branch-1-6/Bio/SeqAnalysisParserI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::SeqAnalysisParserI
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Jason Stajich <jason@bioperl.org>,
   8 # and Hilmar Lapp <hlapp@gmx.net>
   9 #
  10 # Copyright Jason Stajich, Hilmar Lapp
  11 #
  12 # You may distribute this module under the same terms as perl itself
  13
  14 # POD documentation - main docs before the code
  15
  16 =head1 NAME
  17
  18 Bio::SeqAnalysisParserI - Sequence analysis output parser interface
  19
  20 =head1 SYNOPSIS
  21
  22     # get a SeqAnalysisParserI somehow, e.g. by
  23     my $parser = Bio::Factory::SeqAnalysisParserFactory->get_parser(
  24                             '-input' => 'inputfile', '-method' => 'genscan');
  25     while( my $feature = $parser->next_feature() ) {
  26         print "Feature from ", $feature->start, " to ", $feature->end, "\n";
  27     }
  28
  29 =head1 DESCRIPTION
  30
  31 SeqAnalysisParserI is a generic interface for describing sequence analysis
  32 result parsers. Sequence analysis in this sense is a search for similarities
  33 or the identification of features on the sequence, like a databank search or a
  34 a gene prediction result.
  35
  36 The concept behind this interface is to have a generic interface in sequence
  37 annotation pipelines (as used e.g. in high-throughput automated
  38 sequence annotation). This interface enables plug-and-play for new analysis
  39 methods and their corresponding parsers without the necessity for modifying
  40 the core of the annotation pipeline. In this concept the annotation pipeline
  41 has to rely on only a list of methods for which to process the results, and a
  42 factory from which it can obtain the corresponding parser implementing this
  43 interface.
  44
  45 See Bio::Factory::SeqAnalysisParserFactoryI and
  46 Bio::Factory::SeqAnalysisParserFactory for interface and an implementation
  47 of the corresponding factory.
  48
  49 =head1 FEEDBACK
  50
  51 =head2 Mailing Lists
  52
  53 User feedback is an integral part of the evolution of this
  54 and other Bioperl modules. Send your comments and suggestions preferably
  55  to one of the Bioperl mailing lists.
  56 Your participation is much appreciated.
  57
  58   bioperl-l@bioperl.org                  - General discussion
  59   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  60
  61 =head2 Support
  62
  63 Please direct usage questions or support issues to the mailing list:
  64
  65 I<bioperl-l@bioperl.org>
  66
  67 rather than to the module maintainer directly. Many experienced and
  68 reponsive experts will be able look at the problem and quickly
  69 address it. Please include a thorough description of the problem
  70 with code and data examples if at all possible.
  71
  72 =head2 Reporting Bugs
  73
  74 Report bugs to the Bioperl bug tracking system to help us keep track
  75 the bugs and their resolution.  Bug reports can be submitted via the
  76 web:
  77
  78   http://bugzilla.open-bio.org/
  79
  80 =head1 AUTHOR - Hilmar Lapp, Jason Stajich
  81
  82 Email Hilmar Lapp E<lt>hlapp@gmx.netE<gt>, Jason Stajich E<lt>jason@bioperl.orgE<gt>
  83
  84 =head1 APPENDIX
  85
  86 The rest of the documentation details each of the object methods.
  87 Internal methods are usually preceded with a _
  88
  89 =cut
  90
  91 package Bio::SeqAnalysisParserI;
  92 use strict;
  93 use Carp;
  94 use base qw(Bio::Root::RootI);
  95
  96 =head2 next_feature
  97
  98  Title   : next_feature
  99  Usage   : $seqfeature = $obj->next_feature();
 100  Function: Returns the next feature available in the analysis result, or
 101            undef if there are no more features.
 102  Example :
 103  Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
 104            more features.
 105  Args    : none
 106
 107 =cut
 108
 109 sub next_feature {
 110     my ($self) = shift;
 111     $self->throw_not_implemented();
 112 }
 113
 114 1;