| line |
true |
false |
branch |
|
176
|
5 |
20 |
if (not defined($buffer = $self->_readline)) { } |
|
192
|
14 |
231 |
if ($buffer =~ /^\#\s(\S+)\s\:\:\s/) { } |
|
|
14 |
217 |
elsif ($buffer =~ /^\#\sHMMER\s+(\S+)\s+\((.+)\)/) { } |
|
|
14 |
203 |
elsif ($buffer =~ /^\#\squery (?:\w+ )?file\:\s+(\S+)/) { } |
|
|
0 |
203 |
elsif ($buffer =~ /^\#\sshow\salignments\sin\soutput/) { } |
|
|
14 |
189 |
elsif ($buffer =~ /^\#\starget\s\S+\sdatabase\:\s+(\S+)/) { } |
|
|
20 |
169 |
elsif ($buffer =~ s/^Query:\s+//) { } |
|
|
6 |
163 |
elsif ($buffer =~ s/^Accession:\s+//) { } |
|
|
9 |
154 |
elsif ($buffer =~ s/^Description:\s+//) { } |
|
|
154 |
0 |
elsif (defined $self->{'_reporttype'} and $self->{'_reporttype'} eq 'HMMSEARCH' || $self->{'_reporttype'} eq 'HMMSCAN' || $self->{'_reporttype'} eq 'PHMMER' || $self->{'_reporttype'} eq 'NHMMER') { } |
|
220
|
7 |
7 |
if ($self->{'_reporttype'} eq 'HMMSEARCH' or $self->{'_reporttype'} eq 'PHMMER' or $self->{'_reporttype'} eq 'NHMMER') { } |
|
|
7 |
0 |
elsif ($self->{'_reporttype'} eq 'HMMSCAN') { } |
|
249
|
7 |
7 |
if ($self->{'_reporttype'} eq 'HMMSEARCH' or $self->{'_reporttype'} eq 'PHMMER' or $self->{'_reporttype'} eq 'NHMMER') { } |
|
|
7 |
0 |
elsif ($self->{'_reporttype'} eq 'HMMSCAN') { } |
|
273
|
6 |
0 |
if (not exists $self->{'_values'}{'RESULT-algorithm_name'} && exists $self->{'_values'}{'RESULT-algorithm_version'} and exists $self->{'_hmmidline'}) |
|
290
|
6 |
0 |
if (not exists $self->{'_values'}{'RESULT-hmm_name'} && exists $self->{'_values'}{'RESULT-sequence_file'} and exists $self->{'_hmmfileline'} || exists $self->{'_hmmseqline'}) |
|
297
|
4 |
2 |
if ($self->{'_reporttype'} eq 'HMMSEARCH' or $self->{'_reporttype'} eq 'PHMMER' or $self->{'_reporttype'} eq 'NHMMER') { } |
|
|
2 |
0 |
elsif ($self->{'_reporttype'} eq 'HMMSCAN') { } |
|
330
|
0 |
20 |
unless ($buffer =~ s/\s+\[[L|M]\=(\d+)\]$//) |
|
378
|
19 |
135 |
if ($buffer =~ /Scores for complete sequence/) { } |
|
|
1 |
134 |
elsif ($buffer =~ /Scores for complete hits/) { } |
|
|
5 |
129 |
elsif ($buffer =~ /inclusion threshold/) { } |
|
|
17 |
112 |
elsif ($buffer =~ /Domain( and alignment)? annotation for each/ or $buffer =~ /Annotation for each hit\s+\(and alignments\)/) { } |
|
|
20 |
92 |
elsif ($buffer =~ /Internal pipeline statistics/ or $buffer =~ m[^//]) { } |
|
380
|
19 |
106 |
if ($buffer =~ /inclusion threshold/ or $buffer =~ /Domain( and alignment)? annotation for each/ or $buffer =~ /\[No hits detected/ or $buffer =~ m[^//]) { } |
|
|
76 |
30 |
elsif ($buffer =~ /^\s+E-value\s+score/ or $buffer =~ /\-\-\-/ or $buffer =~ /^$/) { } |
|
414
|
