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.\" ========================================================================
.\"
.IX Title "Bio::Seq::LargeLocatableSeq 3pm"
.TH Bio::Seq::LargeLocatableSeq 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.
.if n .ad l
.nh
.SH "NAME"
Bio::Seq::LargeLocatableSeq \- LocatableSeq object that stores sequence as
files in the tempdir
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 6
\&  # normal primary seq usage
\&    use Bio::Seq::LargeLocatableSeq;
\&    my $seq = Bio::Seq::LargeLocatableSeq\->new(\-seq => "CAGT\-GGT",
\&                                              \-id  => "seq1",
\&                                              \-start => 1,
\&                                              \-end   => 7);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Bio::Seq::LargeLocatableSeq \- object with start/end points on it that
can be projected into a \s-1MSA\s0 or have coordinates relative to another
seq.
.PP
This object, unlike Bio::LocatableSeq, stores a sequence as a series
of files in a temporary directory. The aim is to allow someone the
ability to store very large sequences (eg, > 100MBases) in a file
system without running out of memory (eg, on a 64 \s-1MB\s0 real memory
machine!).
.PP
Of course, to actually make use of this functionality, the programs
which use this object \fBmust\fR not call \f(CW$primary_seq\fR\->seq otherwise
the entire sequence will come out into memory and probably crash your
machine. However, calls like \f(CW$primary_seq\fR\->subseq(10,100) will cause
only 90 characters to be brought into real memory.
.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
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 "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Usage   : my $obj = Bio::Seq::LargeLocatableSeq\->new();
\& Function: Builds a new Bio::Seq::LargeLocatableSeq object
\& Returns : an instance of Bio::Seq::LargeLocatableSeq
\& Args    :
.Ve
.SS "length"
.IX Subsection "length"
.Vb 6
\& Title   : length
\& Usage   :
\& Function:
\& Example :
\& Returns :
\& Args    :
.Ve
.SS "seq"
.IX Subsection "seq"
.Vb 6
\& Title   : seq
\& Usage   :
\& Function:
\& Example :
\& Returns :
\& Args    :
.Ve
.SS "subseq"
.IX Subsection "subseq"
.Vb 6
\& Title   : subseq
\& Usage   :
\& Function:
\& Example :
\& Returns :
\& Args    :
.Ve
.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 LargeLocatableSeq 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
.SS "_filename"
.IX Subsection "_filename"
.Vb 6
\& Title   : _filename
\& Usage   : $obj\->_filename($newval)
\& Function:
\& Example :
\& Returns : value of _filename
\& Args    : newvalue (optional)
.Ve
.SS "alphabet"
.IX Subsection "alphabet"
.Vb 6
\& Title   : alphabet
\& Usage   : $obj\->alphabet($newval)
\& Function:
\& Example :
\& Returns : value of alphabet
\& Args    : newvalue (optional)
.Ve