This file is indexed.

/usr/lib/perl5/Ace/Sequence/GappedAlignment.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
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
package Ace::Sequence::GappedAlignment;

use strict;
use Ace;
use Ace::Sequence::Feature;
use vars '$AUTOLOAD';
use overload 
  '""' => 'asString',
  'fallback' => 'TRUE';
  ;
use vars '$VERSION';
$VERSION = '1.20';

*sub_SeqFeature = \&merged_segments;


# autoload delegates everything to the Sequence feature
sub AUTOLOAD {
  my($pack,$func_name) = $AUTOLOAD=~/(.+)::([^:]+)$/;
  my $self = shift;
  $self->{base}->$func_name(@_);
}

sub new {
  my $class = shift;
  my $segments = shift;
  my @segments = sort {$a->start <=> $b->start} @$segments;

  # find the min and max for the alignment
  my ($offset,$len);
  if ($segments[0]->start < $segments[-1]->start) {  # positive direction
    $offset = $segments[0]->{offset};
    $len = $segments[-1]->end - $segments[0]->start + 1;
  } else {
    $offset = $segments[-1]->{offset};
    $len = $segments[0]->end - $segments[-1]->start + 1;
  }

  my $base = { %{$segments[0]} };
  $base->{offset} = $offset;
  $base->{length} = $len;

  bless $base,ref($segments[0]);
  return bless {
		base     => $base,
		segments => $segments,
	       },$class;
}

sub smapped { 1; }

sub asString {
  shift->{base}->info;
}

sub type   { return 'similarity'; }

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

sub segments {
  my $self = shift;
  return $self->{segments} ? @{$self->{segments}} : () unless $self->relative;
  # otherwise, we have to handle relative coordinates
  my $base   = $self->{base};
  my @e = map {Ace::Sequence->new(-refseq=>$base,-seq=>$_)} @{$self->{segments}};
  return $self->strand < 0 ? reverse @e : @e;
}

sub merged_segments {
  my $self = shift;

  return @{$self->{merged_segs}} if exists $self->{merged_segs};

  my @segs = sort {$a->start <=> $b->start} $self->segments;
  # attempt to merge overlapping segments
  my @merged;
  for my $s (@segs) {
    my $previous = $merged[-1];
    if ($previous && $previous->end+1 >= $s->start) {
      $previous->{length} = $s->end - $previous->start + 1;  # extend
    } else {
      my $clone = bless {%$s},ref($s);
      push @merged,$clone;
    }
  }
  $self->{merged_segs} = \@merged;
  return @merged;
}

1;

__END__

=head1 NAME

Ace::Sequence::GappedAlignment - Gapped alignment object

=head1 SYNOPSIS

    # open database connection and get an Ace::Sequence object
    use Ace::Sequence;

    # get a megabase from the middle of chromosome I
    $seq = Ace::Sequence->new(-name   => 'CHROMOSOME_I,
                              -db     => $db,
			      -offset => 3_000_000,
			      -length => 1_000_000);

    # get all the gapped alignments
    @alignments = $seq->alignments('EST_GENOME');

    # get the aligned segments from the first one
    @segs = $alignments[0]->segments;

    # get the position of the first aligned segment on the
    # source sequence:
    ($s_start,$s_end) = ($segs[0]->start,$segs[0]->end);

    # get the target position for the first aligned segment
    ($t_start,$t_end) = ($segs[0]->target->start,$segs[0]->target->end);

=head1 DESCRIPTION

Ace::Sequence::GappedAlignment is a subclass of
Ace::Sequence::Feature.  It inherits all the methods of
Ace::Sequence::Feature, but adds the ability to retrieve the positions
of the aligned segments.  Each segment is an Ace::Sequence::Feature,
from which you can retrieve the source and target coordinates.

=head1  OBJECT CREATION

You will not ordinarily create an I<Ace::Sequence::GappedAlignment>
object directly.  Instead, objects will be created in response to a
alignments() call to an I<Ace::Sequence> object.

=head1 OBJECT METHODS

Most methods are inherited from I<Ace::Sequence::Feature>.  The
following methods are also supported:

=over 4

=item segments()

  @segments = $gene->segments;

Return a list of Ace::Sequence::Feature objects corresponding to
similar segments.

=item relative()

  $relative = $gene->relative;
  $gene->relative(1);

This turns on and off relative coordinates.  By default, the exons and
intron features will be returned in the coordinate system used by the
gene.  If relative() is set to a true value, then coordinates will be
expressed as relative to the start of the gene.  The first exon will
(usually) be 1.

=head1 SEE ALSO

L<Ace>, L<Ace::Object>, L<Ace::Sequence>,L<Ace::Sequence::Homol>,
L<Ace::Sequence::Feature>, L<Ace::Sequence::FeatureList>, L<GFF>

=head1 AUTHOR

Lincoln Stein <lstein@cshl.org> with extensive help from Jean
Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>

Copyright (c) 1999, Lincoln D. Stein

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