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.\" ========================================================================
.\"
.IX Title "Bio::Seq::LargeSeqI 3pm"
.TH Bio::Seq::LargeSeqI 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::Seq::LargeSeqI \- Interface class for sequences that cache their
residues in a temporary file
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\& #
.Ve
.SH "DESCRIPTION"
.IX Header "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 \s-1RAM.\s0
.PP
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 \fBlength()\fR method not
to check the sequence.
.PP
The \fBseq()\fR method is not resettable, if you want to add to the end of the
sequence you have to use \fBadd_sequence_as_string()\fR, for any other sequence changes you'll
have to create a new object.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Albert Vilella"
.IX Header "AUTHOR - Albert Vilella"
Email avilella-AT-gmail-DOT-com
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "add_sequence_as_string"
.IX Subsection "add_sequence_as_string"
.Vb 7
\& 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
.Ve