Bio/Seq/LargeSeqI.pm

   1 #
   2 # BioPerl module for Bio::Seq::LargeSeqI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Albert Vilella
   7 #
   8 # Copyright Albert Vilella
   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::Seq::LargeSeqI - Interface class for sequences that cache their
  17 residues in a temporary file
  18
  19 =head1 SYNOPSIS
  20
  21  #
  22
  23 =head1 DESCRIPTION
  24
  25 The interface class defines a group of sequence classes that do not
  26 keep their sequence information in memory but store it in a file. This
  27 makes it possible to work with very large files even with limited RAM.
  28
  29 The most important consequence of file caching for sequences is that
  30 you do not want to inspect the sequence unless absolutely
  31 necessary. These sequences typically override the length() method not
  32 to check the sequence.
  33
  34 The seq() method is not resetable, if you want to add to the end of the
  35 sequence you have to use add_sequence_as_string(), for any other sequence changes you'll
  36 have to create a new object.
  37
  38 =head1 FEEDBACK
  39
  40 =head2 Mailing Lists
  41
  42 User feedback is an integral part of the evolution of this and other
  43 Bioperl modules. Send your comments and suggestions preferably to
  44 the Bioperl mailing list.  Your participation is much appreciated.
  45
  46   bioperl-l@bioperl.org                  - General discussion
  47   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  48
  49 =head2 Support
  50
  51 Please direct usage questions or support issues to the mailing list:
  52
  53 I<bioperl-l@bioperl.org>
  54
  55 rather than to the module maintainer directly. Many experienced and
  56 reponsive experts will be able look at the problem and quickly
  57 address it. Please include a thorough description of the problem
  58 with code and data examples if at all possible.
  59
  60 =head2 Reporting Bugs
  61
  62 Report bugs to the Bioperl bug tracking system to help us keep track
  63 of the bugs and their resolution. Bug reports can be submitted via
  64 email or the web:
  65
  66   https://github.com/bioperl/bioperl-live/issues
  67
  68 =head1 AUTHOR - Albert Vilella
  69
  70 Email avilella-AT-gmail-DOT-com
  71
  72 =head1 CONTRIBUTORS
  73
  74 Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
  75
  76 =head1 APPENDIX
  77
  78 The rest of the documentation details each of the object methods.
  79 Internal methods are usually preceded with a _
  80
  81 =cut
  82
  83
  84 # Let the code begin...
  85
  86
  87 package Bio::Seq::LargeSeqI;
  88 use strict;
  89
  90
  91 use base qw(Bio::Root::RootI);
  92
  93
  94 =head2 add_sequence_as_string
  95
  96  Title   : add_sequence_as_string
  97  Usage   : $seq->add_sequence_as_string("CATGAT");
  98  Function: Appends additional residues to an existing  object.
  99            This allows one to build up a large sequence without
 100            storing entire object in memory.
 101  Returns : Current length of sequence
 102  Args    : string to append
 103
 104 =cut
 105
 106 sub add_sequence_as_string {
 107     my ($self) = @_;
 108     $self->throw_not_implemented();
 109 }
 110
 111
 112 1;