| line |
true |
false |
branch |
|
44
|
1 |
20 |
if defined $dir |
|
61
|
20 |
0 |
unless $self->{'_summary'} and not $self->{'_summary'}{'multidata'} |
|
65
|
16 |
4 |
if ($seqtype eq 'CODONML' or $seqtype eq 'AAML') { } |
|
|
2 |
2 |
elsif ($seqtype eq 'BASEML') { } |
|
|
2 |
0 |
elsif ($seqtype eq 'YN00') { } |
|
68
|
8 |
65 |
if ($seqtype eq 'CODONML' and /^pairwise comparison, codon frequencies:/) { } |
|
|
1 |
64 |
elsif ($seqtype eq 'AAML' and /^ML distances of aa seqs\.$/) { } |
|
|
9 |
55 |
elsif (/^Model\s+(\d+)/ or not $has_model_line and /^TREE/ and $seqtype eq 'CODONML' and not $self->{'_summary'}{'version'} =~ /4/) { } |
|
|
2 |
53 |
elsif (/for each branch/) { } |
|
|
3 |
50 |
elsif (/^TREE/) { } |
|
|
0 |
50 |
elsif (/Heuristic tree search by stepwise addition$/) { } |
|
|
0 |
50 |
elsif (/Heuristic tree search by NNI perturbation$/) { } |
|
|
0 |
50 |
elsif (/^stage 0:/) { } |
|
105
|
0 |
2 |
unless (defined $data{'-trees'}) |
|
111
|
0 |
2 |
unless ($tree and ref $tree and $tree->isa('Bio::Tree::Tree')) |
|
128
|
14 |
30 |
@nodes_L < 2 ? : |
|
132
|
0 |
44 |
unless ($n) |
|
135
|
30 |
14 |
unless ($n->is_Leaf and $n->id) |
|
196
|
2 |
1 |
if (/^Distances:/) { } |
|
|
1 |
0 |
elsif (/^TREE/) { } |
|
212
|
2 |
1 |
if (/^Estimation by the method|\(B\) Yang & Nielsen \(2000\) method/) |
|
222
|
20 |
0 |
if (%data) { } |
|
263
|
0 |
20 |
$self->{'_already_parsed_seqs'} ? : |
|
267
|
20 |
165 |
if (/^($SEQTYPES) \s+ # seqtype: CODONML, AAML, BASEML, CODON2AAML, YN00, etc
(?: \(in \s+ ([^\)]+?) \s* \) \s* )? # version: "paml 3.12 February 2002"; not present < 3.1 or YN00
(\S+) \s* # tree filename
(?: (.+?) )? # model description (not there in YN00)
\s* $ # trim any trailing space
/ox) { } |
|
|
6 |
159 |
elsif (/\s+?\d+?\s+?\d+?/ and $self->{'_already_parsed_seqs'} != 1) { } |
|
|
1 |
158 |
elsif (/^Data set \d$/) { } |
|
|
0 |
158 |
elsif (/^Before\s+deleting\s+alignment\s+gaps/) { } |
|
|
5 |
153 |
elsif (@lines >= 3 and $self->{'_already_parsed_seqs'} != 1) { } |
|
|
0 |
300 |
elsif (/Printing out site pattern counts/ and $self->{'_already_parsed_seqs'} != 1) { } |
|
279
|
8 |
12 |
unless (defined $self->{'_summary'}{'model'}) |
|
282
|
6 |
2 |
if ($model_line =~ /^Model:/) |
|
288
|
18 |
2 |
if defined $self->{'_summary'}{'model'} |
|
290
|
0 |
20 |
if $self->{'_summary'}{'seqtype'} eq 'AAMODEL' |
|
308
|
2 |
3 |
unless (/^\n$/) |
|
318
|
0 |
20 |
unless (defined $self->{'_summary'}{'seqtype'}) |
|
325
|
14 |
6 |
if ($seqtype eq 'CODONML') { } |
|
|
2 |
4 |
elsif ($seqtype eq 'AAML') { } |
|
|
0 |
4 |
