/usr/share/perl5/SWISS/CCseq_caution.pm is in libswiss-perl 1.67-1.2.
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 | package SWISS::CCseq_caution;
use vars qw($AUTOLOAD @ISA);
use Carp;
use strict;
use SWISS::TextFunc;
use SWISS::ListBase;
use SWISS::BaseClass;
BEGIN {
@ISA = ('SWISS::ListBase');
}
sub new {
my $ref = shift;
my $class = ref($ref) || $ref;
my $self = new SWISS::ListBase;
$self->rebless($class);
return $self;
}
sub fromText {
my $class = shift;
my $textRef = shift;
my $self = new SWISS::CCseq_caution;
my $text = $$textRef;
$self->initialize();
$text =~ s/ +/ /g;
$text =~ s/\s*-!-.*?:\s*//;
while (length $text) {
if ($text =~ s/^\s*Sequence=(.*?); Type=(.*?);(?: Positions=(.*?);)?(?: Note=(.*?);)?(?:\s*|\Z)//s) {
my ($sequence, $type, $positions, $note, $evidence) = ($1, $2, $3, $4);
my $arg = new SWISS::BaseClass;
if (($evidence) = $sequence =~ /($SWISS::TextFunc::evidencePattern)/m) {
my $quotedEvidence = quotemeta $evidence;
$sequence =~ s/$quotedEvidence//m;
}
$arg->{'sequence'} = $sequence;
$arg->{'type'} = $type;
$arg->{'positions'} = $positions if defined $positions;
$arg->{'note'} = $note if defined $note;
$arg->evidenceTags($evidence);
$self->push($arg);
}
else { #dangling text
carp "CC SEQUENCE CAUTION parse error, ignoring $text";
last;
}
}
$self->sort;
$self->{_dirty} = 0;
return $self;
}
sub sort {
my ($self) = @_;
if ($self) {
my @items;
for my $item ($self->elements) {
push @items, $item
}
$self->set(sort {
lc $a->{sequence} cmp lc $b->{sequence}
|| $a->{type} cmp $b->{type}
} @items);
}
}
sub toString {
my $self = shift;
my $text = "-!- SEQUENCE CAUTION:\n" . $self->comment;
$text =~ s/^/CC /mg;
$text =~ s/ //;
return $text;
}
sub topic {
return "SEQUENCE CAUTION";
}
sub comment {
my ($self) = @_;
my $text = '';
if ($self) {
for my $el ($self->elements) {
$text .= 'Sequence=' . $el->{sequence} . $el->getEvidenceTagsString();
$text .= '; Type=' . $el->{type};
$text .= '; Positions=' . $el->{positions} if $el->{positions};
$text .= '; Note=' . $el->{note} if $el->{note};
$text .= ";\n";
}
}
$text;
}
1;
__END__
=head1 Name
SWISS::CCinteraction
=head1 Description
B<SWISS::CCinteraction> represents a comment on the topic 'INTERACTION'
within a Swiss-Prot or TrEMBL entry as specified in the user manual
http://www.expasy.org/sprot/userman.html . Comments on other topics are stored
in other types of objects, such as SWISS::CC (see SWISS::CCs for more information).
Collectively, comments of all types are stored within a SWISS::CCs container
object.
Each element of the list is a hash with the following keys:
accession
identifier
xeno
NbExp
IntAct (array reference)
=head1 Inherits from
SWISS::ListBase.pm
=head1 Methods
=head2 Standard methods
=over
=item new
=item fromText
=item toString
Returns a string representation of this comment.
=back
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