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1 =head1 NAME
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2
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3 Bio::DB::GFF::Homol -- A segment of DNA that is homologous to another
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4
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5 =head1 SYNOPSIS
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6
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7 See L<Bio::DB::GFF>.
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8
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9 =head1 DESCRIPTION
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10
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11 Bio::DB::GFF::Homol is a named subtype of Bio::DB::GFF::Segment. It
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12 inherits all the methods of its parent, and was created primarily to
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13 allow for isa() queries and for compatibility with
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14 Ace::Sequence::Homol.
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15
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16 A Homol object is typically returned as the method result of the
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17 Bio::DB::GFF::Feature-E<gt>target() method.
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18
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19 =head1 METHODS
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20
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21 =cut
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22
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23 package Bio::DB::GFF::Homol;
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24 use strict;
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25
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26 use Bio::DB::GFF::Segment;
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27 use vars qw(@ISA);
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28 @ISA = 'Bio::DB::GFF::Segment';
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29
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30 =head2 name
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31
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32 Title : name
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33 Usage : $name = $homol->name
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34 Function: get the ID of the homology object
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35 Returns : a string
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36 Args : none
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37 Status : Public
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38
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39 =cut
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40
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41 sub name { shift->refseq }
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42
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43 =head2 asString
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44
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45 Title : asString
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46 Usage : $name = $homol->asString
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47 Function: same as name(), for operator overloading
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48 Returns : a string
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49 Args : none
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50 Status : Public
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51
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52 =cut
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53
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54 sub asString { shift->name }
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55
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56
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57 =head2 id
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58
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59 Title : id
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60 Usage : $id = $homol->id
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61 Function: get database ID in class:id format
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62 Returns : a string
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63 Args : none
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64 Status : Public
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65
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66 =cut
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67
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68 sub id {
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69 my $self = shift;
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70 return "$self->{class}:$self->{name}";
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71 }
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72
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73 sub new_from_segment {
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74 my $package = shift;
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75 $package = ref $package if ref $package;
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76 my $segment = shift;
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77 my $new = {};
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78 @{$new}{qw(factory sourceseq start stop strand class ref refstart refstrand)}
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79 = @{$segment}{qw(factory sourceseq start stop strand class ref refstart refstrand)};
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80 return bless $new,__PACKAGE__;
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81 }
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82
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83 =head1 BUGS
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84
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85 This module is still under development.
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86
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87 =head1 SEE ALSO
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88
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89 L<bioperl>, L<Bio::DB::GFF>, L<Bio::DB::RelSegment>
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90
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91 =head1 AUTHOR
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92
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93 Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
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94
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95 Copyright (c) 2001 Cold Spring Harbor Laboratory.
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96
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97 This library is free software; you can redistribute it and/or modify
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98 it under the same terms as Perl itself.
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99
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100 =cut
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101
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102 1;
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