Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Seq::LargePrimarySeq - PrimarySeq object that stores sequence as files in the tempdir
       (as found by File::Temp) or the default method in Bio::Root::Root


         # normal primary seq usage


       This object 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 MB real memory machine!).

       Of course, to actually make use of this functionality, the programs which use this object
       must not call $primary_seq->seq otherwise the entire sequence will come out into memory
       and probably paste your machine. However, calls $primary_seq->subseq(10,100) will cause
       only 90 characters to be brought into real memory.


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AUTHOR - Ewan Birney, Jason Stajich

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       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

        Title   : length
        Usage   :
        Example :
        Returns :
        Args    :

        Title   : seq
        Usage   :
        Example :
        Returns :
        Args    :

        Title   : subseq
        Usage   :
        Example :
        Returns :
        Args    :

        Title   : add_sequence_as_string
        Usage   : $seq->add_sequence_as_string("CATGAT");
        Function: Appends additional residues to an existing LargePrimarySeq 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

        Title   : _filename
        Usage   : $obj->_filename($newval)
        Example :
        Returns : value of _filename
        Args    : newvalue (optional)

        Title   : alphabet
        Usage   : $obj->alphabet($newval)
        Example :
        Returns : value of alphabet
        Args    : newvalue (optional)