Bio/DB/GFF/Homol.pm

   1 =head1 NAME
   2
   3 Bio::DB::GFF::Homol -- A segment of DNA that is homologous to another
   4
   5 =head1 SYNOPSIS
   6
   7 See L<Bio::DB::GFF>.
   8
   9 =head1 DESCRIPTION
  10
  11 Bio::DB::GFF::Homol is a named subtype of Bio::DB::GFF::Segment.  It
  12 inherits all the methods of its parent, and was created primarily to
  13 allow for isa() queries and for compatibility with
  14 Ace::Sequence::Homol.
  15
  16 A Homol object is typically returned as the method result of the
  17 Bio::DB::GFF::Feature-E<gt>target() method.
  18
  19 =head1 METHODS
  20
  21 =cut
  22
  23 package Bio::DB::GFF::Homol;
  24 use strict;
  25
  26 use base qw(Bio::DB::GFF::Segment);
  27
  28 =head2 name
  29
  30  Title   : name
  31  Usage   : $name = $homol->name
  32  Function: get the ID of the homology object
  33  Returns : a string
  34  Args    : none
  35  Status  : Public
  36
  37 =cut
  38
  39 sub name     { shift->refseq }
  40
  41 =head2 asString
  42
  43  Title   : asString
  44  Usage   : $name = $homol->asString
  45  Function: same as name(), for operator overloading
  46  Returns : a string
  47  Args    : none
  48  Status  : Public
  49
  50 =cut
  51
  52 sub asString { shift->name }
  53
  54
  55 =head2 id
  56
  57  Title   : id
  58  Usage   : $id = $homol->id
  59  Function: get database ID in class:id format
  60  Returns : a string
  61  Args    : none
  62  Status  : Public
  63
  64 =cut
  65
  66 sub id       {
  67   my $self = shift;
  68   return "$self->{class}:$self->{name}";
  69 }
  70
  71 sub new_from_segment {
  72   my $package   = shift;
  73   $package      = ref $package if ref $package;
  74   my $segment   = shift;
  75   my $new = {};
  76   @{$new}{qw(factory sourceseq start stop strand class ref refstart refstrand)}
  77     = @{$segment}{qw(factory sourceseq start stop strand class ref refstart refstrand)};
  78   return bless $new,__PACKAGE__;
  79 }
  80
  81 =head1 BUGS
  82
  83 This module is still under development.
  84
  85 =head1 SEE ALSO
  86
  87 L<bioperl>, L<Bio::DB::GFF>, L<Bio::DB::RelSegment>
  88
  89 =head1 AUTHOR
  90
  91 Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
  92
  93 Copyright (c) 2001 Cold Spring Harbor Laboratory.
  94
  95 This library is free software; you can redistribute it and/or modify
  96 it under the same terms as Perl itself.
  97
  98 =cut
  99
 100 1;