRAME|SWN|TSWN)\s+(.+)/i) { } |
|
|
73 |
15167 |
elsif (/^Reference:\s+(.*)$/) { } |
|
|
9 |
15158 |
elsif (/^RID:\s+(.*)$/) { } |
|
|
67 |
15091 |
elsif (/^(Searching|Results from round)/) { } |
|
|
102 |
14989 |
elsif (/^Query=\s*(.*)$/) { } |
|
|
1 |
14988 |
elsif (/^>Unfiltered[+-]1$/) { } |
|
|
56 |
14932 |
elsif (/Sequences producing significant alignments:/) { } |
|
|
26 |
14906 |
elsif (/Sequences producing High-scoring Segment Pairs:/) { } |
|
|
77 |
14829 |
elsif (/^Database:\s*(.+?)\s*$/) { } |
|
|
922 |
13907 |
elsif (/^(?:Subject=|>)\s*(\S+)\s*(.*)?/) { } |
|
|
19 |
13888 |
elsif (/\s+(Plus|Minus) Strand HSPs:/i) { } |
|
|
0 |
13888 |
elsif ($self->in_element('hit') || $self->in_element('hsp') and /Score\s*=\s*(\S+)\s*bits\s* # Bit score
(?:\((\d+)\))?, # Raw score
\s+Log\-Length\sScore\s*=\s*(\d+) # Log-Length score
/ox) { } |
|
|
0 |
13888 |
elsif ($self->in_element('hit') || $self->in_element('hsp') and /Score\s*=\s*([^,\s]+), # Raw score
\s*Expect\s*=\s*([^,\s]+), # E-value
\s*P(?:\(\S+\))?\s*=\s*([^,\s]+) # P-value
/ox) { } |
|
|
423 |
13465 |
elsif ($self->in_element('hit') || $self->in_element('hsp') and /Score\s*=\s*(\S+)\s* # Bit score
\(([\d\.]+)\s*bits\), # Raw score
\s*Expect\s*=\s*([^,\s]+), # E-value
\s*(?:Sum)?\s* # SUM
P(?:\(\d+\))?\s*=\s*([^,\s]+) # P-value
(?:\s*,\s+Group\s*\=\s*(\d+))? # HSP Group
/ox) { } |
|
|
70 |
13395 |
elsif ($self->in_element('hit') || $self->in_element('hsp') and /^\sFeatures\s\w+\sthis\spart/mosx) { } |
|
|
1200 |
12195 |
elsif ($self->in_element('hit') || $self->in_element('hsp') and /Score\s*=\s*(\S+)\s*bits\s* # Bit score
(?:\((\d+)\))?, # Missing for BLAT pseudo-BLAST fmt
\s*Expect(?:\((\d+\+?)\))?\s*=\s*([^,\s]+) # E-value
/ox) { } |
|
|
1623 |
10572 |
elsif ($self->in_element('hsp') and m[Identities\s*=\s*(\d+)\s*/\s*(\d+)\s*[\d\%\(\)]+\s*
(?:,\s*Positives\s*=\s*(\d+)/(\d+)\s*[\d\%\(\)]+\s*)? # pos only valid for Protein alignments
(?:\,\s*Gaps\s*=\s*(\d+)/(\d+))? # Gaps
]iox) { } |
|
|
372 |
10200 |
elsif ($self->in_element('hsp') and m[Strand\s*=\s*(Plus|Minus)\s*/\s*(Plus|Minus)]i) { } |
|
|
342 |
9858 |
elsif ($self->in_element('hsp') and /Links\s*=\s*(\S+)/ox) { } |
|
|
308 |
9550 |
elsif ($self->in_element('hsp') and m[Frame\s*=\s*([\+\-][1-3])\s*(/\s*([\+\-][1-3]))?]) { } |
|
|
83 |
9467 |
elsif (/^Parameters:/ or /^\s+Database:\s+?/ or /^\s+Subset/ or /^\s*Lambda/ or /^\s*Histogram/ or $self->in_element('hsp') and /WARNING|NOTE/) { } |
