lib/Bio/Factory/SequenceStreamI.pm

   1 #
   2 # BioPerl module for Bio::Factory::SequenceStreamI
   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::SequenceStreamI - Interface describing the basics of a Sequence Stream.
  17
  18 =head1 SYNOPSIS
  19
  20   # get a SequenceStreamI object somehow like with SeqIO
  21   use Bio::SeqIO;
  22   my $in = Bio::SeqIO->new(-file => '< fastafile');
  23   while( my $seq = $in->next_seq ) {
  24   }
  25
  26 =head1 DESCRIPTION
  27
  28 This interface is for describing objects which produces
  29 Bio::PrimarySeqI objects or processes Bio::PrimarySeqI objects to a
  30 data stream.
  31
  32 =head1 FEEDBACK
  33
  34 =head2 Mailing Lists
  35
  36 User feedback is an integral part of the evolution of this and other
  37 Bioperl modules. Send your comments and suggestions preferably to
  38 the Bioperl mailing list.  Your participation is much appreciated.
  39
  40   bioperl-l@bioperl.org                  - General discussion
  41   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  42
  43 =head2 Support
  44
  45 Please direct usage questions or support issues to the mailing list:
  46
  47 I<bioperl-l@bioperl.org>
  48
  49 rather than to the module maintainer directly. Many experienced and
  50 reponsive experts will be able look at the problem and quickly
  51 address it. Please include a thorough description of the problem
  52 with code and data examples if at all possible.
  53
  54 =head2 Reporting Bugs
  55
  56 Report bugs to the Bioperl bug tracking system to help us keep track
  57 of the bugs and their resolution. Bug reports can be submitted via the
  58 web:
  59
  60   https://github.com/bioperl/bioperl-live/issues
  61
  62 =head1 AUTHOR - Jason Stajich
  63
  64 Email jason@bioperl.org
  65
  66 =head1 APPENDIX
  67
  68 The rest of the documentation details each of the object methods.
  69 Internal methods are usually preceded with a _
  70
  71 =cut
  72
  73
  74 # Let the code begin...
  75
  76
  77 package Bio::Factory::SequenceStreamI;
  78
  79 use strict;
  80
  81 use base qw(Bio::Root::RootI);
  82
  83 =head2 next_seq
  84
  85  Title   : next_seq
  86  Usage   : $seq = stream->next_seq
  87  Function: Reads the next sequence object from the stream and returns it.
  88
  89            Certain driver modules may encounter entries in the stream that
  90            are either misformatted or that use syntax not yet understood
  91            by the driver. If such an incident is recoverable, e.g., by
  92            dismissing a feature of a feature table or some other non-mandatory
  93            part of an entry, the driver will issue a warning. In the case
  94            of a non-recoverable situation an exception will be thrown.
  95            Do not assume that you can resume parsing the same stream after
  96            catching the exception. Note that you can always turn recoverable
  97            errors into exceptions by calling $stream->verbose(2).
  98  Returns : a Bio::Seq sequence object
  99  Args    : none
 100
 101 See L<Bio::Root::RootI>
 102
 103 =cut
 104
 105 sub next_seq {
 106     shift->throw_not_implemented();
 107 }
 108
 109 =head2 write_seq
 110
 111  Title   : write_seq
 112  Usage   : $stream->write_seq($seq)
 113  Function: writes the $seq object into the stream
 114  Returns : 1 for success and 0 for error
 115  Args    : Bio::Seq object
 116
 117 =cut
 118
 119 sub write_seq {
 120     shift->throw_not_implemented();
 121 }
 122
 123 =head2 sequence_factory
 124
 125  Title   : sequence_factory
 126  Usage   : $seqio->sequence_factory($seqfactory)
 127  Function: Get the Bio::Factory::SequenceFactoryI
 128  Returns : Bio::Factory::SequenceFactoryI
 129  Args    : none
 130
 131
 132 =cut
 133
 134 sub sequence_factory{
 135     shift->throw_not_implemented();
 136 }
 137
 138 1;