Bio/Factory/SequenceFactoryI.pm

   1 #
   2 # BioPerl module for Bio::Factory::SequenceFactoryI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Jason Stajich <jason@bioperl.org>
   7 #
   8 # Copyright Jason Stajich
   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::SequenceFactoryI - This interface allows for generic building of sequences in factories which create sequences (like SeqIO)
  17
  18 =head1 SYNOPSIS
  19
  20 # do not use this object directly it is an interface
  21 # get a Bio::Factory::SequenceFactoryI object like
  22
  23     use Bio::Seq::SeqFactory;
  24     my $seqbuilder = Bio::Seq::SeqFactory->new('-type' => 'Bio::PrimarySeq');
  25
  26     my $seq = $seqbuilder->create(-seq => 'ACTGAT',
  27                                   -display_id => 'exampleseq');
  28
  29     print "seq is a ", ref($seq), "\n";
  30
  31 =head1 DESCRIPTION
  32
  33 A generic way to build Sequence objects via a pluggable factory.  This
  34 reduces the amount of code that looks like
  35
  36   if( $type  eq 'Bio::PrimarySeq' ) { ... }
  37   elsif( $type eq 'Bio::Seq::RichSeq' ) { ... }
  38
  39 =head1 FEEDBACK
  40
  41 =head2 Mailing Lists
  42
  43 User feedback is an integral part of the evolution of this and other
  44 Bioperl modules. Send your comments and suggestions preferably to
  45 the Bioperl mailing list.  Your participation is much appreciated.
  46
  47   bioperl-l@bioperl.org                  - General discussion
  48   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  49
  50 =head2 Support
  51
  52 Please direct usage questions or support issues to the mailing list:
  53
  54 I<bioperl-l@bioperl.org>
  55
  56 rather than to the module maintainer directly. Many experienced and
  57 reponsive experts will be able look at the problem and quickly
  58 address it. Please include a thorough description of the problem
  59 with code and data examples if at all possible.
  60
  61 =head2 Reporting Bugs
  62
  63 Report bugs to the Bioperl bug tracking system to help us keep track
  64 of the bugs and their resolution. Bug reports can be submitted via the
  65 web:
  66
  67   https://github.com/bioperl/bioperl-live/issues
  68
  69 =head1 AUTHOR - Jason Stajich
  70
  71 Email jason-at-bioperl.org
  72
  73 =head1 APPENDIX
  74
  75 The rest of the documentation details each of the object methods.
  76 Internal methods are usually preceded with a _
  77
  78 =cut
  79
  80
  81 # Let the code begin...
  82
  83
  84 package Bio::Factory::SequenceFactoryI;
  85
  86 use strict;
  87
  88 use base qw(Bio::Factory::ObjectFactoryI);
  89
  90 =head2 create
  91
  92  Title   : create
  93  Usage   : my $seq = $seqbuilder->create(-seq => 'CAGT',
  94                                          -id => 'name');
  95  Function: Instantiates new Bio::PrimarySeqI (or one of its child classes)
  96            This object allows us to genericize the instantiation of sequence
  97            objects.
  98  Returns : Bio::PrimarySeqI
  99  Args    : initialization parameters specific to the type of sequence
 100            object we want.  Typically
 101            -seq        => $str,
 102            -display_id => $name
 103
 104 =cut
 105
 106 1;