| line |
true |
false |
branch |
|
166
|
16 |
445 |
if ($buffer =~ /^HMMER\s+(\S+)\s+\((.+)\)/o) { } |
|
|
16 |
429 |
elsif ($buffer =~ s/^HMM file:\s+//o) { } |
|
|
16 |
413 |
elsif ($buffer =~ s/^Sequence\s+(file|database):\s+//o) { } |
|
|
17 |
396 |
elsif ($buffer =~ s/^Query(?:\s+(?:sequence|HMM))?(?:\s+\d+)?:\s+//o) { } |
|
|
8 |
388 |
elsif ($buffer =~ s/^Accession:\s+//o) { } |
|
|
8 |
380 |
elsif ($buffer =~ s/^Description:\s+//o) { } |
|
|
365 |
15 |
elsif (defined $self->{'_reporttype'} and $self->{'_reporttype'} eq 'HMMSEARCH' || $self->{'_reporttype'} eq 'HMMPFAM') { } |
|
168
|
0 |
16 |
if ($seentop) |
|
177
|
16 |
0 |
if (defined $last) |
|
179
|
15 |
1 |
if defined $reporttype |
|
205
|
5 |
11 |
if ($1 eq 'database') |
|
221
|
1 |
16 |
unless ($seentop) |
|
261
|
16 |
349 |
if ($buffer =~ /^Scores for (?:complete sequences|sequence family)/o) { } |
|
|
16 |
333 |
elsif ($buffer =~ /^Parsed for domains:/o) { } |
|
|
12 |
321 |
elsif ($buffer =~ /^Alignments of top/o) { } |
|
|
16 |
305 |
elsif ($buffer =~ /^Histogram/o or $buffer =~ m[^//]o) { } |
|
263
|
16 |
3157 |
if $buffer =~ /^\s+$/ |
|
264
|
21 |
3125 |
if $buffer =~ /^Model\s+Description/o or $buffer =~ /^Sequence\s+Description/o or $buffer =~ /^\-\-\-/o |
|
281
|
16 |
5019 |
if $buffer =~ /^\s+$/ |
|
282
|
0 |
5019 |
if ($buffer =~ m[^//]) |
|
286
|
32 |
4987 |
if $buffer =~ /^(?:Model|Sequence)\s+Domain/ or $buffer =~ /^\-\-\-/ |
|
289
|
4987 |
0 |
if (my($name, $domainct, $domaintotal, $seq_start, $seq_end, $seq_cov, $hmm_start, $hmm_end, $hmm_cov, $score, $evalue) = $buffer =~ m[^(\S+)\s+ # domain name
(\d+)/(\d+)\s+ # domain num out of num
(\d+)\s+(\d+)\s+ # seq start, end
(\S+)\s+ # seq coverage
(\d+)\s+(\d+)\s+ # hmm start, end
(\S+)\s+ # hmm coverage
(\S+)\s+ # score
(\S+) # evalue
\s*$]ox) |
|
307
|
0 |
4987 |
unless (defined $hindex) |
|
315
|
0 |
4987 |
unless (defined $info) |
|
316
|
0 |
0 |
if ($self->{'_reporttype'} eq 'HMMSEARCH') { } |
|
|
0 |
0 |
elsif ($self->{'_reporttype'} eq 'HMMPFAM') { } |
|
330
|
4864 |
123 |
if ($self->{'_reporttype'} eq 'HMMSEARCH') { } |
|
|
123 |
0 |
elsif ($self->{'_reporttype'} eq 'HMMPFAM') { } |
|
334
|
48 |
4816 |
if ($seq_cov =~ /\]$/ and scalar @{$hitinfo[$hindex];} == 5) |
|
341
|
5 |
4859 |
if ($hmm_cov =~ /\]$/ and not exists $self->{'_values'}{'RESULT-query_length'}) |
|
355
|
69 |
54 |
if ($hmm_cov =~ /\]$/ and scalar @{$hitinfo[$hindex];} == 5) |
|
362
|
2 |
121 |
if ($seq_cov =~ /\]$/ and not exists $self->{'_values'}{'RESULT-query_length'}) |
|
388
|
0 |
1204 |
if $buffer =~ /^Align/o |
|
390
|
11 |
1192 |
if ($buffer =~ /^Histogram/o or $buffer =~ m[^//]o or $buffer =~ /^Query(?:\s+(?:sequence|HMM))?(?:\s+\d+)?:/o) |
|
394
|
12 |
0 |
if ($self->in_element('hsp')) |
|
397
|
12 |
0 |
if ($self->within_element('hit')) |
|
405
|
127 |
1065 |
if (my($name, $domainct, $domaintotal, $from, $to) = $buffer =~ /^\s*(.+):
\s+ domain \s+ (\d+) \s+ of \s+ (\d+) ,
\s+ from \s+ (\d+) \s+ to \s+ (\d+)/x) { } |
|
415
|
115 |
12 |
if ($self->within_element('hit')) |
|
416
|
115 |
0 |
if ($self->within_element('hsp')) |
|
423
|
0 |
127 |
if (not defined $info or $info->[0] ne $name) |
|
466
|
75 |
52 |
if (my $hit_end = shift @{$info;}) |
