| line |
true |
false |
branch |
|
117
|
0 |
5 |
unless (defined $parsetype) |
|
121
|
4 |
1 |
if (defined $self->_fh) |
|
122
|
2 |
2 |
if ($parsetype eq 'hmmsearch') { } |
|
|
2 |
0 |
elsif ($parsetype eq 'hmmpfam') { } |
|
152
|
0 |
0 |
if ($self->{'_started_next_feature'} == 1) { } |
|
204
|
4 |
2 |
if (defined $value) |
|
225
|
4 |
2 |
if (defined $value) |
|
249
|
0 |
3037 |
if (not exists $self->{'seq'}{$name}) { } |
|
311
|
0 |
0 |
if ($_->evalue > $eval) |
|
319
|
0 |
0 |
if (not defined $prev or $seen == 0) |
|
326
|
0 |
0 |
if ($sep < 1) |
|
329
|
0 |
0 |
if ($dom->bits < 25 and $prev->bits > 25) |
|
366
|
0 |
0 |
unless (defined $idt) |
|
398
|
0 |
1 |
unless (defined $domthr) |
|
405
|
448 |
303 |
if $seq->bits < $seqthr |
|
408
|
106 |
604 |
if $unit->bits < $domthr |
|
435
|
0 |
0 |
unless (defined $fh) |
|
470
|
0 |
0 |
unless (defined $file) |
|
477
|
0 |
0 |
if ($seq->bits < $seqt) |
|
482
|
0 |
0 |
if ($unit->bits < $domt) |
|
493
|
0 |
0 |
if ($aa eq $bb) { } |
|
517
|
0 |
0 |
unless (defined $file) |
|
524
|
0 |
0 |
if ($seq->bits < $seqt) |
|
529
|
0 |
0 |
if ($unit->bits < $domt) |
|
554
|
0 |
0 |
unless (defined $file) |
|
574
|
0 |
0 |
if ($seq->bits < $seqt and $seq->bits > $hseq) |
|
579
|
0 |
0 |
if ($seq->bits < $seqt || $seq->bits > $seqt && $unit->bits < $domt and $unit->bits > $hdom) |
|
598
|
0 |
0 |
unless (defined $domt) |
|
607
|
0 |
0 |
if ($seq->bits >= $seqt and $seq->bits < $lowseq) |
|
611
|
0 |
0 |
if ($seq->bits < $seqt) |
|
616
|
0 |
0 |
if ($unit->bits >= $domt and $unit->bits < $lowdom) |
|
648
|
0 |
1807 |
if (exists $self->{'seq'}{$name}) |
|
718
|
2 |
17 |
if (/^HMM file:\s+(\S+)/) { } |
|
|
2 |
15 |
elsif (/^Sequence file:\s+(\S+)/) { } |
|
|
2 |
13 |
elsif (/^Query(\s+sequence)?:\s+(\S+)/) { } |
|
732
|
1 |
15 |
if (/Accession:\s+(\S+)/) { } |
|
|
1 |
14 |
elsif (s/^Description:\s+//) { } |
|
734
|
2 |
12 |
if /^Parsed for domains/ |
|
739
|
1 |
11 |
if (($id, $acc, $sc, $ev, $nd) = /^\s*(\S+)\s+(\S+).+?\s(\S+)\s+(\S+)\s+(\d+)\s*$/) { } |
|
|
1 |
10 |
elsif (($id, $sc, $ev, $nd) = /^\s*(\S+).+?\s(\S+)\s+(\S+)\s+(\d+)\s*$/) { } |
|
755
|
2 |
9 |
if /^Align/ |
|
756
|
0 |
9 |
if m[^//] |
|
763
|
3 |
6 |
if (($id, $sqfrom, $sqto, $hmmf, $hmmt, $sc, $ev) = /(\S+)\s+\S+\s+(\d+)\s+(\d+).+?(\d+)\s+(\d+)\s+\S+\s+(\S+)\s+(\S+)\s*$/) |
|
775
|
0 |
3 |
unless (exists $hash{$id}) |
|
781
|
1 |
2 |
if (defined $acc{$id}) |
|
789
|
0 |
2 |
if (m[^//]) |
|
796
|
2 |
3 |
if not defined $_ or m[^//] |
|
800
|
3 |
0 |
if (/^\s*(\S+):.*from\s+(\d+)\s+to\s+(\d+)/) { } |
|
809
|
0 |
3 |
unless (defined $unit) |
|
815
|
2 |
41 |
if m[^//] |
|
816
|
1 |
40 |
if /^\s*\S+:.*from\s+\d+\s+to\s+\d+/ |
|
842
|
0 |
3 |
unless (defined $seq) |
|
847
|
3 |
1 |
if ($unit->hmmname eq $domname and $unit->start == $start and $unit->end == $end) |
|
875
|
2 |
24 |
if (/^HMM file:\s+(\S+)/) |
|
876
|
0 |
26 |
if (/^Accession:\s+(\S+)/) |
|
877
|
2 |
24 |
if (/^Query HMM:\s+(\S+)/) |
|
878
|
2 |
24 |
if (/^Sequence database:\s+(\S+)/) |
|
879
|
2 |
24 |
if /^Scores for complete sequences/ |
|
882
|
0 |
2 |
unless $hmmfname |
|
885
|
2 |
1508 |
if /^Parsed for domains/ |
|
886
|
1502 |
6 |
if (($id, $sc, $ev, $nd) = /(\S+).+?\s(\S+)\s+(\S+)\s+(\d+)\s*$/) |
|
898
|
0 |
2804 |
if /^Alignments of top-scoring domains/ |
|
899
|
2430 |
374 |
if (($id, $sqfrom, $sqto, $hmmf, $hmmt, $sc, $ev) = /(\S+)\s+\S+\s+(\d+)\s+(\d+).+?(\d+)\s+(\d+)\s+\S+\s+(\S+)\s+(\S+)\s*$/) |
|
921
|
2 |
0 |
unless (defined $_) |
|
924
|
0 |
0 |
if /^Histogram of all scores/ |
|
928
|
0 |
0 |
if (/^\s*(\S+):.*from\s+(\d+)\s+to\s+(\d+)/) { } |
|
936
|
0 |
0 |
unless (defined $unit) |
|
941
|
0 |
0 |
if /^Histogram of all scores/ |
|
942
|
0 |
0 |
if /^\s*\S+:.*from\s+\d+\s+to\s+\d+/ |
|
967
|
5 |
1 |
if (defined $value) |