Bio/SeqFeature/TypedSeqFeatureI.pm

   1 #
   2 # BioPerl module for Bio::SeqFeature::TypedSeqFeatureI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Ewan Birney <birney@ebi.ac.uk>
   7 #
   8 # Copyright Ewan Birney
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::SeqFeature::TypedSeqFeatureI - a strongly typed SeqFeature
  17
  18 =head1 SYNOPSIS
  19
  20
  21    # get Sequence Features in some manner, eg
  22    # from a Sequence object
  23
  24     foreach $sf ( $seq->get_SeqFeatures() ) {
  25         # all sequence features must have primary_tag() return a string
  26         $type_as_string = $sf->primary_tag();
  27         if( $sf->isa("Bio::SeqFeature::TypedSeqFeatureI") ) {
  28             $ot = $sf->ontology_term();
  29             print "Ontology identifier:",$ot->identifier(),
  30                   " name:",$ot->name(),
  31                   " Description:",$ot->description(),"\n";
  32
  33         } else {
  34             print "Sequence Feature does not have an ontology type\n";
  35         }
  36
  37     }
  38
  39 =head1 DESCRIPTION
  40
  41 This interface describes the extension of SeqFeatureI
  42 to being a strongly typed SeqFeature.
  43
  44 Bio::SeqFeature::TypedSeqFeatureI extends the Bio::SeqFeatureI
  45 interface (ie, a TypedSeqFeatureI feature must also implement
  46 all the Bio::SeqFeatureI interface as well).
  47
  48 It is suggested that the primary_tag() method of SeqFeatureI
  49 return the same as the ontology_term()-E<gt>name() of the OntologyTypedI
  50 (ie, the "string" name of the ontology type is used as the primary
  51 tag), but this should not be assumed by client code as they
  52 are scenarios where one would like to maintain the difference.
  53
  54
  55 =head1 FEEDBACK
  56
  57 =head2 Mailing Lists
  58
  59 User feedback is an integral part of the evolution of this and other
  60 Bioperl modules. Send your comments and suggestions preferably to
  61 the Bioperl mailing list.  Your participation is much appreciated.
  62
  63   bioperl-l@bioperl.org                  - General discussion
  64   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  65
  66 =head2 Support
  67
  68 Please direct usage questions or support issues to the mailing list:
  69
  70 I<bioperl-l@bioperl.org>
  71
  72 rather than to the module maintainer directly. Many experienced and
  73 reponsive experts will be able look at the problem and quickly
  74 address it. Please include a thorough description of the problem
  75 with code and data examples if at all possible.
  76
  77 =head2 Reporting Bugs
  78
  79 Report bugs to the Bioperl bug tracking system to help us keep track
  80 of the bugs and their resolution. Bug reports can be submitted via the
  81 web:
  82
  83   https://github.com/bioperl/bioperl-live/issues
  84
  85 =head1 AUTHOR - Ewan Birney
  86
  87 Email - please email the BioPerl mailing list above.
  88
  89 =head1 APPENDIX
  90
  91 The rest of the documentation details each of the object methods.
  92 Internal methods are usually preceded with a _
  93
  94 =cut
  95
  96
  97 # Let the code begin...
  98
  99
 100 package Bio::SeqFeature::TypedSeqFeatureI;
 101
 102 use strict;
 103 use Bio::Root::RootI;
 104
 105 use base qw(Bio::SeqFeatureI);
 106
 107
 108 =head2 ontology_term
 109
 110   Title   : ontology_term
 111   Usage   : my $ot = $seqfeature->ontology_term()
 112   Returns : a Bio::Ontology::TermI compliant object
 113   Args    : none
 114   Status  : public
 115
 116 This method returns the ontology term for a
 117 strongly typed sequence feature.
 118
 119 =cut
 120
 121 sub ontology_term {
 122     shift->throw_not_implemented();
 123 }
 124
 125 1;