lib/Bio/Factory/SeqAnalysisParserFactoryI.pm

   1 #
   2 # BioPerl module for Bio::Factory::SeqAnalysisParserFactoryI
   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::Factory::SeqAnalysisParserFactoryI - interface describing objects capable
  18               of creating SeqAnalysisParserI compliant parsers
  19
  20 =head1 SYNOPSIS
  21
  22     # initialize an object implementing this interface, e.g.
  23     $factory = Bio::Factory::SeqAnalysisParserFactory->new();
  24     # obtain a parser object
  25     $parser = $factory->get_parser(-input=>$inputobj,
  26                                    -params=>[@params],
  27                                    -method => $method);
  28     # $parser is an object implementing Bio::SeqAnalysisParserI
  29     # annotate sequence with features produced by parser
  30     while(my $feat = $parser->next_feature()) {
  31         $seq->add_SeqFeature($feat);
  32     }
  33
  34 =head1 DESCRIPTION
  35
  36 This is an interface for factory classes capable of instantiating
  37 SeqAnalysisParserI implementing parsers.
  38
  39 The concept behind the interface is a generic analysis result parsing
  40 in high-throughput automated sequence annotation pipelines. See
  41 L<Bio::SeqAnalysisParserI> for more documentation of this concept.
  42
  43 =head1 FEEDBACK
  44
  45 =head2 Mailing Lists
  46
  47 User feedback is an integral part of the evolution of this
  48 and other Bioperl modules. Send your comments and suggestions preferably
  49  to one of the Bioperl mailing lists.
  50 Your participation is much appreciated.
  51
  52   bioperl-l@bioperl.org                  - General discussion
  53   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  54
  55 =head2 Support
  56
  57 Please direct usage questions or support issues to the mailing list:
  58
  59 I<bioperl-l@bioperl.org>
  60
  61 rather than to the module maintainer directly. Many experienced and
  62 reponsive experts will be able look at the problem and quickly
  63 address it. Please include a thorough description of the problem
  64 with code and data examples if at all possible.
  65
  66 =head2 Reporting Bugs
  67
  68 Report bugs to the Bioperl bug tracking system to help us keep track
  69 the bugs and their resolution.  Bug reports can be submitted via the
  70 web:
  71
  72   https://github.com/bioperl/bioperl-live/issues
  73
  74 =head1 AUTHOR - Hilmar Lapp, Jason Stajich
  75
  76 Email Hilmar Lapp E<lt>hlapp@gmx.netE<gt>, Jason Stajich E<lt>jason@bioperl.orgE<gt>
  77
  78 =head1 APPENDIX
  79
  80 The rest of the documentation details each of the object
  81 methods. Internal methods are usually preceded with a _
  82
  83 =cut
  84
  85 package Bio::Factory::SeqAnalysisParserFactoryI;
  86 use strict;
  87
  88 use Carp;
  89
  90 use base qw(Bio::Root::RootI);
  91
  92 =head2 get_parser
  93
  94  Title   : get_parser
  95  Usage   : $factory->get_parser(-input=>$inputobj,
  96                                 [ -params=>[@params] ],
  97                                 -method => $method)
  98  Function: Creates and returns a parser object for the given input and method.
  99            The type of input which is suitable depends on the implementation,
 100            but a good-style implementation should allow both file names and
 101            streams (filehandles).
 102
 103            A particular implementation may not be able to create a parser for
 104            the requested method. In this case it shall return undef.
 105
 106            Parameters (-params argument) are passed on to the parser object
 107            and therefore are specific to the parser to be created. An
 108            implementation of this interface should make this argument optional.
 109  Example :
 110  Returns : A Bio::SeqAnalysisParserI implementing object.
 111  Args    : B<input>  - object/file where analysis results are coming from,
 112            B<params> - parameter to use when parsing/running analysis
 113            B<method> - method of analysis
 114
 115 =cut
 116
 117 sub get_parser {
 118     my ( $self, @args) = @_;
 119     $self->throw_not_implemented();
 120 }
 121
 122 1;