Condition Coverage

lib/Bio/BPWrapper/AlnManipulations.pm
Criterion Covered Total %
condition 23 73 31.5


and 3 conditions

line !l l&&!r l&&r condition
160 0 28 0 $in_format and $in_format =~ /blast/
308 0 0 0 $refSeq->alphabet eq "dna" and $seqB->alphabet eq "dna"
0 0 0 $mA =~ /^[ATCG]$/i && $mB =~ /^[ATCG]$/i
0 0 0 $refSeq->alphabet eq "dna" and $seqB->alphabet eq "dna" and not $mA =~ /^[ATCG]$/i && $mB =~ /^[ATCG]$/i
359 0 0 0 $seqA->alphabet eq "dna" and $seqB->alphabet eq "dna"
0 0 0 $mA =~ /^[ATCG]$/i && $mB =~ /^[ATCG]$/i
0 0 0 $seqA->alphabet eq "dna" and $seqB->alphabet eq "dna" and not $mA =~ /^[ATCG]$/i && $mB =~ /^[ATCG]$/i
695 24 1 1 $i + 1 == $num_seqs and $nuc_count == $aln_length
24 0 1 $i + 1 == $num_seqs and $nuc_count < $aln_length
1070 0 0 90 $pos >= $range{$gene}{'start'} and $pos <= $range{$gene}{'end'}

or 2 conditions

line l !l condition
148 1 28 $opts{'input'} || 'clustalw'
159 28 0 shift @ARGV || 'STDIN'
378 0 0 '<' . $cls_file || die("cdhit clstr file not found: $cls_file\n")
596 0 0 $gap_presence{$u_gap->{'id'}}{$sid} || 0
900 0 0 $opts{'bin-ref'} || die("need ref id as an argument\n")

or 3 conditions

line l !l&&r !l&&!r condition
181 1 28 0 $opts{'output'} || $default_format
236 1 1 27 $option eq "input" or $option eq "output"
2 0 27 $option eq "input" or $option eq "output" or $option eq "noflatname"
1 0 27 $option eq "input" or $option eq "output" or $option eq "noflatname" or $option eq "binary"
310 0 0 0 $mA eq "-" or $mB eq "-"
362 0 0 0 $mA eq "-" or $mB eq "-"
459 0 0 0 @three_end_gaps or @five_end_gaps
534 0 0 0 $start == 1 || $end == $aln->length
585 0 0 0 $start == 1 || $end == $aln->length
687 13 13 1534 $j + 1 == $aln_length or ($j + 1) % $block_length == 0
1170 0 0 1 not $nmatch or $nmatch > 1