| line |
true |
false |
branch |
|
105
|
0 |
46 |
if defined $percentages |
|
126
|
29 |
0 |
unless $first_line =~ /^$/ |
|
129
|
0 |
29 |
if (defined($first_line = $self->_readline) and not $first_line =~ /CLUSTAL/) |
|
146
|
58 |
2215 |
if /^\s+$/ and not $first_block |
|
147
|
217 |
1998 |
if (/^\s$/) |
|
154
|
0 |
1998 |
if (/CLUSTAL/) |
|
160
|
48 |
1950 |
if (m[^\s*(\S+)\s*/\s*(\d+)-(\d+)\s+(\S+)\s*$]ox) { } |
|
|
1715 |
235 |
elsif (/^\s*(\S+)\s+(\S+)\s*\d*\s*$/ox) { } |
|
169
|
1 |
1714 |
if ($seqname =~ /^[\*\.\+\:]+$/) |
|
179
|
211 |
1551 |
unless ($seen_block) |
|
180
|
0 |
211 |
if (exists $order{$seqname}) { } |
|
194
|
6 |
205 |
if ($name =~ /(\S+):(\d+)-(\d+)/) { } |
|
219
|
29 |
0 |
if $aln->num_sequences |
|
238
|
0 |
2 |
unless ($aln and $aln->isa('Bio::Align::AlignI')) |
|
245
|
0 |
2 |
if ($self->force_displayname_flat) |
|
249
|
0 |
2 |
unless $self->_print(sprintf("CLUSTAL W (%s) multiple sequence alignment\n\n\n", $Bio::AlignIO::clustalw::CLUSTALPRINTVERSION)) |
|
257
|
0 |
12 |
if length $aln->displayname($seq->get_nse) > $max |
|
272
|
84 |
12 |
if (length $seqchars >= $count + $line_len) { } |
|
|
12 |
0 |
elsif (length $seqchars >= $count) { } |
|
274
|
14 |
70 |
if ($first) |
|
283
|
2 |
10 |
if ($first) |
|
292
|
0 |
96 |
unless $self->_print(sprintf('%-' . $max . "s %s\n", $aln->displayname($seq->get_nse), $substring)) |
|
300
|
0 |
16 |
if ($self->percentages) |
|
312
|
0 |
16 |
unless $self->_print("\n\n") |
|
316
|
2 |
0 |
if $self->_flush_on_write and defined $self->_fh |
|
334
|
0 |
16 |
if (defined $value) |
|
353
|
46 |
2 |
if (defined $value) |