/usr/share/perl5/GO/ObjCache.pm is in libgo-perl 0.15-1.
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 | # $Id: ObjCache.pm,v 1.3 2005/05/20 18:46:57 cmungall Exp $
#
# This GO module is maintained by Chris Mungall <cjm@fruitfly.org>
#
# see also - http://www.geneontology.org
# - http://www.godatabase.org/dev
#
# You may distribute this module under the same terms as perl itself
package GO::ObjCache;
=head1 NAME
GO::ObjCache - private method
=head1 DESCRIPTION
This is a kind of L<GO::ObjFactory> - you should not need to use this
method directly
=cut
use Carp;
use strict;
use Exporter;
use GO::Utils qw(rearrange);
#use strict;
use FileHandle;
use Exporter;
use vars qw(@ISA);
use strict;
use base qw(GO::Model::Graph GO::ObjFactory);
sub _valid_params {
return qw(dbh);
}
sub _initialize {
my $self = shift;
$self->SUPER::_initialize(@_);
}
sub apph {
my $self = shift;
$self->{apph} = shift if @_;
return $self->{apph} || $self;
}
sub n_deep_associations {
my $self = shift;
my $acc = shift;
$self->extend_down([$acc]); # make sure all terms loaded
$self->SUPER::n_deep_associations($acc);
}
sub deep_association_list {
my $self = shift;
my $acc = shift;
$self->extend_down([$acc]); # make sure all terms loaded
$self->SUPER::deep_association_list($acc);
}
#------
sub extend_graph_by_acc {
my $self = shift;
my $graph = shift;
my $acc = shift;
my $depth = shift;
my $term = $self->get_term($acc);
$self->extend_up($graph, [$acc]);
$self->extend_down($graph, [$acc], $depth);
}
sub extend_up {
my $self = shift;
my $graph = shift;
my @accs = @{shift || []};
my $i=0;
while ($i < scalar(@accs)) {
my $acc = $accs[$i];
$i++;
my $term = $self->get_term($acc);
$graph->add_term($term);
my $parent_rels = $self->get_parent_relationships($acc);
foreach my $rel (@$parent_rels) {
$graph->add_relationship($rel);
if (!(grep {$_ == $rel->acc1} @accs)) {
# only put new accs in
push(@accs, $rel->acc1);
}
}
} @accs;
}
sub extend_down {
my $self = shift;
my $graph = shift;
my @accs = @{shift || []};
my $max_depth = shift;
my $i=0;
while ($i < scalar(@accs)) {
printf STDERR
"======== %d %d %s\n",
$i,
$#accs,
join(", ", @accs);
my $acc = $accs[$i];
$i++;
my $term = $self->get_term($acc);
$graph->add_term($term);
my $child_rels = $self->get_child_relationships($acc);
foreach my $rel (@$child_rels) {
$graph->add_relationship($rel);
if (!(grep {$_ == $rel->acc2} @accs)) {
# only put new accs in
push(@accs, $rel->acc2);
}
}
} @accs;
}
sub get_deep_product_count { 0 }
1;
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