Bio/SeqAnalysisParserI.pm

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