Branch Coverage

Bio/Search/HSP/GenericHSP.pm
Criterion Covered Total %
branch 274 354 77.4


line true false branch
192 705 626 if defined $self->{'VERBOSE'}
193 0 1331 if (exists $self->{'GAP_SYMBOL'}) { }
198 0 0 if CORE::length $self->{'GAP_SYMBOL'} != 1
206 0 1331 unless (defined $self->{'QUERY_LENGTH'} and defined $self->{'HIT_LENGTH'})
218 105 208 unless (defined $self->{'_sbjct_offset'} and defined $self->{'_query_offset'})
221 209 104 $type =~ /sbjct|hit|tot/i ? :
244 0 7397 if (defined $value or not defined $previous)
245 0 0 unless defined $value
266 0 63 if (defined $value)
285 0 170 if (defined $value)
311 105 497 unless ($self->{'_did_prefrac'})
315 602 0 if defined $type
316 0 602 if defined $type and $type =~ /subject|sbjct/
318 85 517 if not defined $type or $type eq 'hsp' or not $type =~ /query|hit|subject|sbjct|total/
321 313 289 if (defined $value or not defined $previous)
322 0 313 unless defined $value
323 208 105 if ($type eq 'hit' or $type eq 'query')
353 0 440 unless ($self->{'_did_prefrac'})
357 434 6 if defined $type
358 0 440 if defined $type and $type =~ /subject|sbjct/
359 4 430 if not defined $type or $type eq 'hsp' or not $type =~ /query|hit|subject|sbjct|total/
362 313 127 if (defined $value or not defined $previous)
363 0 313 unless defined $value
386 378 2747 unless ($self->{'_did_pregaps'})
390 2039 1086 if defined $type
391 0 2039 if not defined $type or $type eq 'hsp' or not $type =~ /query|hit|subject|sbjct|total/
393 38 3087 if $type =~ /sbjct|subject/
395 1110 2015 if (defined $value or not defined $previous)
396 11 1099 unless defined $value
416 3 607 if (defined $value or not defined $previous)
417 3 0 unless defined $value
440 1 617 if (defined $value or not defined $previous)
441 1 0 unless defined $value
466 3 6902 if (defined $value or not defined $previous)
467 3 0 unless defined $value
493 0 8 if (defined $value or not defined $previous)
494 0 0 unless defined $value
520 2 7 if (defined $value or not defined $previous)
521 2 0 unless defined $value
552 675 3164 unless defined $type
555 1615 2224 if ($type =~ /^q/i) { }
989 1235 elsif ($type =~ /^(hit|subject|sbjct)/) { }
561 105 1130 if (defined $v)
595 42 42 unless ($self->{'_did_prepi'})
635 0 610 unless (defined $val)
644 284 326 if ($val =~ /^q/i) { }
326 0 elsif ($val =~ /^hi|^s/i) { }
0 0 elsif ($val =~ /^list|array/i) { }
0 0 elsif ($val =~ /^\d+$/) { }
657 0 0 wantarray ? :
707 16 3 $q_nm ? :
718 19 0 $s_nm ? :
739 1 1913 unless ($self->{'_did_presimilar'})
743 0 1914 if (defined $value)
763 437 1486 unless ($self->{'_did_presimilar'})
767 0 1923 if (defined $value)
785 0 4514 if (defined $value)
845 94 100 if $seqType eq 'hit'
847 100 94 if ($t eq 'q') { }
94 0 elsif ($t eq 's' or $t eq 'h') { }
858 8 186 if ($t eq 'c') { }
0 186 elsif ($t eq 'i') { }
18 168 elsif ($t eq 'n') { }
10 158 elsif ($t eq 'm') { }
150 8 elsif ($t eq 'g') { }
8 0 elsif ($t eq 'f') { }
859 0 8 if ($class =~ /conserved\-not\-identical/) { }
884 150 44 if ($class eq '_gap') { }
8 36 elsif ($class eq '_conservedall') { }
907 48 146 if $collapse
909 48 146 $collapse ? :
936 1 1 $self->{'_sbjct_offset'} == 3 ? :
2 2 $self->{'_query_offset'} == 3 ? :
2 4 $self->{'_query_offset'} == 3 && $self->{'_sbjct_offset'} == 3 ? :
956 1167 4423 unless ($self->{'_created_qff'})
964 1331 5608 if (not $self->{'_finished_new'} or $self->{'_making_qff'})
965 0 1331 if $self->{'_sim1'}
969 9 5599 unless ($self->{'_created_qff'})
987 550 3840 unless ($self->{'_created_sff'})
995 0 4408 if (not $self->{'_finished_new'} or $self->{'_making_sff'})
996 0 0 if $self->{'_sim2'}
1000 12 4396 unless ($self->{'_created_sff'})
1021 19 0 if (not defined $self->{'SIGNIFICANCE'} or defined $val)
1022 0 8 defined $self->pvalue ? :
11 8 defined $self->evalue ? :
0 19 defined $val ? :
1045 2 585 if ($type =~ /^q/i and defined $self->{'QUERY_STRAND'}) { }
2 862 elsif ($type =~ /^(hit|subject|sbjct)/i and defined $self->{'HIT_STRAND'}) { }
