/usr/lib/perl5/TFBS/PatternI.pm is in libtfbs-perl 0.5.svn.20100421-1build1.
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 | # TFBS module for TFBS::PatternI
#
# Copyright Boris Lenhard
#
# You may distribute this module under the same terms as perl itself
#
# POD
=head1 NAME
TFBS::PatternI - interface definition for all pattern objects (currently
includes matrices and word (consensus and regular expressions )
=head1 DESCRIPTION
TFBS::PatternI is a draft class that should contain general interface for matrix and other (future) pattern objects. It is not defined and not used yet, as I need to ponder over certain unresolved issues in general pattern definition. User feedback is more than welcome.
=head1 FEEDBACK
Please send bug reports and other comments to the author.
=head1 AUTHOR - Boris Lenhard
Boris Lenhard E<lt>Boris.Lenhard@cgb.ki.seE<gt>
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are preceded with an underscore.
=cut
# The code begins here:
# The code begins HERE:
package TFBS::PatternI;
use vars '@ISA';
use Bio::Root::Root;
use strict;
@ISA = qw(Bio::Root::Root);
#sub new {
#}
=head2 ID
Title : ID
Usage : my $ID = $icm->ID()
$pfm->ID('M00119');
Function: Get/set on the ID of the pattern (unique in a DB or a set)
Returns : pattern ID (a string)
Args : none for get, string for set
=cut
sub ID {
my ($self, $ID) = @_;
$self->{'ID'} = $ID if $ID;
return $self->{'ID'};
}
=head2 name
Title : name
Usage : my $name = $pwm->name()
$pfm->name('PPARgamma');
Function: Get/set on the name of the pattern
Returns : pattern name (a string)
Args : none for get, string for set
=cut
sub name {
my ($self, $name) = @_;
$self->{'name'} = $name if $name;
return $self->{'name'};
}
=head2 class
Title : class
Usage : my $class = $pwm->class()
$pfm->class('forkhead');
Function: Get/set on the structural class of the pattern
Returns : class name (a string)
Args : none for get, string for set
=cut
sub class {
my ($self, $class) = @_;
$self->{'class'} = $class if $class;
return $self->{'class'};
}
=head2 tag
Title : tag
Usage : my $acc = $pwm->tag('acc')
$pfm->tag(source => "Gibbs");
Function: Get/set on the structural class of the pattern
Returns : tag value (a scalar/reference)
Args : tag name (string) for get,
tag name (string) and value (any scalar/reference) for set
=cut
sub tag {
my $self = shift;
my $tag = shift || return;
if (scalar @_) {
$self->{'tags'}->{$tag} =shift;
}
return $self->{'tags'}->{$tag};
}
=head2 all_tags
Title : all_tags
Usage : my %tag = $pfm->all_tags();
Function: get a hash of all tags for a matrix
Returns : a hash of all tag values keyed by tag name
Args : none
=cut
sub all_tags {
return %{$_[0]->{'tags'}};
}
=head2 delete_tag
Title : delete_tag
Usage : $pfm->delete_tag('score');
Function: get a hash of all tags for a matrix
Returns : nothing
Args : a string (tag name)
=cut
sub delete_tag {
my ($self, $tag) = @_;
delete $self->{'tags'}->{$tag};
}
1;
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