/usr/lib/perl5/TFBS/_Iterator/_SiteSetIterator.pm is in libtfbs-perl 0.6.0+dfsg-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 | package TFBS::_Iterator::_SiteSetIterator;
use vars '@ISA';
use strict;
use Carp;
use TFBS::_Iterator;
@ISA = qw(TFBS::_Iterator);
sub _sort {
my ($self, $sort_by) = @_;
$sort_by or $sort_by = $self->{_sort_by} or $sort_by = 'name';
# we can sort by name, start, end, score
my %sort_fn =
(start => sub { $a->start() <=> $b->start()
|| $a->pattern->name() cmp $b->pattern->name()
|| $a->strand() <=> $b->strand()
},
end => sub { $a->end() <=> $b->end()
|| $a->pattern->name() cmp $b->pattern->name()
|| $a->strand() <=> $b->strand()
},
ID => sub { $a->pattern->ID() cmp $b->pattern->ID()
|| $a->start() <=> $b->start()
|| $a->end() <=> $b->end()
|| $a->strand() <=> $b->strand()
},
name => sub { $a->pattern->name() cmp $b->pattern->name()
|| $a->start() <=> $b->start()
|| $a->end() <=> $b->end()
|| $a->strand() <=> $b->strand()
},
score => sub { $b->score() <=> $a->score()
|| $a->pattern->name() cmp $b->pattern->name()
|| $a->strand() <=> $b->strand()
}
);
if (defined (my $sort_function = $sort_fn{lc $sort_by})) {
$self->{'_iterator_array_ref'} =
[ sort $sort_function @{$self->{'_orig_array_ref'}} ];
}
else {
$self->throw("Cannot sort ".ref($self)." object by '$sort_by'.");
}
}
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