0 |
30 |
unless defined $desc |
|
425
|
1 |
6 |
if ($buffer =~ /inclusion threshold/ or $buffer =~ /Annotation for each hit/ or $buffer =~ /\[No hits detected/ or $buffer =~ m[^//]) { } |
|
|
4 |
2 |
elsif ($buffer =~ /^\s+E-value\s+score/ or $buffer =~ /\-\-\-/ or $buffer =~ /^$/) { } |
|
455
|
0 |
2 |
unless defined $desc |
|
465
|
5 |
30 |
if ($buffer =~ /Domain( and alignment)? annotation for each/ or $buffer =~ /Internal pipeline statistics summary/ or $buffer =~ /Annotation for each hit\s+\(and alignments\)/) { } |
|
|
10 |
20 |
elsif ($buffer =~ /inclusion threshold/ or $buffer =~ /^$/) { } |
|
498
|
0 |
20 |
unless defined $desc |
|
516
|
17 |
94 |
if ($buffer =~ /\[No targets detected/ or $buffer =~ /Internal pipeline statistics/) |
|
523
|
46 |
48 |
if ($buffer =~ /^\>\>\s(\S*)\s+(.*)/) { } |
|
|
46 |
2 |
elsif ($buffer =~ /Alignment(?:s for each domain)?:/) { } |
|
531
|
6 |
40 |
if (length $hit_list[$hitinfo{"$name.$annot_counter"}][1] < length $desc) |
|
540
|
46 |
217 |
if ($buffer =~ /Internal pipeline statistics/ or $buffer =~ /Alignments for each domain/ or $buffer =~ /^\s+Alignment:/ or $buffer =~ /^\>\>/) { } |
|
|
138 |
79 |
elsif ($buffer =~ /^\s+score\s+bias/ or $buffer =~ /^\s+\#\s+score/ or $buffer =~ /^\s+------\s+/ or $buffer =~ /^\s\-\-\-\s+/ or $buffer =~ /^$/) { } |
|
559
|
79 |
0 |
if ($self->{'_reporttype'} =~ /(?:HMMSCAN|HMMSEARCH|PHMMER|NHMMER)/) |
|
568
|
77 |
2 |
if (($domain_num, $score, $bias, $ceval, $ieval, $hmm_start, $hmm_stop, $hmm_cov, $seq_start, $seq_stop, $seq_cov, $env_start, $env_stop, $env_cov, $acc) = $buffer =~ /^\s+(\d+)\s\!*\?*\s+ # domain number
(\S+)\s+(\S+)\s+ # score, bias
(\S+)\s+(\S+)\s+ # c-eval, i-eval
(\d+)\s+(\d+)\s+(\S+)\s+ # hmm start, stop, coverage
(\d+)\s+(\d+)\s+(\S+)\s+ # seq start, stop, coverage
(\d+)\s+(\d+)\s+(\S+)\s+ # env start, stop, coverage
(\S+) # posterior probability accuracy
\s*$/ox) { } |
|
|
2 |
0 |
elsif (($score, $bias, $ceval, $hmm_start, $hmm_stop, $hmm_cov, $seq_start, $seq_stop, $seq_cov, $env_start, $env_stop, $env_cov, $hitlength, $acc) = $buffer =~ /^\s+[!?]\s+
(\S+)\s+(\S+)\s+(\S+)\s+ # score, bias, evalue
(\d+)\s+(\d+)\s+(\S+)\s+ # hmm start, stop, coverage
(\d+)\s+(\d+)\s+(\S+)\s+ # seq start, stop, coverage
(\d+)\s+(\d+)\s+(\S+)\s+ # env start, stop, coverage
(\d+)\s+(\S+) # target length, pp accuracy
.*$/ox) { } |
|
590
|
22 |
55 |
if ($self->{'_reporttype'} eq 'HMMSEARCH' or $self->{'_reporttype'} eq 'PHMMER') { } |
|
|
55 |
0 |
elsif ($self->{'_reporttype'} eq 'HMMSCAN') { } |
|
594
|
2 |
20 |
if ($seq_cov =~ /\]$/) |
|
602
|
5 |
50 |
if ($hmm_cov =~ /\]$/) |
|
631
|
0 |
