Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::DB::UpdateableSeqI - An interface for writing to a database of sequences.

SYNOPSIS

           # get a Bio::DB::UpdateableSeqI somehow
           eval {
               my ( @updatedseqs, @newseqs, @deadseqs);
               my $seq = $db->get_Seq_by_id('ROA1_HUMAN');
               $seq->desc('a new description');

               push @updatedseqs, $seq;

               $db->write_seq(\@updatedseqs, \@newseqs, \@deadseqs);
           };
           if( $@ ) {
               print STDERR "an error when trying to write seq : $@\n";
           }

DESCRIPTION

       This module seeks to provide a simple method for pushing sequence changes back to a
       Sequence Database - which can be an SQL compliant database, a file based database, AceDB,
       etc.

AUTHOR

       Jason Stajich <jason@bioperl.org>

   Support
       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 Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

APPENDIX

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

   write_seq
         Title   : write_seq
         Usage   : write_seq(\@updatedseqs, \@addedseqs, \@deadseqs)
         Function: updates sequences in first array,
                   adds sequences in the second array,
                   and removes sequences in the third array.
         Example :
         Returns :
         Args    : arrays of sequence objects that must be obtained from
                   Bio::DB::UpdateableSeqI.

   _add_seq
        Title   : _add_seq
        Usage   : _add_seq($seq)
        Function: Adds a new sequence
        Example :
        Returns : will throw an exception if
                  sequences accession number already exists
        Args    : a new seq object - should have an accession number

   _remove_seq
        Title   : _remove_seq
        Usage   : _remove_seq($seq)
        Function: Removes an existing sequence
        Example :
        Returns : will throw an exception if
                  sequence does not exists for the primary_id
        Args    : a seq object that was retrieved from Bio::DB::UpdateableSeqI

   _update_seq
        Title   : _update_seq
        Usage   : _update_seq($seq)
        Function: Updates a sequence
        Example :
        Returns : will throw an exception if
                  sequence is out of sync from expected val.
        Args    : a seq object that was retrieved from Bio::DB::UpdateableSeqI

Methods inherieted from Bio::DB::RandomAccessI

   get_Seq_by_id
        Title   : get_Seq_by_id
        Usage   : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
        Function: Gets a Bio::Seq object by its name
        Returns : a Bio::Seq object
        Args    : the id (as a string) of a sequence
        Throws  : "id does not exist" exception

   get_Seq_by_acc
        Title   : get_Seq_by_acc
        Usage   : $seq = $db->get_Seq_by_acc('X77802');
        Function: Gets a Bio::Seq object by accession number
        Returns : A Bio::Seq object
        Args    : accession number (as a string)
        Throws  : "acc does not exist" exception

Methods inheirited from Bio::DB::SeqI

   get_PrimarySeq_stream
        Title   : get_PrimarySeq_stream
        Usage   : $stream = get_PrimarySeq_stream
        Function: Makes a Bio::DB::SeqStreamI compliant object
                  which provides a single method, next_primary_seq
        Returns : Bio::DB::SeqStreamI
        Args    : none

   get_all_primary_ids
        Title   : get_all_ids
        Usage   : @ids = $seqdb->get_all_primary_ids()
        Function: gives an array of all the primary_ids of the
                  sequence objects in the database. These
                  maybe ids (display style) or accession numbers
                  or something else completely different - they
                  *are not* meaningful outside of this database
                  implementation.
        Example :
        Returns : an array of strings
        Args    : none

   get_Seq_by_primary_id
        Title   : get_Seq_by_primary_id
        Usage   : $seq = $db->get_Seq_by_primary_id($primary_id_string);
        Function: Gets a Bio::Seq object by the primary id. The primary
                  id in these cases has to come from $db->get_all_primary_ids.
                  There is no other way to get (or guess) the primary_ids
                  in a database.

                  The other possibility is to get Bio::PrimarySeqI objects
                  via the get_PrimarySeq_stream and the primary_id field
                  on these objects are specified as the ids to use here.
        Returns : A Bio::Seq object
        Args    : accession number (as a string)
        Throws  : "acc does not exist" exception