Bio/Factory/SeqAnalysisParserFactoryI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Factory::SeqAnalysisParserFactoryI
   4 #
   5 # Cared for by Jason Stajich <jason@bioperl.org>,
   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::Factory::SeqAnalysisParserFactoryI - interface describing objects capable
  17               of creating SeqAnalysisParserI compliant parsers
  18
  19 =head1 SYNOPSIS
  20
  21     # initialize an object implementing this interface, e.g.
  22     $factory = Bio::Factory::SeqAnalysisParserFactory->new();
  23     # obtain a parser object
  24     $parser = $factory->get_parser(-input=>$inputobj,
  25                                    -params=>[@params],
  26                                    -method => $method);
  27     # $parser is an object implementing Bio::SeqAnalysisParserI
  28     # annotate sequence with features produced by parser
  29     while(my $feat = $parser->next_feature()) {
  30         $seq->add_SeqFeature($feat);
  31     }
  32
  33 =head1 DESCRIPTION
  34
  35 This is an interface for factory classes capable of instantiating
  36 SeqAnalysisParserI implementing parsers.
  37
  38 The concept behind the interface is a generic analysis result parsing
  39 in high-throughput automated sequence annotation pipelines. See
  40 L<Bio::SeqAnalysisParserI> for more documentation of this concept.
  41
  42 =head1 FEEDBACK
  43
  44 =head2 Mailing Lists
  45
  46 User feedback is an integral part of the evolution of this
  47 and other Bioperl modules. Send your comments and suggestions preferably
  48  to one of the Bioperl mailing lists.
  49 Your participation is much appreciated.
  50
  51   bioperl-l@bioperl.org                  - General discussion
  52   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  53
  54 =head2 Reporting Bugs
  55
  56 Report bugs to the Bioperl bug tracking system to help us keep track
  57 the bugs and their resolution.  Bug reports can be submitted via the
  58 web:
  59
  60   http://bugzilla.open-bio.org/
  61
  62 =head1 AUTHOR - Hilmar Lapp, Jason Stajich
  63
  64 Email Hilmar Lapp E<lt>hlapp@gmx.netE<gt>, Jason Stajich E<lt>jason@bioperl.orgE<gt>
  65
  66 =head1 APPENDIX
  67
  68 The rest of the documentation details each of the object
  69 methods. Internal methods are usually preceded with a _
  70
  71 =cut
  72
  73 package Bio::Factory::SeqAnalysisParserFactoryI;
  74 use strict;
  75
  76 use Carp;
  77
  78 use base qw(Bio::Root::RootI);
  79
  80 =head2 get_parser
  81
  82  Title   : get_parser
  83  Usage   : $factory->get_parser(-input=>$inputobj,
  84                                 [ -params=>[@params] ],
  85                                 -method => $method)
  86  Function: Creates and returns a parser object for the given input and method.
  87            The type of input which is suitable depends on the implementation,
  88            but a good-style implementation should allow both file names and
  89            streams (filehandles).
  90
  91            A particular implementation may not be able to create a parser for
  92            the requested method. In this case it shall return undef.
  93
  94            Parameters (-params argument) are passed on to the parser object
  95            and therefore are specific to the parser to be created. An
  96            implementation of this interface should make this argument optional.
  97  Example :
  98  Returns : A Bio::SeqAnalysisParserI implementing object.
  99  Args    : B<input>  - object/file where analysis results are coming from,
 100            B<params> - parameter to use when parsing/running analysis
 101            B<method> - method of analysis
 102
 103 =cut
 104
 105 sub get_parser {
 106     my ( $self, @args) = @_;
 107     $self->throw_not_implemented();
 108 }
 109
 110 1;