|
|
9058 |
409 |
elsif ($self->in_element('hsp')) { } |
|
474
|
0 |
85 |
if ($reportversion and $reportversion =~ /WashU$/) |
|
478
|
5 |
80 |
if ($self->{'_seentop'}) |
|
484
|
4 |
76 |
if ($reporttype =~ /RPS-BLAST/) |
|
543
|
65 |
2 |
unless $1 =~ /Results from round/ |
|
546
|
1 |
1 |
if $self->in_element('hsp') |
|
548
|
1 |
1 |
if $self->in_element('hit') |
|
550
|
1 |
1 |
if (defined $seeniteration) { } |
|
551
|
1 |
0 |
if $self->within_element('iteration') |
|
564
|
8 |
94 |
if (defined $seenquery) |
|
566
|
4 |
4 |
if $reportline |
|
569
|
14 |
80 |
unless (defined $reporttype) |
|
571
|
0 |
14 |
if (defined $seeniteration) { } |
|
572
|
0 |
0 |
if $self->in_element('iteration') |
|
584
|
0 |
142 |
if (/^Database:/) |
|
590
|
94 |
48 |
if (/\((\-?[\d,]+)\s+letters.*\)/ or /^Length=(\-?[\d,]+)/) { } |
|
597
|
13 |
35 |
$q =~ /\w$/ && $_ =~ /^\w/ ? : |
|
606
|
89 |
5 |
if $nm |
|
618
|
55 |
39 |
if defined $desc |
|
626
|
27 |
67 |
defined $version && length $version ? : |
|
627
|
89 |
5 |
if $acc |
|
641
|
20 |
74 |
if $self->{'_blsdb_length'} |
|
647
|
20 |
74 |
if $self->{'_blsdb_letters'} |
|
653
|
20 |
74 |
if $self->{'_blsdb_letters'} |
|
676
|
50 |
6 |
unless ($self->in_element('iteration')) |
|
686
|
105 |
1249 |
if ($descline =~ /^\s*$/) |
|
687
|
50 |
55 |
if $seen_block |
|
693
|
3 |
1246 |
if ($descline =~ /^(\S+)\s+Begin:\s\d+\s+End:\s+\d+/msx) |
|
699
|
1243 |
6 |
if ($descline =~ /(?
|
|
|
0 |
6 |
elsif ($descline =~ /^CONVERGED/i) { } |
|
718
|
0 |
1243 |
if ($3) |
|
744
|
23 |
3 |
unless ($self->in_element('iteration')) |
|
766
|
75 |
80 |
if (/^\s+(\-?[\d\,]+|\S+)\s+sequences\;
\s+(\-?[\d,]+|\S+)\s+ # Deal with NCBI 2.2.8 OSX problems
total\s+letters/ox) { } |
|
811
|
834 |
88 |
if $self->in_element('hsp') |
|
813
|
834 |
88 |
if $self->in_element('hit') |
|
818
|
2 |
920 |
if (not $self->within_element('result')) { } |
|
|
2 |
918 |
elsif (not $self->within_element('iteration')) { } |
|
852
|
14 |
628 |
if (not $tableid =~ /\Q$id\E/) { } |
|
860
|
3 |
1458 |
if /^\s+$/ |
|
862
|
922 |
536 |
if (/Length\s*=\s*([\d,]+)/) { } |
|
874
|
519 |
17 |
unless ($restofline =~ /\s$/) |
|
877
|
12 |
524 |
$restofline =~ /\w$/ && $_ =~ /^\w/ ? : |
|
902
|
0 |
0 |
if $self->in_element('hsp') |
|
939
|
0 |
0 |
if $self->in_element('hsp') |
|
947
|
0 |
0 |
if $evalue =~ /^e/ |
|
948
|
0 |
0 |
if $pvalue =~ /^e/ |
|
981
|
330 |
93 |
