This file is indexed.

/usr/share/perl5/GO/ObjFactory.pm is in libgo-perl 0.15-5.

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
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
# $Id: ObjFactory.pm,v 1.6 2007/01/24 01:16:19 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::ObjFactory;

=head1 NAME

  GO::ObjFactory     - GO Object Factory

=head1 SYNOPSIS

You should not use this method directly

=head1 DESCRIPTION

You only need to be aware of this class if you are generating new
objects. You should not directly create objects like this:

  $term = GO::Model::Term->new($h);

Instead you should create them like this:

  $fac = GO::ObjFactory->new();
  $term = $fac->create_term_obj($h);

Usually you do not need to instantiate a factory, as all objects
created with a factory carry around a reference to that factory, so
you can do this:

  # $graph object was previously created via a factory
  $term = $graph->create_term_obj($h);

If you are only using the go-perl module, then factories do not buy
you much. However, if you are also using go-db-perl and GO::AppHandle,
then factories can be useful - all objects generated from the database
will be attached to an AppHandle which means that "lazy loading" can
be used. See GO::AppHandle in go-db-perl for details

=cut


use strict;
use Carp;
use GO::Model::Seq;
use GO::Model::Term;
use GO::Model::Xref;
use GO::Model::GeneProduct;
use GO::Model::CrossProduct;
use GO::Model::LogicalDefinition;
use GO::Model::Graph;
use GO::Model::DB;
use GO::Model::Ontology;
use GO::Model::Property;
use GO::Model::Restriction;
use GO::Model::Species;
use base qw(GO::Model::Root);

sub apph{
  my $self = shift;
  $self->{apph} = shift if @_;

  my $apph = $self->{apph} || $self;
  return $apph;
}




=head2 create_term_obj

  Usage   - $term = $apph->create_term_obj;
  Returns - L<GO::Model::Term>
  Args    -

=cut

sub create_term_obj {
    my $self = shift;
    my $term = GO::Model::Term->new(@_);
    $term->apph( $self->apph );
    return $term;
}

=head2 create_relationship_obj

  Usage   - $relationship = $apph->create_relationship_obj;
  Returns - L<GO::Model::Relationship>
  Args    -

=cut

sub create_relationship_obj {
    my $self = shift;
    my $term = GO::Model::Relationship->new(@_);
    $term->apph( $self->apph );
    return $term;
}

=head2 create_xref_obj

  Usage   - $xref = $apph->create_xref_obj;
  Returns - L<GO::Model::Xref>
  Args    -

=cut

sub create_xref_obj {
    my $self = shift;
    my $xref = GO::Model::Xref->new(@_);
#    $xref->apph($self);
    return $xref;
}

=head2 create_evidence_obj

  Usage   - $evidence = $apph->create_evidence_obj;
  Returns - L<GO::Model::Evidence>
  Args    -

=cut

sub create_evidence_obj {
    my $self = shift;
    my $ev = GO::Model::Evidence->new(@_);
    return $ev;
}

=head2 create_seq_obj

  Usage   - $seq = $apph->create_seq_obj;
  Returns - L<GO::Model::Seq>
  Args    -

=cut

sub create_seq_obj {
    my $self = shift;
    my $seq = GO::Model::Seq->new(@_);
    $seq->apph( $self->apph );
    return $seq;
}

=head2 create_db_obj

  Usage   - $db = $apph->create_db_obj;
  Returns - L<GO::Model::DB>
  Args    -

=cut

sub create_db_obj {
    my $self = shift;
    my $db = GO::Model::DB->new(@_);
    $db->apph( $self->apph );
    return $db;
}

=head2 create_association_obj

  Usage   - $association = $apph->create_association_obj;
  Returns - L<GO::Model::Association>
  Args    -

=cut

sub create_association_obj {
    my $self = shift;
    my $association = GO::Model::Association->new();
    $association->apph( $self->apph );
    $association->_initialize(@_);
    return $association;
}

=head2 create_gene_product_obj

  Usage   - $gene_product = $apph->create_gene_product_obj;
  Synonym - create_product_obj
  Returns - L<GO::Model::GeneProduct>
  Args    -

=cut

sub create_gene_product_obj {
    my $self = shift;
    my $gene_product = GO::Model::GeneProduct->new(@_);
    $gene_product->apph( $self->apph );
    return $gene_product;
}
*create_product_obj = \&create_gene_product_obj;

=head2 create_species_obj

  Usage   - $species = $apph->create_species_obj;
  Returns - L<GO::Model::Species>
  Args    -

=cut

sub create_species_obj {
    my $self = shift;
    my $sp = GO::Model::Species->new(@_);
    $sp->apph( $self->apph );
    return $sp;
}

=head2 create_graph_obj

  Usage   - $graph = $apph->create_graph_obj;
  Returns - L<GO::Model::Graph>
  Args    -

=cut

sub create_graph_obj {
    my $self = shift;
    my $graph = GO::Model::Graph->new(@_);
    $graph->apph( $self->apph );
    return $graph;
}

# deprecated synonym for Graph
sub create_ontology_obj {
    my $self = shift;
    my $ontology = GO::Model::Ontology->new(@_);
    $ontology->apph( $self->apph );
    return $ontology;
}

# alpha code
sub create_property_obj {
    my $self = shift;
    my $property = GO::Model::Property->new(@_);
    $property->apph( $self->apph );
    return $property;
}


# alpha code
sub create_restriction_obj {
    my $self = shift;
    my $restriction = GO::Model::Restriction->new(@_);
    $restriction->apph( $self->apph );
    return $restriction;
}

sub create_logical_definition_obj {
    my $self = shift;
    my $ldef = GO::Model::LogicalDefinition->new(@_);
    $ldef->apph( $self->apph );
    return $ldef;
}


# experimental/deprecated code
sub create_cross_product_obj {
    my $self = shift;
    my $cross_product = GO::Model::CrossProduct->new(@_);
    $cross_product->apph( $self->apph );
    return $cross_product;
}

1;