| line |
true |
false |
branch |
|
74
|
1 |
0 |
if defined $xml
|
|
210
|
0 |
0 |
unless (defined $$self{'dom'}{'alignmentInfo'}{'qstart'})
|
|
212
|
0 |
0 |
defined $1 ? :
|
|
213
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
240
|
0 |
0 |
unless (defined $$self{'dom'}{'alignmentInfo'}{'qend'})
|
|
243
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
245
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
599
|
0 |
0 |
if (defined $score) { }
|
|
774
|
0 |
0 |
unless (ref $$al{'target_ss'})
|
|
791
|
0 |
0 |
if substr($ss, $i, 1) eq '-'
|
|
793
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
794
|
0 |
0 |
if (not defined $lti) { }
|
|
|
0 |
0 |
elsif ($qi % 10 == 0 and $i - $lti >= 9) { }
|
|
799
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
805
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
807
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
815
|
0 |
0 |
if $seqs[$ti]
|
|
906
|
0 |
0 |
if (@select_me = $self->get_identities)
|
|
915
|
0 |
0 |
if (@select_me = $self->get_similarities)
|
|
924
|
0 |
0 |
if (@select_me = $self->get_mismatches)
|
|
933
|
0 |
0 |
if (@select_me = $self->get_deletions)
|
|
942
|
0 |
0 |
if (@select_me = $self->get_inserts)
|
|
958
|
0 |
0 |
if (length $I > 20)
|
|
1017
|
0 |
0 |
unless $templateStructure->isa('Bio::Structure::Entry')
|
|
1021
|
0 |
0 |
if ($#template_align != $#target_align)
|
|
1033
|
0 |
0 |
if $resseq == $start
|
|
1041
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
1042
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
1044
|
0 |
0 |
if ($template_align[$i] eq '-') { }
|
|
|
0 |
0 |
elsif ($target_align[$i] eq '-') { }
|
|
|
0 |
0 |
elsif ($target_align[$i] eq $template_align[$i]) { }
|
|
|
0 |
0 |
elsif ($target_align[$i] ne $template_align[$i]) { }
|
|
1047
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
1053
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
1059
|
0 |
0 |
if ($alignment[$i] ne '|')
|
|
1068
|
0 |
0 |
if ($alignment[$i] ne '.') { }
|
|
1081
|
0 |
0 |
if ($self->_a_to_aaa_code($template_align[$i]) ne $resname)
|
|
1087
|
0 |
0 |
if $resseq == $end
|
|
1191
|
0 |
0 |
if (exists $$self{'inserted'}[$res_i])
|
|
1258
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
1281
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
1304
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
1328
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
1333
|
0 |
0 |
if @_
|
|
1354
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
1378
|
0 |
0 |
unless (defined $$self{'a2aaa'})
|
|
1408
|
0 |
0 |
$i + $bin < $#ids ? :
|
|
1437
|
0 |
1 |
if defined $$self{'dom'}
|
|
1478
|
0 |
0 |
if $#template_align != $#target_align
|
|
1484
|
0 |
0 |
unless $line =~ /^(ATOM |HETATM|SIGATM)/
|
|
1497
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
1498
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
1499
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
1500
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
1503
|
0 |
0 |
if ($template_align[$i] eq '-') { }
|
|
|
0 |
0 |
elsif ($target_align[$i] eq '-') { }
|
|
|
0 |
0 |
elsif ($target_align[$i] eq $template_align[$i]) { }
|
|
|
0 |
0 |
elsif ($target_align[$i] ne $template_align[$i]) { }
|
|
1505
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
1512
|
0 |
0 |
if $ENV{'DEBUG'}
|
|
1518
|
0 |
0 |
if ($alignment[$i] ne '|')
|
|
1527
|
0 |
0 |
if ($alignment[$i] ne '.') { }
|
|
1534
|
0 |
0 |
if ($self->_a_to_aaa_code($target_align[$i]) ne $resname)
|
|
1539
|
0 |
0 |
if $resseq == $end
|