Bio/SeqAnalysisParserI.pm

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