|
479
|
0 |
127 |
if ($id ne $name) |
|
486
|
4 |
123 |
if ($self->{'_reporttype'} eq 'HMMSEARCH') { } |
|
|
123 |
0 |
elsif ($self->{'_reporttype'} eq 'HMMPFAM') { } |
|
551
|
121 |
6 |
if ($domaincounter{$name} == $domaintotal) |
|
561
|
104 |
961 |
if ($buffer =~ /^\s+(?:CS|RF)\s+/o and $count == 0) { } |
|
|
127 |
834 |
elsif ($buffer =~ /^(\s+ \*->) (\S+)/ox) { } |
|
|
25 |
809 |
elsif ($buffer =~ /^(\s+) (\S+) <-?\*? \s*$/ox) { } |
|
|
247 |
562 |
elsif ($count != 1 and $buffer =~ /^\s+$/o or length $buffer == 0 or $buffer =~ /^\s+\-?\*\s*$/ or $buffer =~ /^\s+\S+\s+\-\s+\-\s*$/) { } |
|
|
86 |
476 |
elsif ($count == 0) { } |
|
|
238 |
238 |
elsif ($count == 1) { } |
|
|
238 |
0 |
elsif ($count == 2) { } |
|
574
|
102 |
25 |
if ($data =~ s/<-?\*?\s*$//) |
|
579
|
4 |
123 |
if ($self->{'_reporttype'} eq 'HMMSEARCH') { } |
|
|
123 |
0 |
elsif ($self->{'_reporttype'} eq 'HMMPFAM') { } |
|
600
|
10 |
15 |
unless $second_tier++ |
|
601
|
4 |
21 |
if ($self->{'_reporttype'} eq 'HMMSEARCH') { } |
|
|
21 |
0 |
elsif ($self->{'_reporttype'} eq 'HMMPFAM') { } |
|
628
|
15 |
71 |
unless $second_tier++ |
|
629
|
0 |
86 |
unless (defined $prelength) |
|
634
|
20 |
66 |
if ($self->{'_reporttype'} eq 'HMMSEARCH') { } |
|
|
66 |
0 |
elsif ($self->{'_reporttype'} eq 'HMMPFAM') { } |
|
652
|
0 |
238 |
unless (defined $prelength) |
|
655
|
127 |
111 |
if ($width) { } |
|
662
|
54 |
73 |
if ($csline ne '') |
|
680
|
50 |
61 |
if ($csline ne '') |
|
692
|
238 |
0 |
if ($buffer =~ /^\s+(\S+)\s+(\d+|\-)\s+(\S*)\s+(\d+|\-)/o) { } |
|
693
|
28 |
210 |
if ($self->{'_reporttype'} eq 'HMMSEARCH') { } |
|
|
210 |
0 |
elsif ($self->{'_reporttype'} eq 'HMMPFAM') { } |
|
714
|
238 |
476 |
if $count++ >= 2 |
|
726
|
0 |
4860 |
unless defined $info |
|
754
|
56 |
4804 |
if (my $hit_end = shift @{$info;}) |
|
805
|
3004 |
1856 |
if ($domaincounter{$id} == $domaintotal) |
|
820
|
16 |
3 |
if $seentop |
|
841
|
9990 |
80976 |
if ($type) |
|
842
|
9990 |
0 |
if ($self->_eventHandler->will_handle($type)) |
|
848
|
16 |
90950 |
if (defined $type and $type eq 'result') |
|
873
|
16 |
90950 |
if ($nm eq 'HMMER_program') |
|
874
|
15 |
1 |
if ($self->{'_last_data'} =~ /(HMM\S+)/i) |
|
881
|
4987 |
85979 |
if ($nm eq 'Hsp') |
|
884
|
127 |
19821 |
if ($data and $line eq 'Hsp_hseq') |
|
896
|
4987 |
14961 |
if ($line eq 'Hsp_midline') |
|
897
|
127 |
4860 |
if ($data) { } |
|
934
|
9990 |
80976 |
if ($type) { } |
|
|
80976 |
0 |
elsif ($Bio::SearchIO::hmmer2::MAPPING{$nm}) { } |
|
935
|
9990 |
0 |
if ($self->_eventHandler->will_handle($type)) |
|
945
|
104966 |
89885 |
if $key =~ /^$name-/ |
|
949
|
0 |
80976 |
if (ref($Bio::SearchIO::hmmer2::MAPPING{$nm}) =~ /hash/i) { } |
|
963
|
16 |
90950 |
if defined $type and $type eq 'result' |
|
999
|
1253 |
59536 |
if ($self->in_element('hsp') and $data->{'Name'} =~ /Hsp\_(?:qseq|hseq|csline|midline)/o and defined $data->{'Data'}) |
|
1005
|
19516 |
61460 |
unless defined $data->{'Data'} and not $data->{'Data'} =~ /^\s+$/o |
|
1028
|
0 |
254 |
if not defined $name && defined $self->{'_elements'} or scalar @{$self->{'_elements'};} == 0 |
|
1030
|
242 |
127 |
if $element eq $name |
|
1050
|
0 |
80988 |
unless defined $self->{'_elements'}[0] |