Bio::Seq LargeSeqI
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Summary
Bio::Seq::LargeSeqI - Interface class for sequences that cache their
residues in a temporary file
Package variables
No package variables defined.
Inherit
Bio::Root::RootI
Synopsis
 #
Description
The interface class defines a group of sequence classes that do not
keep their sequence information in memory but store it in a file. This
makes it possible to work with very large files even with limited RAM.
The most important consequence of file caching for sequences is that
you do not want to inspect the sequence unless absolutely
necessary. These sequences typically override the length() method not
to check the sequence.
The seq() method is not resetable, if you want to add to the end of the
sequence you have to use add_sequence_as_string(), for any other sequence changes you'll
have to create a new object.
Methods
add_sequence_as_stringDescriptionCode
Methods description
add_sequence_as_stringcode    nextTop
 Title   : add_sequence_as_string
Usage : $seq->add_sequence_as_string("CATGAT");
Function: Appends additional residues to an existing object.
This allows one to build up a large sequence without
storing entire object in memory.
Returns : Current length of sequence
Args : string to append
Methods code
add_sequence_as_stringdescriptionprevnextTop
sub add_sequence_as_string {
    my ($self) = @_;
    $self->throw_not_implemented();
}


1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Albert VilellaTop
Email avilella-AT-gmail-DOT-com
CONTRIBUTORSTop
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _