Bio/AnalysisParserI.pm

   1 #---------------------------------------------------------------
   2 # $Id$
   3 #
   4 # BioPerl module Bio::AnalysisParserI
   5 #
   6 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   7 #
   8 # Cared for by Steve Chervitz <sac@bioperl.org>
   9 #
  10 # Derived from Bio::SeqAnalysisParserI by Jason Stajich, Hilmar Lapp.
  11 #
  12 # You may distribute this module under the same terms as perl itself
  13 #---------------------------------------------------------------
  14
  15 =head1 NAME
  16
  17 Bio::AnalysisParserI - Generic analysis output parser interface
  18
  19 =head1 SYNOPSIS
  20
  21     # get a AnalysisParserI somehow.
  22     # Eventually, there may be an Bio::Factory::AnalysisParserFactory.
  23     # For now a SearchIO object, an implementation of AnalysisParserI, can be created
  24     # directly, as in the following:
  25     my $parser = Bio::SearchIO->new(
  26                                     '-file'   => 'inputfile',
  27                                     '-format' => 'blast');
  28
  29     while( my $result = $parser->next_result() ) {
  30         print "Result:  ", $result->analysis_method,
  31               ", Query:  ", $result->query_name, "\n";
  32
  33           while( my $feature = $result->next_feature() ) {
  34               print "Feature from ", $feature->start, " to ",
  35                     $feature->end, "\n";
  36           }
  37     }
  38
  39 =head1 DESCRIPTION
  40
  41 AnalysisParserI is a interface for describing generic analysis
  42 result parsers. This module makes no assumption about the nature of
  43 analysis being parsed, only that zero or more result sets can be
  44 obtained from the input source.
  45
  46 This module was derived from Bio::SeqAnalysisParserI, the differences being
  47
  48 =over 4
  49
  50 =item 1. next_feature() was replaced with next_result().
  51
  52 Instead of flattening a stream containing potentially multiple
  53 analysis results into a single set of features, AnalysisParserI
  54 segments the stream in terms of analysis result sets
  55 (Bio::AnalysisResultI objects). Each AnalysisResultI can then be
  56 queried for its features (if any) as well as other information
  57 about the result
  58
  59 =item 2. AnalysisParserI is a pure interface.
  60
  61 It does not inherit from Bio::Root::RootI and does not provide a new()
  62 method. Implementations are free to choose how to implement it.
  63
  64 =back
  65
  66 =head2 Rationale (copied from Bio::SeqAnalysisParserI)
  67
  68 The concept behind this interface is to have a generic interface in sequence
  69 annotation pipelines (as used e.g. in high-throughput automated
  70 sequence annotation). This interface enables plug-and-play for new analysis
  71 methods and their corresponding parsers without the necessity for modifying
  72 the core of the annotation pipeline. In this concept the annotation pipeline
  73 has to rely on only a list of methods for which to process the results, and a
  74 factory from which it can obtain the corresponding parser implementing this
  75 interface.
  76
  77 =head2 TODO
  78
  79 Create Bio::Factory::AnalysisParserFactoryI and
  80 Bio::Factory::AnalysisParserFactory for interface and an implementation.
  81 Note that this factory could return Bio::SearchIO-derived objects.
  82
  83 =head1 FEEDBACK
  84
  85 =head2 Mailing Lists
  86
  87 User feedback is an integral part of the evolution of this
  88 and other Bioperl modules. Send your comments and suggestions preferably
  89  to one of the Bioperl mailing lists.
  90 Your participation is much appreciated.
  91
  92   bioperl-l@bioperl.org                  - General discussion
  93   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  94
  95 =head2 Support
  96
  97 Please direct usage questions or support issues to the mailing list:
  98
  99 I<bioperl-l@bioperl.org>
 100
 101 rather than to the module maintainer directly. Many experienced and
 102 reponsive experts will be able look at the problem and quickly
 103 address it. Please include a thorough description of the problem
 104 with code and data examples if at all possible.
 105
 106 =head2 Reporting Bugs
 107
 108 Report bugs to the Bioperl bug tracking system to help us keep track
 109 the bugs and their resolution.  Bug reports can be submitted via the
 110 web:
 111
 112   http://bugzilla.open-bio.org/
 113
 114 =head1 AUTHOR - Steve Chervitz, Jason Stajich, Hilmar Lapp
 115
 116 Email sac@bioperl.org
 117
 118 Authors of Bio::SeqAnalysisParserI on which this module is based:
 119 Email jason@bioperl.org
 120 Email hlapp@gmx.net
 121
 122 =head1 COPYRIGHT
 123
 124 Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
 125
 126 =head1 DISCLAIMER
 127
 128 This software is provided "as is" without warranty of any kind.
 129
 130 =head1 APPENDIX
 131
 132 The rest of the documentation details each of the object methods.
 133 Internal methods are usually preceded with a _
 134
 135 =cut
 136
 137 package Bio::AnalysisParserI;
 138 use strict;
 139
 140
 141 use base qw(Bio::Root::RootI);
 142
 143 =head2 next_result
 144
 145  Title   : next_result
 146  Usage   : $result = $obj->next_result();
 147  Function: Returns the next result available from the input, or
 148            undef if there are no more results.
 149  Example :
 150  Returns : A Bio::Search::Result::ResultI implementing object,
 151            or undef if there are no more results.
 152  Args    : none
 153
 154 =cut
 155
 156 sub next_result {
 157     my ($self);
 158     $self->throw_not_implemented;
 159 }
 160
 161
 162 1;
 163 __END__
 164
 165 NOTE (sac): My ten-month old son Russell added the following line.
 166 It doesn't look like it will compile so I'm putting it here:
 167 mt6 j7qa