elsif ($seqtype eq 'CODON2AAML') { } |
|
|
2 |
2 |
elsif ($seqtype eq 'BASEML') { } |
|
|
2 |
0 |
elsif ($seqtype eq 'YN00') { } |
|
374
|
10 |
29 |
if (/^((?:Codon frequencies)|(?:Site-class models))\s*:\s+(.+)/) { } |
|
|
4 |
25 |
elsif (/^\s+$/) { } |
|
|
16 |
9 |
elsif (/^ns\s+=\s+/ or /^Frequencies/) { } |
|
393
|
2 |
1493 |
if (/^Nei|\(A\) Nei/) |
|
394
|
14 |
1479 |
if $done |
|
395
|
557 |
922 |
if /^\s+/ |
|
397
|
866 |
56 |
unless $okay or /^Codon position x base \(3x4\) table\, overall/ |
|
399
|
42 |
14 |
if (s/^position\s+(\d+):\s+//) |
|
408
|
14 |
28 |
if $pos == 3 |
|
413
|
8 |
29 |
if (/^Nei\s\&\sGojobori|\(A\)\sNei-Gojobori/) |
|
417
|
8 |
21 |
if $done |
|
418
|
8 |
13 |
if (/^Codon frequencies under model, for use in evolver/) |
|
420
|
8 |
128 |
if /^\s+$/ |
|
434
|
0 |
2 |
unless $self->{'_summary'}{'seqs'} |
|
436
|
1 |
33 |
if (/^TREE/ or /^AA distances/) |
|
440
|
1 |
32 |
if $done |
|
441
|
12 |
20 |
if /^\s+$/ or /^\(Ambiguity/ |
|
442
|
2 |
18 |
if (/^Frequencies\./) { } |
|
|
0 |
18 |
elsif (not $okay) { } |
|
|
2 |
16 |
elsif (not $header) { } |
|
|
2 |
14 |
elsif (/^\#\s+constant\s+sites\:\s+
(\d+)\s+ # constant sites
\(\s*([\d\.]+)\s*\%\s*\)/x) { } |
|
|
1 |
13 |
elsif (/^ln\s+Lmax\s+\(unconstrained\)\s+\=\s+(\S+)/x) { } |
|
494
|
0 |
3 |
unless $self->{'_summary'}{'seqs'} |
|
497
|
2 |
21 |
if $done |
|
498
|
0 |
21 |
if (/^TREE/) |
|
499
|
2 |
19 |
if (/^\s+$/) |
|
500
|
0 |
2 |
if $seen |
|
503
|
3 |
16 |
if (/^(AA|ML) distances/) |
|
509
|
16 |
0 |
if ($okay) |
|
515
|
0 |
5 |
if ($type eq 'ML' and not @names and @vl) |
|
525
|
0 |
35 |
unless @vl |
|
532
|
3 |
13 |
if scalar @names == $numseqs |
|
542
|
0 |
86 |
unless defined $v |
|
560
|
0 |
18 |
if exists $self->{'_summary'}{'patterns'} |
|
563
|
11 |
88 |
if (/^Codon\s+(usage|position)/ or /Model/) { } |
|
|
52 |
36 |
elsif ($patternct) { } |
|
|
18 |
18 |
elsif (/^ns\s+\=\s*(\d+)\s+ls\s+\=\s*(\d+)/) { } |
|
|
7 |
11 |
elsif (/^\# site patterns \=\s*(\d+)/) { } |
|
570
|
7 |
45 |
if /^\s+$/ |
|
601
|
8 |
18 |
if $self->{'_already_parsed_seqs'} |
|
604
|
5 |
86 |
if (/^(Printing|After|TREE|Codon)/) |
|
608
|
13 |
73 |
if /^\s+$/ and @seqs > 0 |
|
609
|
6 |
67 |
if /^\s+$/ |
|
610
|
1 |
66 |
if /^\d+\s+$/ |
|
615
|
53 |
13 |
if (@firstseq) { } |
|
640
|
13 |
5 |
if (@seqs > 0) |
|
656
|
8 |
16 |
if /^\s+$/ |
|
659
|
1 |
15 |
if (/^\(A\)\sNei-Gojobori\s\(1986\)\smethod/) |
|
662
|
1 |
8 |
if ($_ =~ /.*\d+?\.\d+?\s*\(.*/) |
|
675
|
14 |
2 |
if ($self->{'_summary'}{'seqtype'} eq 'CODONML') |
|
682
|
2 |
14 |
if ($self->{'_summary'}{'seqtype'} eq 'YN00') |
|
683
|