1089 132 73 unless $self->{'_sequenceschanged'}
1097 18 55 $qdir <= 0 ? :
1099 14 59 $sdir <= 0 ? :
1104 4 69 if ($prog =~ /FAST|SSEARCH|SMITH-WATERMAN/i)
1112 4 0 if ($seqString =~ /^(\s+)?(.*?)\s*$/)
1113 3 1 $1 ? :
1139 2 71 unless (defined $self->{'_sbjct_offset'} and defined $self->{'_query_offset'})
1150 30602 0 $pos < CORE::length $qseq ? :
30602 0 $pos < CORE::length $sseq ? :
1157 757 29845 if ($mchar eq '+' or $mchar eq '.') { }
25371 4474 elsif ($mchar eq ':' or $mchar ne ' ') { }
4474 0 elsif ($mchar eq ' ') { }
1166 2 4472 $qchar eq '\\' ? :
0 4474 $qchar eq '/' ? :
1169 0 4474 $schar eq '\\' ? :
0 4474 $schar eq '/' ? :
1172 2 4472 if ($qfs) { }
0 4472 elsif ($sfs) { }
512 3960 elsif ($qchar eq $self->{'GAP_SYMBOL'}) { }
491 3469 elsif ($schar eq $self->{'GAP_SYMBOL'}) { }
1218 3981 493 unless ($sgap)
1221 3960 514 unless ($qgap)
1237 30088 514 unless $qgap
1238 30109 493 unless $sgap
1247 68 39 if ($prog =~ /^(?:PSI)?T(BLAST|FAST)(N|X|Y)/io) { }
3 36 elsif ($prog =~ /^(BLAST|FAST)(X|Y|XY)/io) { }
1249 67 1 if ($1 eq 'BLAST' and $2 eq 'X')
1266 0 113 if (@_)
1268 10 103 defined $self->{'N'} ? :
1281 758 901 if $seqType eq 'hit'
1284 840 819 if ($seqType eq 'query') { }
1311 0 54 if @_
1330 0 12 if @_
1350 0 6 if @_
1406 0 8 if defined $arg
1408 7 1 unless (defined $self->{'_cigar_string'})
1431 0 7 unless (scalar @qchars == scalar @hchars)
1442 1837 80 if ($qchar ne $self->{'GAP_SYMBOL'} and $hchar ne $self->{'GAP_SYMBOL'}) { }
13 67 elsif ($qchar eq $self->{'GAP_SYMBOL'}) { }
67 0 elsif ($hchar eq $self->{'GAP_SYMBOL'}) { }
1462 1835 89 if ($self->{'_state_for_cigar_string'} eq $new_state) { }
1466 55 34 unless $self->{'_count_for_cigar_string'} == 1
1481 7 1170 if ($algo =~ /^(?:PSI)?T(?:BLAST|FAST|SW)[NY]/io) { }
25 1145 elsif ($algo =~ /^(?:FAST|BLAST)(?:X|Y|XY)/io or $algo =~ /^P?GENEWISE/io) { }
286 859 elsif ($algo =~ /^T(BLAST|FAST|SW)(X|Y|XY)/io or $algo =~ /^(BLAST|FAST|SW)N/io or $algo =~ /^WABA|AXT|BLAT|BLASTZ|PSL|MEGABLAST|EXONERATE|SW|SSEARCH|SMITH\-WATERMAN|SIM4$/) { }
1 858 elsif ($algo =~ /^RPS-BLAST/) { }
1490 126 160 if ($2)
1497 0 1 if ($algo =~ /^RPS-BLAST\(BLASTX\)/)
1505 602 256 $stranded eq 'q' || $stranded eq 'b' ? :
1506 617 241 $stranded eq 'h' || $stranded eq 's' || $stranded eq 'b' ? :
1520 1133 43 unless (defined $self->{'_query_factor'})
1525 0 1176 unless (defined $qe and defined $qs)
1528 1106 70 if ($qe > $qs) { }
1529 843 263 if ($queryfactor) { }
1537 70 0 if ($queryfactor) { }
1562 14 1162 if $self->can('meta')
1567 603 573 if (defined $strand and not defined $qframe and $queryfactor) { }
263 310 elsif (not defined $strand) { }
1574 1176 0 if ($qframe =~ /^([+-])?([0-3])/) { }
1576 0 623 if ($qframe and $dir eq '-' && $strand >= 0 || $dir eq '+' && $strand <= 0)
1579 623 553 $2 != 0 ? :
1598 44 518 unless (defined $self->{'_hit_factor'})
1603 0 562 unless (defined $he and defined $hs)
1606 455 107 if ($he > $hs) { }
1607 199 256 if ($hitfactor) { }
1615 106 1 if ($hitfactor) { }
1635 15 547 if $self->can('meta')
1638 3 559 if (defined $strand and not defined $hframe and $hitfactor) { }
257 302 elsif (not defined $strand) { }
1645 562 0 if ($hframe =~ /^([+-])?([0-3])/) { }
1647 0 132 if ($hframe and $dir eq '-' && $strand >= 0 || $dir eq '+' && $strand <= 0)
1650 132 430 $2 != 0 ? :
1670 0 438 unless (defined $identical)
1671 0 0 if (not defined $percent_id) { }
1680 0 438 unless (defined $conserved)
1682 0 0 unless $self->{'ALGORITHM'} =~ /^((FAST|BLAST)N)|EXONERATE|SIM4|AXT|PSL|BLAT|BLASTZ|WABA/io
1704 105 0 if ($hsp_len)
1710 104 1 if ($hit_len)
1715 104 1 if ($query_len)
1736 0 378 if (defined $query_gaps) { }
363 15 elsif (defined $query_seq) { }
1739 0 294 $self->algorithm eq 'ERPIN' ? :
69 294 defined $self->{'_query_offset'} ? :
1745 0 378 if (defined $hit_gaps) { }
358 20 elsif (defined $hit_seq) { }
1748 2 288 $self->algorithm eq 'ERPIN' ? :
68 290 defined $self->{'_sbjct_offset'} ? :
1754 329 49 unless (defined $gaps)
1764 42 0 if $self->{'HSP_LENGTH'} > 0