Bio/AnalysisParserI.pm

   1 #---------------------------------------------------------------
   2 # $Id$
   3 #
   4 # BioPerl module Bio::AnalysisParserI
   5 #
   6 # Cared for by Steve Chervitz <sac@bioperl.org>
   7 #
   8 # Derived from Bio::SeqAnalysisParserI by Jason Stajich, Hilmar Lapp.
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11 #---------------------------------------------------------------
  12
  13 =head1 NAME
  14
  15 Bio::AnalysisParserI - Generic analysis output parser interface
  16
  17 =head1 SYNOPSIS
  18
  19     # get a AnalysisParserI somehow.
  20     # Eventually, there may be an Bio::Factory::AnalysisParserFactory.
  21     # For now a SearchIO object, an implementation of AnalysisParserI, can be created
  22     # directly, as in the following:
  23     my $parser = Bio::SearchIO->new(
  24                                     '-file'   => 'inputfile',
  25                                     '-format' => 'blast');
  26
  27     while( my $result = $parser->next_result() ) {
  28         print "Result:  ", $result->analysis_method,
  29               ", Query:  ", $result->query_name, "\n";
  30
  31           while( my $feature = $result->next_feature() ) {
  32               print "Feature from ", $feature->start, " to ",
  33                     $feature->end, "\n";
  34           }
  35     }
  36
  37 =head1 DESCRIPTION
  38
  39 AnalysisParserI is a interface for describing generic analysis
  40 result parsers. This module makes no assumption about the nature of
  41 analysis being parsed, only that zero or more result sets can be
  42 obtained from the input source.
  43
  44 This module was derived from Bio::SeqAnalysisParserI, the differences being
  45
  46 =over 4
  47
  48 =item 1. next_feature() was replaced with next_result().
  49
  50 Instead of flattening a stream containing potentially multiple
  51 analysis results into a single set of features, AnalysisParserI
  52 segments the stream in terms of analysis result sets
  53 (Bio::AnalysisResultI objects). Each AnalysisResultI can then be
  54 queried for its features (if any) as well as other information
  55 about the result
  56
  57 =item 2. AnalysisParserI is a pure interface.
  58
  59 It does not inherit from Bio::Root::RootI and does not provide a new()
  60 method. Implementations are free to choose how to implement it.
  61
  62 =back
  63
  64 =head2 Rationale (copied from Bio::SeqAnalysisParserI)
  65
  66 The concept behind this interface is to have a generic interface in sequence
  67 annotation pipelines (as used e.g. in high-throughput automated
  68 sequence annotation). This interface enables plug-and-play for new analysis
  69 methods and their corresponding parsers without the necessity for modifying
  70 the core of the annotation pipeline. In this concept the annotation pipeline
  71 has to rely on only a list of methods for which to process the results, and a
  72 factory from which it can obtain the corresponding parser implementing this
  73 interface.
  74
  75 =head2 TODO
  76
  77 Create Bio::Factory::AnalysisParserFactoryI and
  78 Bio::Factory::AnalysisParserFactory for interface and an implementation.
  79 Note that this factory could return Bio::SearchIO-derived objects.
  80
  81 =head1 FEEDBACK
  82
  83 =head2 Mailing Lists
  84
  85 User feedback is an integral part of the evolution of this
  86 and other Bioperl modules. Send your comments and suggestions preferably
  87  to one of the Bioperl mailing lists.
  88 Your participation is much appreciated.
  89
  90   bioperl-l@bioperl.org                  - General discussion
  91   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  92
  93 =head2 Reporting Bugs
  94
  95 Report bugs to the Bioperl bug tracking system to help us keep track
  96 the bugs and their resolution.  Bug reports can be submitted via the
  97 web:
  98
  99   http://bugzilla.open-bio.org/
 100
 101 =head1 AUTHOR - Steve Chervitz, Jason Stajich, Hilmar Lapp
 102
 103 Email sac@bioperl.org
 104
 105 Authors of Bio::SeqAnalysisParserI on which this module is based:
 106 Email jason@bioperl.org
 107 Email hlapp@gmx.net
 108
 109 =head1 COPYRIGHT
 110
 111 Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
 112
 113 =head1 DISCLAIMER
 114
 115 This software is provided "as is" without warranty of any kind.
 116
 117 =head1 APPENDIX
 118
 119 The rest of the documentation details each of the object methods.
 120 Internal methods are usually preceded with a _
 121
 122 =cut
 123
 124 package Bio::AnalysisParserI;
 125 use strict;
 126
 127
 128 use base qw(Bio::Root::RootI);
 129
 130 =head2 next_result
 131
 132  Title   : next_result
 133  Usage   : $result = $obj->next_result();
 134  Function: Returns the next result available from the input, or
 135            undef if there are no more results.
 136  Example :
 137  Returns : A Bio::Search::Result::ResultI implementing object,
 138            or undef if there are no more results.
 139  Args    : none
 140
 141 =cut
 142
 143 sub next_result {
 144     my ($self);
 145     $self->throw_not_implemented;
 146 }
 147
 148
 149 1;
 150 __END__
 151
 152 NOTE (sac): My ten-month old son Russell added the following line.
 153 It doesn't look like it will compile so I'm putting it here:
 154 mt6 j7qa