1 |
1 |
if ($firstseq) |
|
693
|
16 |
0 |
if /^\s+$/ and exists $self->{'_summary'}{'ngmatrix'} |
|
694
|
0 |
82 |
if /^\s+$/ or /^NOTE:/i |
|
698
|
12 |
70 |
if ($self->{'_summary'}{'seqtype'} eq 'YN00') { } |
|
706
|
14 |
68 |
unless defined $rest |
|
708
|
12 |
70 |
if ($self->{'_summary'}{'seqtype'} eq 'YN00') |
|
723
|
2 |
14 |
if ($self->{'_summary'}{'seqtype'} eq 'YN00' and @seqs) |
|
735
|
1 |
7 |
if ($self->{'_summary'}{'model'} =~ /kappa = (\d+?\.\d+?) fixed/) |
|
739
|
8 |
672 |
if (/^pairwise comparison, codon frequencies\:\s*(\S+)\./) { } |
|
|
112 |
560 |
elsif (/^(\d+)\s+\((\S+)\)\s+\.\.\.\s+(\d+)\s+\((\S+)\)/) { } |
|
|
112 |
448 |
elsif (/^lnL\s+\=\s*(\-?\d+(\.\d+)?)/) { } |
|
|
112 |
336 |
elsif (/^t\=\s*(\d+(\.\d+)?)\s+/) { } |
|
|
336 |
0 |
elsif (/^\s+$/) { } |
|
|
0 |
0 |
elsif (/^\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)/) { } |
|
751
|
112 |
0 |
if (defined($_ = $self->_readline)) |
|
757
|
1 |
111 |
if ($omega eq '') |
|
784
|
112 |
0 |
defined $t && length $t ? : |
|
|
112 |
0 |
defined $omega && length $omega ? : |
|
812
|
2 |
9 |
if /^seq\.\s+seq\./ |
|
815
|
43 |
8 |
if (/^\s+(\d+)\s+ # seq #
(\d+)\s+ # seq #
(\d+(\.\d+))\s+ # S
(\d+(\.\d+))\s+ # N
(\d+(\.\d+))\s+ # t
(\d+(\.\d+))\s+ # kappa
(\d+(\.\d+))\s+ # omega
\-??(\d+(\.\d+))\s+ # dN
\+\-\s+
\-??(\d+(\.\d+))\s+ # dN SE
\-??(\d+(\.\d+))\s+ # dS
\+\-\s+
\-??(\d+(\.\d+))\s+ # dS SE
/ox) { } |
|
|
4 |
4 |
elsif (/^\s+$/) { } |
|
|
1 |
3 |
elsif (/^\(C\) LWL85, LPB93 & LWLm methods/) { } |
|
863
|
0 |
175 |
if $done |
|
864
|
13 |
162 |
if (s/^TREE\s+\#\s*\d+:\s+//) { } |
|
|
11 |
151 |
elsif (/^Node\s+\&/ or /^\s+N37/ or /^(CODONML|AAML|YN00|BASEML)/ or /^\*\*/ or /^Detailed output identifying parameters/) { } |
|
|
13 |
138 |
elsif (/^tree\s+length\s+\=\s+(\S+)/) { } |
|
|
13 |
125 |
elsif (/^\s*lnL\(.+np\:\s*(\d+)\)\:\s+(\S+)/) { } |
|
|
26 |
99 |
elsif (/^\(/) { } |
|
|
3 |
96 |
elsif (/^SEs for parameters/) { } |
|
|
13 |
83 |
elsif (/^\s*\d+\.\.\d+/) { } |
|
896
|
26 |
0 |
if ($tree) |
|
899
|
13 |
13 |
if ($okay > 0) |
|
902
|
13 |
0 |
if (not %match and @ids) |
|
910
|
93 |
27 |
if ($match{$child}) { } |
|
917
|
0 |
13 |
if ($self->verbose > 1) |
|
926
|
3 |
10 |
if (defined $self->{'_SEs'}) |
|
936
|
21 |
12 |
@nodes_L < 2 ? : |
|
940
|
0 |
33 |
unless ($n) |
|
974
|
5 |
115 |
if $done |
|
975
|
47 |
68 |
if /^\s+$/ |
|
976
|
0 |
9 |
unless $okay or /^Model\s+\d+/ or /^TREE/ |
|
978
|
7 |
61 |
if (/^Model\s+(\d+)/) { } |
|
|
7 |
54 |
elsif (/^Time used\:\s+(\S+)/) { } |
|
|
9 |
45 |
elsif (m[^kappa\s+\(ts/tv\)\s+\=\s+(\S+)]) { } |
