/usr/share/perl5/SWISS/OGs.pm is in libswiss-perl 1.67-1.1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 | package SWISS::OGs;
use vars qw($AUTOLOAD @ISA @EXPORT_OK %fields);
use Exporter;
use Carp;
use strict;
use SWISS::TextFunc;
use SWISS::ListBase;
use SWISS::OG;
BEGIN {
@EXPORT_OK = qw();
@ISA = ( 'Exporter', 'SWISS::ListBase');
%fields = (
);
}
sub new {
my $ref = shift;
my $class = ref($ref) || $ref;
my $self = new SWISS::ListBase;
$self->rebless($class);
return $self;
}
sub initialize {
}
sub fromText {
my $self = new(shift);
my $textRef = shift;
my $line;
my @tmp;
if ($$textRef =~ /($SWISS::TextFunc::linePattern{'OG'})/m){
$line = join ' ', map {
$self->{indentation} += s/^ //;
SWISS::TextFunc->cleanLine($_);
} (split /\n/m, $1 );
# drop 'AND'
$line =~ s/\s*,\s*(AND\s+)*/, /gi;
# Step one: Split on dots separating organelle classes (Plasmid, Mitochondrion).
# complex expression for separator to make sure commas within brackets are
# not regarded as separators.
@tmp = SWISS::TextFunc->listFromText($line, '\.\s+', '\.');
# Step two: Split on commas separating elements of organelle classes.
my @resultList;
foreach my $organelle (@tmp) {
push @resultList, SWISS::TextFunc->listFromText($organelle, ',\s+(?![^\(]+\))', '\.');
}
@resultList = map {SWISS::OG->fromText($_)} @resultList;
push (@{$self->list()}, @resultList);
}
$self->{_dirty} = 0;
return $self;
}
sub toText {
my $self = shift;
my $textRef = shift;
my (@tmp, @lines);
my (@plasmids, @nonPlasmids);
my $nonPlasmidText = '';
my $plasmidText = '';
my $lastElementRef;
my $listRef;
@tmp = $self->elements();
foreach my $element (@tmp) {
if ($element->isPlasmid()) {
push @plasmids, $element;
} else {
push @nonPlasmids, $element;
}
}
# First format all non-plasmid elements
foreach my $nonPlasmid (@nonPlasmids) {
my $indent = $self->{indentation} ? " " : "";
$nonPlasmidText .= "${indent}OG " . $nonPlasmid->toText() . ".\n";
}
# Format plasmids
if ($#plasmids > -1) {
# insert an 'AND' before the last species if appropriate
@tmp = map {$_->toText} @plasmids;
if ($#tmp > 0) {
push(@tmp, 'and '. pop(@tmp));
}
$plasmidText = join(", ", @tmp);
$plasmidText .= ".";
my $prefix = "OG ";
my $col = $SWISS::TextFunc::lineLength;
$col++, $prefix=" $prefix" if $self->{indentation};
$plasmidText = SWISS::TextFunc->wrapOn($prefix, $prefix, $col,
$plasmidText,
',\s+and\s+', ',\s+', '(?=\()', '\s+');
};
$self->{_dirty} = 0;
return SWISS::TextFunc->insertLineGroup($textRef,
$nonPlasmidText . $plasmidText,
$SWISS::TextFunc::linePattern{'OG'});
}
# OGs must never be sorted, overwrite the inherited sort method.
sub sort {
return 1;
}
1;
__END__
=head1 Name
SWISS::OGs
=head1 Description
B<SWISS::OGs> represents the OG lines within an SWISS-PROT + TrEMBL
entry as specified in the user manual
http://www.expasy.org/sprot/userman.html . The OGs object is a container object which holds a list of SWISS::OG objects.
=head1 Inherits from
SWISS::ListBase.pm
=head1 Attributes
=over
=item C<list>
Each list element is a SWISS::OG object.
=back
=head1 Methods
=head2 Standard methods
=over
=item new
=item fromText
=item toText
=back
|