Bio/Seq/LargeSeqI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Seq::LargeSeqI
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Albert Vilella
   8 #
   9 # Copyright Albert Vilella
  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::Seq::LargeSeqI - Interface class for sequences that cache their
  18 residues in a temporary file
  19
  20 =head1 SYNOPSIS
  21
  22  #
  23
  24 =head1 DESCRIPTION
  25
  26 The interface class defines a group of sequence classes that do not
  27 keep their sequence information in memory but store it in a file. This
  28 makes it possible to work with very large files even with limited RAM.
  29
  30 The most important consequence of file caching for sequences is that
  31 you do not want to inspect the sequence unless absolutely
  32 necessary. These sequences typically override the length() method not
  33 to check the sequence.
  34
  35 The seq() method is not resetable, if you want to add to the end of the
  36 sequence you have to use add_sequence_as_string(), for any other sequence chnages you'll
  37 have to create a new object.
  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 L<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
  65 email or the web:
  66
  67   http://bugzilla.open-bio.org/
  68
  69 =head1 AUTHOR - Albert Vilella
  70
  71 Email avilella-AT-gmail-DOT-com
  72
  73 =head1 CONTRIBUTORS
  74
  75 Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
  76
  77 =head1 APPENDIX
  78
  79 The rest of the documentation details each of the object methods.
  80 Internal methods are usually preceded with a _
  81
  82 =cut
  83
  84
  85 # Let the code begin...
  86
  87
  88 package Bio::Seq::LargeSeqI;
  89 use strict;
  90
  91
  92 use base qw(Bio::Root::RootI);
  93
  94
  95 =head2 add_sequence_as_string
  96
  97  Title   : add_sequence_as_string
  98  Usage   : $seq->add_sequence_as_string("CATGAT");
  99  Function: Appends additional residues to an existing  object.
 100            This allows one to build up a large sequence without
 101            storing entire object in memory.
 102  Returns : Current length of sequence
 103  Args    : string to append
 104
 105 =cut
 106
 107 sub add_sequence_as_string {
 108     my ($self) = @_;
 109     $self->throw_not_implemented();
 110 }
 111
 112
 113 1;