|
|
9 |
36 |
elsif (/^TREE/) { } |
|
|
1 |
35 |
elsif (m[^omega\s+\(dn/ds\)\s+\=\s+(\S+)]i) { } |
|
|
6 |
29 |
elsif (/^(Naive Empirical Bayes)|(Bayes Empirical Bayes)|(Positively\sselected\ssites)/i) { } |
|
|
15 |
14 |
elsif (/^dN/i) { } |
|
|
0 |
14 |
elsif (/^Parameters in beta:/) { } |
|
|
0 |
14 |
elsif (/^Parameters in beta\&w\>1:/) { } |
|
|
3 |
11 |
elsif (/^alpha\s+\(gamma\)\s+\=\s+(\S+)/) { } |
|
979
|
0 |
7 |
if ($okay) { } |
|
1003
|
9 |
0 |
if (defined $data{'-trees'} and scalar @{$data{'-trees'};}) |
|
1036
|
7 |
8 |
if (/K\=(\d+)/) { } |
|
|
8 |
0 |
elsif (/for each branch/) { } |
|
1039
|
7 |
5 |
unless ($_ =~ /^\s+$/) |
|
1044
|
1 |
6 |
if (/^site class/) { } |
|
1079
|
0 |
8 |
unless (defined $data{'-trees'}) |
|
1085
|
0 |
8 |
unless ($tree and ref $tree and $tree->isa('Bio::Tree::Tree')) |
|
1102
|
40 |
72 |
@nodes_L < 2 ? : |
|
1106
|
0 |
112 |
unless ($n) |
|
1110
|
72 |
40 |
unless ($n->is_Leaf and $n->id) |
|
1124
|
0 |
0 |
if (/p\=\s+(\S+)\s+q\=\s+(\S+)/) { } |
|
1142
|
0 |
0 |
if (/p0\=\s+(\S+)\s+p\=\s+(\S+)\s+q\=\s+(\S+)/) { } |
|
1151
|
0 |
0 |
if (/\(p1\=\s+(\S+)\)\s+w\=\s*(\S+)/) { } |
|
1171
|
3 |
0 |
if (s/^r\s+\(\s*\d+\)\:\s+//) |
|
1175
|
3 |
0 |
if (s/^f\s*\:\s+//) |
|
1199
|
36 |
80 |
if /^\s+$/ or /^\s+Pr\(w\>1\)/ |
|
1200
|
4 |
76 |
if (/^Time used/ or /^TREE/) |
|
1204
|
5 |
71 |
if (/^Naive Empirical Bayes/i) { } |
|
|
2 |
69 |
elsif (/^Bayes Empirical Bayes/i) { } |
|
|
4 |
65 |
elsif (/^Positively selected sites/) { } |
|
|
9 |
56 |
elsif ($okay and /^\s+(\d+)\s+(\S+)\s+(\-?\d+(?:\.\d+)?)(\**)\s+(\-?\d+(?:\.\d+)?)\s+\+\-\s+(\-?\d+(?:\.\d+)?)/) { } |
|
|
8 |
48 |
elsif ($okay and /^\s+(\d+)\s+(\S+)\s+(\-?\d*(?:.\d+))(\**)\s+(\-?\d+(?:\.\d+)?)/) { } |
|
|
8 |
42 |
elsif ($okay and /^\s+(\d+)\s+(\S)\s+([\d\.\-\+]+)(\**)/) { } |
|
1218
|
0 |
9 |
unless defined $signif |
|
1226
|
0 |
8 |
unless defined $signif |
|
1231
|
0 |
8 |
unless defined $signif |
|
1244
|
38 |
98 |
if /^\s+$/ |
|
1245
|
0 |
98 |
unless $okay or /^\s+branch\s+t/ |
|
1246
|
10 |
88 |
if (/^\s+branch\s+(.+)/) { } |
|
|
78 |
10 |
elsif (/^\s*(\d+\.\.\d+)/) { } |
|
1275
|
0 |
2 |
unless $self->{'_summary'}{'seqs'} |
|
1277
|
0 |
28 |
if (/^TREE/ or /^Distances/) |
|
1278
|
2 |
26 |
if $done |
|
1279
|
10 |
16 |
if /^\s+$/ or /^\(Ambiguity/ |
|
1280
|
2 |
14 |
if (/^Frequencies\./) { } |
|
|
0 |
14 |
elsif (not $okay) { } |
|
|
2 |
12 |
elsif (not $header) { } |
|
|
2 |
10 |
elsif (/^\#\s+constant\s+sites\:\s+
(\d+)\s+ # constant sites
\(\s*([\d\.]+)\s*\%\s*\)/ox) { } |
|
|
2 |
8 |
elsif (/^ln\s+Lmax\s+\(unconstrained\)\s+\=\s+(\S+)/ox) { } |