if $self->in_element('hsp') |
|
1016
|
29 |
394 |
if (defined $group) |
|
1033
|
66 |
4 |
if $self->in_element('hsp') |
|
1063
|
1130 |
70 |
unless ($self->{'_seen_hsp_features'}) |
|
1064
|
305 |
825 |
if $self->in_element('hsp') |
|
1090
|
31 |
1169 |
if defined $n |
|
1096
|
0 |
1200 |
unless defined $score |
|
1120
|
1251 |
372 |
if (defined $3) { } |
|
1136
|
787 |
836 |
if (defined $6) |
|
1148
|
44 |
1579 |
if (/(Frame\s*=\s*.+)$/) |
|
1159
|
2 |
370 |
unless (defined $reporttype) |
|
1182
|
4 |
304 |
unless (defined $reporttype) |
|
1184
|
1 |
3 |
if ($frame1 and $frame2) { } |
|
1201
|
3 |
3 |
if ($line =~ /^(?:Query|Sbjct):?\s+(\-?\d+)?\s*(\S+)\s+(\-?\d+)?/) |
|
1213
|
1 |
2 |
$a_position < $b_position ? : |
|
1215
|
2 |
1 |
$coord_length == $ali_length * 3 ? : |
|
1224
|
187 |
121 |
if ($reporttype eq 'TBLASTX') { } |
|
|
95 |
26 |
elsif ($reporttype eq 'TBLASTN' or $reporttype eq 'PSITBLASTN') { } |
|
|
26 |
0 |
elsif ($reporttype eq 'BLASTX' or $reporttype eq 'RPS-BLAST(BLASTP)') { } |
|
1235
|
0 |
26 |
if ($reporttype eq 'RPS-BLAST(BLASTP)') |
|
1270
|
78 |
5 |
if $self->in_element('hsp') |
|
1272
|
78 |
5 |
if $self->in_element('hit') |
|
1277
|
6 |
77 |
if scalar @hit_signifs |
|
1278
|
81 |
2 |
if $self->within_element('iteration') |
|
1281
|
0 |
83 |
if /^\s+Subset/ |
|
1282
|
57 |
26 |
/^(\s+Database\:)|(\s*Lambda)/ ? : |
|
1283
|
0 |
83 |
if (/^\s*Histogram/) |
|
1299
|
15 |
2804 |
if (/^\s+[\d+\.]+\s+[\d+\.]+\s+[\d+\.]/ and $last eq '') { } |
|
|
5 |
2799 |
elsif (/^((?:\S+)?BLAST[NPX]?)\s+(.+)$/i or /^(P?GENEWISE|HFRAME|SWN|TSWN)\s+(.+)/i) { } |
|
|
4 |
2795 |
elsif (/^Query=/) { } |
|
1317
|
4 |
0 |
if $reportline |
|
1323
|
125 |
2670 |
if (/Number of Sequences:\s+([\d\,]+)/i or /of sequences in database:\s+(\-?[\d,]+)/i) { } |
|
|
73 |
2597 |
elsif (/letters in database:\s+(\-?[\d,]+)/i) { } |
|
|
0 |
2597 |
elsif ($blast eq 'btk') { } |
|
|
985 |
1612 |
elsif ($blast eq 'wublast') { } |
|
|
1612 |
0 |
elsif ($blast eq 'ncbi') { } |
|
1351
|
29 |
956 |
if (/E=(\S+)/) { } |
|
|
2 |
954 |
elsif (/nogaps/) { } |
|
|
26 |
928 |
elsif (/ctxfactor=(\S+)/) { } |
|
|
34 |
894 |
elsif (/(postsw|links|span[12]?|warnings|notes|gi|noseqs|qres|qype)/) { } |
|
|
141 |
753 |
elsif (/(\S+)=(\S+)/) { } |
|
|
26 |
727 |
elsif ($last =~ /(Frame|Strand)\s+MatID\s+Matrix name/i) { } |
|
|
26 |
701 |
elsif ($last =~ /(Frame|Strand)\s+MatID\s+Length/i) { } |
|
|
23 |
678 |
