Bio/Factory/SequenceStreamI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Factory::SequenceStreamI
   4 #
   5 # Cared for by Jason Stajich <jason@bioperl.org>
   6 #
   7 # Copyright Jason Stajich
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::Factory::SequenceStreamI - Interface describing the basics of a Sequence Stream.
  16
  17 =head1 SYNOPSIS
  18
  19   # get a SequenceStreamI object somehow like with SeqIO
  20   use Bio::SeqIO;
  21   my $in = Bio::SeqIO->new(-file => '< fastafile');
  22   while( my $seq = $in->next_seq ) {
  23   }
  24
  25 =head1 DESCRIPTION
  26
  27 This interface is for describing objects which produces
  28 Bio::PrimarySeqI objects or processes Bio::PrimarySeqI objects to a
  29 data stream.
  30
  31 =head1 FEEDBACK
  32
  33 =head2 Mailing Lists
  34
  35 User feedback is an integral part of the evolution of this and other
  36 Bioperl modules. Send your comments and suggestions preferably to
  37 the Bioperl mailing list.  Your participation is much appreciated.
  38
  39   bioperl-l@bioperl.org                  - General discussion
  40   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  41
  42 =head2 Reporting Bugs
  43
  44 Report bugs to the Bioperl bug tracking system to help us keep track
  45 of the bugs and their resolution. Bug reports can be submitted via the
  46 web:
  47
  48   http://bugzilla.open-bio.org/
  49
  50 =head1 AUTHOR - Jason Stajich
  51
  52 Email jason@bioperl.org
  53
  54 =head1 APPENDIX
  55
  56 The rest of the documentation details each of the object methods.
  57 Internal methods are usually preceded with a _
  58
  59 =cut
  60
  61
  62 # Let the code begin...
  63
  64
  65 package Bio::Factory::SequenceStreamI;
  66 use strict;
  67
  68 use base qw(Bio::Root::RootI);
  69
  70 =head2 next_seq
  71
  72  Title   : next_seq
  73  Usage   : $seq = stream->next_seq
  74  Function: Reads the next sequence object from the stream and returns it.
  75
  76            Certain driver modules may encounter entries in the stream that
  77            are either misformatted or that use syntax not yet understood
  78            by the driver. If such an incident is recoverable, e.g., by
  79            dismissing a feature of a feature table or some other non-mandatory
  80            part of an entry, the driver will issue a warning. In the case
  81            of a non-recoverable situation an exception will be thrown.
  82            Do not assume that you can resume parsing the same stream after
  83            catching the exception. Note that you can always turn recoverable
  84            errors into exceptions by calling $stream->verbose(2).
  85  Returns : a Bio::Seq sequence object
  86  Args    : none
  87
  88 See L<Bio::Root::RootI>
  89
  90 =cut
  91
  92 sub next_seq {
  93     shift->throw_not_implemented();
  94 }
  95
  96 =head2 write_seq
  97
  98  Title   : write_seq
  99  Usage   : $stream->write_seq($seq)
 100  Function: writes the $seq object into the stream
 101  Returns : 1 for success and 0 for error
 102  Args    : Bio::Seq object
 103
 104 =cut
 105
 106 sub write_seq {
 107     shift->throw_not_implemented();
 108 }
 109
 110 =head2 sequence_factory
 111
 112  Title   : sequence_factory
 113  Usage   : $seqio->sequence_factory($seqfactory)
 114  Function: Get the Bio::Factory::SequenceFactoryI
 115  Returns : Bio::Factory::SequenceFactoryI
 116  Args    : none
 117
 118
 119 =cut
 120
 121 sub sequence_factory{
 122     shift->throw_not_implemented();
 123 }
 124
 125 1;