Bio::DB UpdateableSeqI
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Summary
Bio::DB::UpdateableSeqI - An interface for writing to a database of sequences.
Package variables
No package variables defined.
Inherit
Bio::DB::SeqI
Synopsis
No synopsis!
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.
Methods
write_seqDescriptionCode
_add_seqDescriptionCode
_remove_seqDescriptionCode
_update_seqDescriptionCode
Methods description
write_seqcode    nextTop
  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_seqcodeprevnextTop
 Title   : _add_seq
 Usage   : _add_seq($seq)
 Function: Adds a new sequence
 Example : 
 Returns : will throw an exception if
           sequences accession number already exists
 Args    : a new seq object - should have an accession number
_remove_seqcodeprevnextTop
 Title   : _remove_seq
 Usage   : _remove_seq($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_seqcodeprevnextTop
 Title   : _update_seq
 Usage   : _update_seq($seq)
 Function: Updates a sequence
 Example : 
 Returns : will throw an exception if
           sequence is out of sync from expected val.
 Args    : a seq object that was retrieved from Bio::DB::UpdateableSeqI
Methods code
write_seqdescriptionprevnextTop
sub write_seq {
    my ($self) = @_;
    
    $self->throw("Abstract database call of write_seq. Your database has not implemented this method!");
}
_add_seqdescriptionprevnextTop
sub _add_seq {
    my ($self ) = @_;
    
    $self->throw("Abstract database call of _add_seq. Your database has not implemented this method!");
}
_remove_seqdescriptionprevnextTop
sub _remove_seq {
    my ($self) = @_;
    
    $self->throw("Abstract database call of _remove_seq. Your database has not implemented this method!");
}
_update_seqdescriptionprevnextTop
sub _update_seq {
    my ($self) = @_;
    
    $self->throw("Abstract database call of _update_seq. Your database has not implemented this method!");
}
General documentation
SYNOPSIS Top
    # 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";
    }
AUTHORTop
Jason Stajich <jason@bioperl.org>
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
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Methods inherieted from Bio::DB::RandomAccessITop
get_Seq_by_idTop
 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_accTop
 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::SeqITop
get_PrimarySeq_streamTop
 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_idsTop
 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_idTop
 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