/usr/share/perl5/SWISS/ACs.pm is in libswiss-perl 1.67-1.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 | package SWISS::ACs;
use vars qw($AUTOLOAD @ISA @EXPORT_OK %fields);
use Exporter;
use Carp;
use strict;
use SWISS::TextFunc;
use SWISS::ListBase;
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 fromText {
my $self = new(shift);
my $textRef = shift;
my $line;
my @tmp;
if ($$textRef =~ /($SWISS::TextFunc::linePattern{'AC'})/m){
foreach $line (split /\n/m, $1) {
# drop ** Comment lines
if (($line =~ /^\*\*/)
&&
($line !~ /^\*\* [OPQ][\w]{5};/)) {
if ($main::opt_warn) {
carp "Dropped \'$line\' from AC line block";
}
next;
}
$self->{indentation} += $line =~ s/^ //;
$line = SWISS::TextFunc->cleanLine($line);
@tmp = SWISS::TextFunc->listFromText($line, ';\s*', ';\s*');
push (@{$self->list()}, @tmp);
}
}
$self->{_dirty} = 0;
return $self;
}
sub toText {
my $self = shift;
my $textRef = shift;
my (@lines, $newText);
$newText = join('; ', @{$self->list}) . ";";
my $prefix = "AC ";
my $col = $SWISS::TextFunc::lineLength;
$col++, $prefix=" $prefix" if $self->{indentation};
$newText = SWISS::TextFunc->wrapOn($prefix, $prefix, $col, $newText, '; ');
$self->{_dirty} = 0;
return SWISS::TextFunc->insertLineGroup($textRef, $newText,
$SWISS::TextFunc::linePattern{'AC'});
}
# sort secondary ACs
sub sort {
my $self = shift;
my $l = $self->{list};
if (@$l > 1) {
@$l = ($l->[0], sort @$l[1..$#$l]);
}
return 1;
}
sub update {
my $self = shift;
my $force = shift;
# Potential duplicates should be removed.
$self->unique();
# The secondary ACs should be sorted.
$self->sort();
return 1;
}
1; # says use was ok
__END__
=head1 Name
SWISS::ACs
=head1 Description
B<SWISS::ACs> represents the AC (accession) lines within an SWISS-PROT + TrEMBL
entry as specified in the user manual
http://www.expasy.org/sprot/userman.html .
The SWISS-PROT format has recently been changed to multiple AC lines.
This module will read
Ordinary AC lines
AC P10585;
The old temporary format (for internal use only)
AC Q57333; O08291; O08202; O08292; O08203; O08293; O08204; O08294;
** O08205; O08295; O08206; O08296; O08207; O08297; O08208; O08298;
** O08213;
and the new format.
AC Q57333; O08291; O08202; O08292; O08203; O08293; O08204; O08294;
AC O08205; O08295; O08206; O08296; O08207; O08297; O08208; O08298;
AC O08213;
But, SWISS::ACs will DROP funny ** comment lines that are sometimes
found following an AC line:
AC Q48558; P71434;
** MERGED 2 TREMBL ENTRIES.
This module will always write the new format with multiple AC lines.
=head1 Inherits from
SWISS::ListBase.pm
=head1 Attributes
=over
=item C<list>
This is an array containing a list of all the accession numbers associated
with this entry. The first member will be the primary accession number, and
any following are the secondary accession numbers.
=back
=head1 Methods
=head2 Standard methods
=over
=item new
=item fromText
=item toText
=item sort
This method sorts the secondary AC numbers alphanumerically, i.e.
all but the first. The primary AC number must never be sorted.
=back
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