| line |
!l |
l&&!r |
l&&r |
condition |
|
272
|
20 |
0 |
0 |
$self->{'_summary'} and not $self->{'_summary'}{'multidata'} |
|
279
|
2 |
63 |
8 |
$seqtype eq 'CODONML' and /^pairwise comparison, codon frequencies:/ |
|
|
63 |
1 |
1 |
$seqtype eq 'AAML' and /^ML distances of aa seqs\.$/ |
|
|
5 |
47 |
5 |
not $has_model_line and /^TREE/ |
|
|
52 |
1 |
4 |
not $has_model_line and /^TREE/ and $seqtype eq 'CODONML' |
|
|
48 |
2 |
2 |
not $has_model_line and /^TREE/ and $seqtype eq 'CODONML' and not $self->{'_summary'}{'version'} =~ /4/ |
|
322
|
0 |
2 |
0 |
$tree and ref $tree |
|
|
0 |
2 |
0 |
$tree and ref $tree and $tree->isa('Bio::Tree::Tree') |
|
346
|
30 |
0 |
14 |
$n->is_Leaf and $n->id |
|
478
|
108 |
51 |
6 |
/\s+?\d+?\s+?\d+?/ and $self->{'_already_parsed_seqs'} != 1 |
|
|
19 |
134 |
5 |
@lines >= 3 and $self->{'_already_parsed_seqs'} != 1 |
|
|
147 |
6 |
0 |
/Printing out site pattern counts/ and $self->{'_already_parsed_seqs'} != 1 |
|
726
|
11 |
4 |
1 |
$type eq 'ML' and not @names |
|
|
15 |
1 |
0 |
$type eq 'ML' and not @names and @vl |
|
819
|
67 |
6 |
13 |
/^\s+$/ and @seqs > 0 |
|
904
|
82 |
16 |
0 |
/^\s+$/ and exists $self->{'_summary'}{'ngmatrix'} |
|
922
|
15 |
67 |
218 |
$rest and $rest =~ /(\-?\d+(\.\d+)?)\s*\(\-?(\d+(\.\d+)?)\s+(\-?\d+(\.\d+)?)\)/g |
|
934
|
14 |
0 |
2 |
$self->{'_summary'}{'seqtype'} eq 'YN00' and @seqs |
|
995
|
0 |
0 |
112 |
defined $t && length $t |
|
|
0 |
0 |
112 |
defined $omega && length $omega |
|
1113
|
0 |
0 |
13 |
not %match and @ids |
|
1296
|
0 |
8 |
0 |
$tree and ref $tree |
|
|
0 |
8 |
0 |
$tree and ref $tree and $tree->isa('Bio::Tree::Tree') |
|
1321
|
72 |
0 |
40 |
$n->is_Leaf and $n->id |
|
1415
|
2 |
54 |
9 |
$okay and /^\s+(\d+)\s+(\S+)\s+(\-?\d+(?:\.\d+)?)(\**)\s+(\-?\d+(?:\.\d+)?)\s+\+\-\s+(\-?\d+(?:\.\d+)?)/ |
|
|
2 |
46 |
8 |
$okay and /^\s+(\d+)\s+(\S+)\s+(\-?\d*(?:.\d+))(\**)\s+(\-?\d+(?:\.\d+)?)/ |
|
|
2 |
38 |
8 |
$okay and /^\s+(\d+)\s+(\S)\s+([\d\.\-\+]+)(\**)/ |
|
1652
|
19 |
0 |
1 |
$self->{'_dir'} and -d $self->{'_dir'} |
|
|
19 |
0 |
1 |
$self->{'_dir'} and -d $self->{'_dir'} and -r $self->{'_dir'} |
|
1655
|
0 |
0 |
1 |
-e $rstfile and not -z $rstfile |
|
1825
|
61 |
0 |
0 |
$seqcount and $seqcount == @seqs |
| line |
l |
!l&&r |
!l&&!r |
condition |
|
276
|
14 |
2 |
4 |
$seqtype eq 'CODONML' or $seqtype eq 'AAML' |
|
279
|
7 |
0 |
57 |
/^Model\s+(\d+)/ or not $has_model_line and /^TREE/ and $seqtype eq 'CODONML' and not $self->{'_summary'}{'version'} =~ /4/ |
|
585
|
16 |
0 |
9 |
/^ns\s+=\s+/ or /^Frequencies/ |
|
608
|
42 |
14 |
866 |
$okay or /^Codon position x base \(3x4\) table\, overall/ |
|
647
|
0 |
1 |
33 |
/^TREE/ or /^AA distances/ |
|
652
|
11 |
1 |
20 |
/^\s+$/ or /^\(Ambiguity/ |
|
774
|
11 |
0 |
88 |
/^Codon\s+(usage|position)/ or /Model/ |
|
905
|
0 |
0 |
82 |
/^\s+$/ or /^NOTE:/i |
|
1075
|
0 |
0 |
162 |
/^Node\s+\&/ or /^\s+N37/ |
|
|
0 |
0 |
162 |
/^Node\s+\&/ or /^\s+N37/ or /^(CODONML|AAML|YN00|BASEML)/ |
|
|
0 |
0 |
162 |
/^Node\s+\&/ or /^\s+N37/ or /^(CODONML|AAML|YN00|BASEML)/ or /^\*\*/ |
|
|
0 |
11 |
151 |
/^Node\s+\&/ or /^\s+N37/ or /^(CODONML|AAML|YN00|BASEML)/ or /^\*\*/ or /^Detailed output identifying parameters/ |
|
1187
|
59 |
7 |
2 |
$okay or /^Model\s+\d+/ |
|
|
66 |
2 |
0 |
$okay or /^Model\s+\d+/ or /^TREE/ |
|
1410
|
33 |
3 |
80 |
/^\s+$/ or /^\s+Pr\(w\>1\)/ |
|
1411
|
4 |
0 |
76 |
/^Time used/ or /^TREE/ |
|
1456
|
88 |
10 |
0 |
$okay or /^\s+branch\s+t/ |
|
1488
|
0 |
0 |
28 |
/^TREE/ or /^Distances/ |
|
1490
|
10 |
0 |
16 |
/^\s+$/ or /^\(Ambiguity/ |
|
1666
|
1 |
0 |
613 |
/^Check\sroot\sfor\sdirections\sof\schange\./ or /^Summary\sof\schanges\salong\sbranches\./ |
|
1696
|
1 |
3 |
131 |
/^Site/i or /^\s+$/ |
|
1803
|
0 |
0 |
0 |
@overall_seq != @overall_site or @overall_seq != @seqs |