79 |
unless (defined $info) |
|
675
|
46 |
760 |
if ($buffer =~ /^\>\>/ or $buffer =~ /Internal pipeline statistics/) { } |
|
|
149 |
611 |
elsif ($buffer =~ /^$/) { } |
|
692
|
79 |
532 |
if ($buffer =~ /\s\s\=\=\sdomain\s(\d+)\s+/ or $buffer =~ /\s\sscore:\s\S+\s+/) { } |
|
|
56 |
476 |
elsif ($buffer =~ /\s+\S+\s(?:CS|RF)$/ and $align_length == 0) { } |
|
|
238 |
238 |
elsif ($count == $max_count - 3 or $count == $max_count - 1) { } |
|
|
119 |
119 |
elsif ($count == $max_count - 2) { } |
|
|
119 |
0 |
elsif ($count == $max_count) { } |
|
730
|
238 |
0 |
if ($line_offset != 0) |
|
735
|
132 |
106 |
if ($self->{'_reporttype'} eq 'HMMSCAN') { } |
|
737
|
66 |
66 |
if $count == $max_count - 3 |
|
739
|
66 |
66 |
if $count == $max_count - 1 |
|
743
|
53 |
53 |
if $count == $max_count - 1 |
|
745
|
53 |
53 |
if $count == $max_count - 3 |
|
784
|
0 |
20 |
if ($self->within_element('hit')) |
|
785
|
0 |
0 |
if ($self->within_element('hsp')) |
|
793
|
17 |
186 |
if $buffer =~ m[^//$] |
|
831
|
79 |
0 |
if (defined $hsp) |
|
836
|
79 |
0 |
if ($hsp->[-3] ne '') { } |
|
869
|
55 |
24 |
if ($self->{'_reporttype'} eq 'HMMSCAN') { } |
|
|
14 |
10 |
elsif ($self->{'_reporttype'} eq 'HMMSEARCH' or $self->{'_reporttype'} eq 'NHMMER') { } |
|
926
|
17 |
62 |
if ($hitlength != 0) |
|
960
|
2 |
77 |
if ($self->{'_reporttype'} eq 'NHMMER') |
|
963
|
1 |
1 |
$hstart < $hend ? : |
|
967
|
2 |
0 |
$qstart < $qend ? : |
|
1019
|
145 |
1825 |
if ($type) |
|
1020
|
145 |
0 |
if ($self->_eventHandler->will_handle($type)) |
|
1026
|
14 |
1956 |
if (defined $type and $type eq 'result') |
|
1051
|
20 |
1956 |
if ($nm eq 'HMMER_program') |
|
1052
|
20 |
0 |
if ($self->{'_last_data'} =~ /([NP]?HMM\S+)/i) |
|
1059
|
79 |
1897 |
if ($nm eq 'Hsp') |
|
1062
|
79 |
316 |
if ($data and $line eq 'Hsp_hseq') |
|
1075
|
151 |
1825 |
if ($type) { } |
|
|
1825 |
0 |
elsif ($Bio::SearchIO::hmmer3::MAPPING{$nm}) { } |
|
1076
|
151 |
0 |
if ($self->_eventHandler->will_handle($type)) |
|
1086
|
1742 |
1160 |
if $key =~ /^$name-/ |
|
1090
|
0 |
1825 |
if (ref($Bio::SearchIO::hmmer3::MAPPING{$nm}) =~ /hash/i) { } |
|
1106
|
20 |
1956 |
if defined $type and $type eq 'result' |
|
1156
|
790 |
692 |
if ($self->in_element('hsp') and $data->{'Name'} =~ /Hsp\_(?:qseq|hseq|csline|pline|midline)/o and defined $data->{'Data'}) |
|
1162
|
0 |
1825 |
unless defined $data->{'Data'} and not $data->{'Data'} =~ /^\s+$/o |
|
1184
|
6 |
14 |
if not defined $name && defined $self->{'_elements'} or scalar @{$self->{'_elements'};} == 0 |
|
1186
|
0 |
14 |
if $element eq $name |
|
1205
|
46 |
1779 |
unless defined $self->{'_elements'}[0] |