/usr/lib/perl5/Ace/Graphics/Fk.pm is in libace-perl 1.92-2build3.
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 | package Ace::Graphics::Fk;
use strict;
*stop = \&end;
*primary_tag = \&name;
*exons = \&segments;
# usage:
# Ace::Graphics::Fk->new(
# -start => 1,
# -end => 100,
# -name => 'fred feature',
# -info => $additional_stuff_to_store,
# -strand => +1);
#
# Alternatively, use -segments => [ [start,stop],[start,stop]...]
# to create a multisegmented feature.
sub new {
my $class= shift;
my %arg = @_;
my $self = bless {},$class;
$arg{-strand} ||= 0;
$self->{strand} = $arg{-strand} >= 0 ? +1 : -1;
$self->{name} = $arg{-name};
$self->{info} = $arg{-info};
if (my $s = $arg{-segments}) {
my @segments;
for my $seg (@$s) {
if (ref($seg) eq 'ARRAY') {
push @segments,$class->new(-start=>$seg->[0],
-stop=>$seg->[1],
-strand=>$self->{strand});
} else {
push @segments,$seg;
}
}
$self->{segments} = [ sort {$a->start <=> $b->start } @segments ];
} else {
$self->{start} = $arg{-start};
$self->{end} = $arg{-end} || $arg{-stop};
}
$self;
}
sub segments {
my $self = shift;
my $s = $self->{segments} or return;
@$s;
}
sub strand { shift->{strand} }
sub name { shift->{name} }
sub start {
my $self = shift;
if (my @segments = $self->segments) {
return $segments[0]->start;
}
return $self->{start};
}
sub end {
my $self = shift;
if (my @segments = $self->segments) {
return $segments[-1]->end;
}
return $self->{end};
}
sub length {
my $self = shift;
return $self->end - $self->start + 1;
}
sub introns {
my $self = shift;
return;
}
sub source_tag { 'dummy' }
sub target { }
sub info {
my $self = shift;
return $self->{info} || $self->name;
}
1;
__END__
=head1 NAME
Ace::Graphics::Fk - A dummy feature object used for generating panel key tracks
=head1 SYNOPSIS
None. Used internally by Ace::Graphics::Panel.
=head1 DESCRIPTION
None. Used internally by Ace::Graphics::Panel.
=head1 SEE ALSO
L<Ace::Sequence>,L<Ace::Sequence::Feature>,
L<Ace::Graphics::Track>,L<Ace::Graphics::Glyph>,
L<GD>
=head1 AUTHOR
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2001 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
=cut
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