elsif (/(\S+\s+\S+)\s+DFA:\s+(\S+)\s+\((.+)\)/) { } |
|
|
0 |
678 |
elsif (/^\s+Time to generate neighborhood:\s+
(\S+\s+\S+\s+\S+)/x) { } |
|
|
23 |
655 |
elsif (/processors\s+used:\s+(\d+)/) { } |
|
|
46 |
609 |
elsif (/^\s+(\S+)\s+cpu\s+time:\s+ # cputype
(\S+\s+\S+\s+\S+) # cputime
\s+Elapsed:\s+(\S+)/x) { } |
|
|
23 |
586 |
elsif (/^\s+Start:/) { } |
|
|
21 |
565 |
elsif (/^\s+Database:\s+(.+)$/) { } |
|
|
21 |
544 |
elsif (/^\s+Posted:\s+(.+)/) { } |
|
1400
|
24 |
84 |
if ($firstgapinfo and s/Q=(\d+),R=(\d+)\s+//x) { } |
|
1425
|
0 |
72 |
if $type eq 'n/a' |
|
1426
|
0 |
72 |
unless (@fields) |
|
1442
|
26 |
58 |
unless (defined $frame) |
|
1483
|
48 |
456 |
unless defined $f |
|
1484
|
72 |
384 |
if ($f eq 'same') |
|
1510
|
0 |
0 |
if (@fields <= 3) { } |
|
1512
|
0 |
0 |
unless @fields |
|
1544
|
23 |
0 |
if ($1 eq 'states in') { } |
|
|
0 |
0 |
elsif ($1 eq 'size of') { } |
|
1641
|
55 |
1557 |
if (/^Matrix:\s+(.+)\s*$/iox) { } |
|
|
49 |
1508 |
elsif (/^Gapped/) { } |
|
|
107 |
1401 |
elsif (/^Lambda/) { } |
|
|
54 |
1347 |
elsif (/effective\s+search\s+space\s+used:\s+(\d+)/iox) { } |
|
|
48 |
1299 |
elsif (/effective\s+search\s+space:\s+(\d+)/iox) { } |
|
|
48 |
1251 |
elsif (/Gap\s+Penalties:\s+Existence:\s+(\d+)\,
\s+Extension:\s+(\d+)/ox) { } |
|
|
45 |
1206 |
elsif (/effective\s+HSP\s+length:\s+(\d+)/) { } |
|
|
34 |
1172 |
elsif (/Number\s+of\s+HSP's\s+better\s+than\s+(\S+)\s+without\s+gapping:\s+(\d+)/) { } |
|
|
7 |
1165 |
elsif (/Number\s+of\s+HSP's\s+gapped:\s+(\d+)/) { } |
|
|
7 |
1158 |
elsif (/Number\s+of\s+HSP's\s+successfully\s+gapped:\s+(\d+)/) { } |
|
|
6 |
1152 |
elsif (/Length\s+adjustment:\s+(\d+)/) { } |
|
|
48 |
1104 |
elsif (/effective\s+length\s+of\s+query:\s+([\d\,]+)/i) { } |
|
|
51 |
1053 |
elsif (/effective\s+length\s+of\s+database:\s+([\d\,]+)/i) { } |
|
|
325 |
728 |
elsif (/^(T|A|X1|X2|X3|S1|S2):\s+(\d+(\.\d+)?)\s+(?:\(\s*(\d+\.\d+) bits\))?/) { } |
|
|
14 |
714 |
elsif (/frameshift\s+window\,
\s+decay\s+const:\s+(\d+)\,\s+([\.\d]+)/x) { } |
|
|
52 |
662 |
elsif (/^Number\s+of\s+Hits\s+to\s+DB:\s+(\S+)/ox) { } |
|
|
51 |
611 |
elsif (/^Number\s+of\s+extensions:\s+(\S+)/ox) { } |
|
|
51 |
560 |
elsif (/^Number\s+of\s+successful\s+extensions:\s+
(\S+)/ox) { } |
|
|
52 |
508 |
elsif (/^Number\s+of\s+sequences\s+better\s+than\s+
(\S+):\s+(\d+)/ox) { } |
|
|
50 |
458 |
elsif (/^\s+Posted\s+date:\s+(.+)/) { } |
|
|
225 |
233 |
elsif (not /^\s+$/) { } |