|
1323
|
0 |
2 |
unless $self->{'_summary'}{'seqs'} |
|
1326
|
0 |
13 |
if (/^TREE/) |
|
1327
|
1 |
12 |
if $done |
|
1328
|
2 |
10 |
if /^This matrix is not used in later/ |
|
1329
|
2 |
8 |
if (/^\s+$/) |
|
1330
|
0 |
2 |
if $seen |
|
1333
|
2 |
6 |
if (/^Distances:(\S+)\s+\(([^\)]+)\)\s+\(alpha set at (\-?\d+\.\d+)\)/) |
|
1340
|
6 |
0 |
if ($okay) |
|
1344
|
4 |
2 |
if (defined $vl) |
|
1352
|
0 |
4 |
unless ($i) |
|
1359
|
2 |
4 |
if scalar @names == $numseqs |
|
1399
|
0 |
0 |
if (/^Rate\s+parameters:\s+/) { } |
|
|
0 |
0 |
elsif (/^Base\s+frequencies:\s+/) { } |
|
|
0 |
0 |
elsif (m[^Rate\s+matrix\s+Q,\s+Average\s+Ts/Tv\s+(\([^\)+]+\))?\s*\=\s+
(\-?\d+\.\d+)]x) { } |
|
|
0 |
0 |
elsif (/^alpha\s+\(gamma,\s+K=\s*(\d+)\s*\)\s*\=\s*(\-?\d+\.\d+)/) { } |
|
|
0 |
0 |
elsif (s/^(r|f):\s+//) { } |
|
1416
|
0 |
0 |
if /^\s+$/ |
|
1417
|
0 |
0 |
if (/^alpha/) |
|
1441
|
0 |
1 |
unless $self->{'_dir'} and -d $self->{'_dir'} and -r $self->{'_dir'} |
|
1444
|
0 |
1 |
unless -e $rstfile and not -z $rstfile |
|
1455
|
1 |
615 |
if (/^TREE\s+\#\s+(\d+)/) { } |
|
|
1 |
614 |
elsif (/^Prob\sof\sbest\scharacter\sat\seach\snode,\slisted\sby\ssite/) { } |
|
|
1 |
613 |
elsif (/^Check\sroot\sfor\sdirections\sof\schange\./ or /^Summary\sof\schanges\salong\sbranches\./) { } |
|
|
0 |
613 |
elsif (/^Overall\s+accuracy\s+of\s+the\s+(\d+)\s+ancestral\s+sequences:/) { } |
|
|
3 |
610 |
elsif (/^List of extant and reconstructed sequences/o) { } |
|
1457
|
1 |
9 |
if (/tree\s+with\s+node\s+labels\s+for/) |
|
1470
|
11 |
1 |
if (defined(my $blen = $n->branch_length)) |
|
1485
|
4 |
131 |
if /^Site/i or /^\s+$/ |
|
1486
|
130 |
1 |
if (s/^\s+(\d+)\s+(\d+)\s+([^:]+)\s*:\s*(.+)//) { } |
|
|
1 |
0 |
elsif (/^Summary\sof\schanges\salong\sbranches\./) { } |
|
1524
|
0 |
1 |
unless ($tree) |
|
1536
|
36 |
57 |
if /^\s+$/ |
|
1537
|
1 |
56 |
if (/^List\sof\sextant\sand\sreconstructed\ssequences/) { } |
|
|
11 |
45 |
elsif (/^Branch\s+(\d+):\s+(\d+)\.\.(\d+)\s+/) { } |
|
|
45 |
0 |
elsif (/^\s+(\d+)\s+([A-Z*])\s+(\S+)\s+\-\>\s+([A-Z*])\s+(\S+)?/) { } |
|
1545
|
0 |
11 |
unless ($node) |
|
1551
|
11 |
0 |
if (/\(n=\s*(\S+)\s+s=\s*(\S+)\)/) |
|
1562
|
0 |
45 |
unless ($node) |
|
1572
|
28 |
17 |
if defined $dprob |
|
1592
|
0 |
0 |
if (@overall_seq != @overall_site or @overall_seq != @seqs) |
|
1612
|
2 |
309 |
if /^Overall accuracy of the/ |
|
1613
|
61 |
248 |
if (/^\s+$/) |
|
1614
|
0 |
61 |
if $seqcount and $seqcount == @seqs |
|
1617
|
0 |
248 |
if (/^\s*(\d+)\s+(\d+)\s+$/) |
|
1622
|
20 |
228 |
if (/^node/) |
|
1626
|
19 |
1 |
if (@firstseq) { } |