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.
Included modules
Bio::DB::SeqI
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
_add_seqDescriptionCode
_remove_seqDescriptionCode
_update_seqDescriptionCode
write_seqDescriptionCode
Methods description
_add_seqcode    nextTop
 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($seq)
 Function: Updates a sequence
 Example : 
 Returns : will throw an exception if
           sequence is out of sync from expected val.
 Args    : a seq object that was retrieved from Bio::DB::UpdateableSeqI
write_seqcodeprevnextTop
  Title   : write_seq
  Usage   : write_seq(\@updatedseqs, \@addedseqs, \@deadseqs)
  Function: updates sequences in first array,
            adds sequences in the second array,
            and removes sequences in the third array.
  Example :
  Returns :
  Args    : arrays of sequence objects that must be obtained from
            Bio::DB::UpdateableSeqI.
Methods code
_add_seqdescriptionprevnextTop
sub _add_seq {
    my ($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) = @_;
    
    $self->throw("Abstract database call of _update_seq. Your database has not implemented this method!");
}
write_seqdescriptionprevnextTop
sub write_seq {
    my ($self) = @_;
    
    $self->throw("Abstract database call of write_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>
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 email
or the web:
    bioperl-bugs@bioperl.org                   
    http://bugzilla.bioperl.org/
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