|
1656
|
49 |
58 |
if ($gapped_stats) { } |
|
1803
|
235 |
90 |
if (defined $4) |
|
1905
|
0 |
27150 |
if ($i == 0 and /^\s+$/ or /^\s*(?:Lambda|Minus|Plus|Score)/i) |
|
1908
|
0 |
0 |
if defined $_ |
|
1913
|
18116 |
9034 |
if (/^((Query|Sbjct):?\s+(\-?\d+)?\s*)(\S+)\s+(\-?\d+)?/) { } |
|
|
0 |
9034 |
elsif (/^((Query|Sbjct):?\s+(\-?0+)\s*)/) { } |
|
1917
|
48 |
18068 |
if ($str eq '-') { } |
|
1918
|
24 |
24 |
if $type eq 'Sbjct' |
|
1925
|
3246 |
14870 |
unless $$self{"_$type"}{'begin'} |
|
1932
|
0 |
9034 |
unless defined $_ and defined $len |
|
1963
|
96 |
6 |
if ($self->{'_seentop'}) |
|
1964
|
9 |
87 |
if $self->within_element('hsp') |
|
1966
|
9 |
87 |
if $self->within_element('hit') |
|
1969
|
2 |
94 |
if scalar @hit_signifs |
|
1970
|
11 |
85 |
if $self->within_element('iteration') |
|
1972
|
6 |
90 |
if ($bl2seq_fix) |
|
2038
|
8178 |
338 |
defined $self->{'_will_handle_cache'}{$type} ? : |
|
2041
|
8516 |
0 |
$will_handle ? : |
|
2060
|
4258 |
0 |
if ($type) |
|
2062
|
4258 |
0 |
if ($handler) |
|
2073
|
96 |
4162 |
if ($type eq 'result') { } |
|
2078
|
4162 |
0 |
if (defined $self->{'_values'}) |
|
2109
|
86 |
42921 |
if ($nm eq 'BlastOutput_program') |
|
2110
|
83 |
3 |
if ($self->{'_last_data'} =~ /(t?blast[npx])/i) |
|
2116
|
80 |
42927 |
if ($nm eq 'BlastOutput_version') |
|
2122
|
1623 |
41384 |
if ($nm eq 'Hsp') |
|
2129
|
4845 |
1647 |
if defined $self->{'_last_hspdata'}{$_} |
|
2161
|
4258 |
38749 |
if ($type = $Bio::SearchIO::blast::MODEMAP{$nm}) { } |
|
|
38562 |
187 |
elsif ($Bio::SearchIO::blast::MAPPING{$nm}) { } |
|
2163
|
4258 |
0 |
if ($handler) |
|
2171
|
2900 |
35662 |
if (ref($Bio::SearchIO::blast::MAPPING{$nm}) =~ /hash/i) { } |
|
2188
|
96 |
42911 |
if defined $type and $type eq 'result' |
|
2226
|
32019 |
33904 |
if ($self->in_element('hsp') and $data->{'Name'} =~ /^Hsp\_(qseq|hseq|midline)$/) |
|
2230
|
31995 |
24 |
if defined $data->{'Data'} |
|
2232
|
70 |
65853 |
unless defined $data->{'Data'} and not $data->{'Data'} =~ /^\s+$/ |
|
2254
|
2 |
2212 |
if not defined $name || defined $self->{'_elements'} or scalar @{$self->{'_elements'};} == 0 |
|
2256
|
1949 |
1185 |
if ($_ eq $name) |
|
2279
|
119 |
263910 |
unless defined $self->{'_elements'}[0] |
|
2323
|
0 |
5 |
unless (defined $self->writer) |
|
2425
|
0 |
1524 |
unless defined $v |
|
2442
|
1524 |
0 |
if (defined $v) |
|
2449
|
0 |
1524 |
if (exists $self->{'_wublast'}) { } |