This file is indexed.

/usr/share/perl5/GO/Handlers/base.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
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
# $Id: base.pm,v 1.5 2004/11/24 02:28:00 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

=head1 NAME

  GO::Handlers::base     - default handler 

=head1 SYNOPSIS

  use GO::Handlers::base

=cut

=head1 DESCRIPTION

Default Handler, other handlers inherit from this class

this class catches events (start, end and body) and allows the
subclassing module to intercept these. unintercepted events get pushed
into a tree

See GO::Parser for details on parser/handler architecture

=head1 PUBLIC METHODS - 

=cut

package GO::Handlers::base;

use strict;
use Exporter;
use Carp;
use GO::Model::Root;
use vars qw(@ISA @EXPORT_OK @EXPORT);
use base qw(Data::Stag::Writer Exporter);

@EXPORT_OK = qw(lookup);

sub EMITS    { () }
sub CONSUMES {
    qw(
       header
       source
       term
       typedef
       prod
      )
}

sub is_transform { 0 }

=head2 strictorder

  Usage   - $handler->strictorder(1);
  Returns -
  Args    -

boolean accessor; if set, then terms passed must be in order

=cut

sub strictorder {
    my $self = shift;
    $self->{_strictorder} = shift if @_;
    return $self->{_strictorder};
}

sub proddb {
    my $self = shift;
    $self->{_proddb} = shift if @_;
    return $self->{_proddb};
}

sub ontology_type {
    my $self = shift;
    $self->{_ontology_type} = shift if @_;
    return $self->{_ontology_type};
}

sub root_to_be_added {
    my $self = shift;
    $self->{_root_to_be_added} = shift if @_;
    return $self->{_root_to_be_added};
}



# DEPRECATED
sub messages {
    my $self = shift;
    $self->{_messages} = shift if @_;
    return $self->{_messages};
}

*error_list = \&messages;

sub message {
    my $self = shift;
    push(@{$self->messages},
         shift);
}


sub lookup {
    my $tree = shift;
    my $k = shift;
#    use Data::Dumper;
#    print Dumper $tree;
#    confess;
    if (!ref($tree)) {
        confess($tree);
    }
    my @v = map {$_->[1]} grep {$_->[0] eq $k} @$tree;
    if (wantarray) {
        return @v;
    }
    $v[0];
}


#sub print {
#    my $self = shift;
#    print "@_";
#}
sub print {shift->addtext(@_)}

sub printf {
    my $self = shift;
    my $fmt = shift;
    $self->addtext(sprintf($fmt, @_));
}

sub throw {
    my $self = shift;
    my @msg = @_;
    confess("@msg");
}
sub warn {
    my $self = shift;
    my @msg = @_;
    warn("@msg");
}

sub dbxref2str {
    my $self = shift;
    my $dbxref = shift;
    return
      $dbxref->sget_dbname . ':' . $dbxref->sget_acc;
}

sub xslt {
    my $self = shift;
    $self->{_xslt} = shift if @_;
    return $self->{_xslt};
}


1;