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Summary

Bio::DB::SeqVersion - front end to querying databases for identifier
versions

Package variables

Inherit

Bio::Root::Root Bio::WebAgent

Synopsis

  use Bio::DB::SeqVersion;

  my $query = Bio::DB::SeqVersion->new(-type => 'gi');

  my @all_gis = $query->get_all(2);

  my $live_gi = $query->get_recent(2);

Description

The default type is 'gi'.

Methods

Methods description

 Usage   : my $obj = Bio::DB::SeqVersion->new();
 Function: Create a Bio::DB::SeqVersion object 
 Returns : An instance of Bio::DB::SeqVersion
 Args    : -type      Identifier namespace, default is 'gi'

 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : _load_seqversion_module
 Usage   : Used internally
 Function: Loads up a module at run time on demand
 Example :
 Returns :
 Args    : Name of identifier type

 Title   : default_id_type
 Usage   : my $type = $self->default_id_type
 Function: Returns default identifier type for this module
 Returns : string
 Args    : none

Methods code

sub new {

  my($class,@args) = @_;

  if( $class =~ /Bio::DB::SeqVersion::\S+/ ) {
    my ($self) = $class->SUPER::new(@args);
    $self->_initialize(@args);
    return $self;
  } 
  else {
    my %param = @args;
    @param{ map { lc $_ } keys %param } = values %param; # lowercase keys

    # we delete '-type' so it doesn't get passed to the sub-class constructor
    # note: delete() returns the value of the item deleted (undef if non-existent)
    my $type = lc( delete($param{'-type'}) || $DEFAULTIDTYPE );

    return unless( $class->_load_seqversion_module($type) );
    
    # we pass %param here, not @args, as we have filtered out -type
    return "Bio::DB::SeqVersion::$type"->new(%param);
  }

}

sub get_recent {

  my ($self,@args) = @_;
  $self->throw_not_implemented();

}

sub get_all {

	my ($self,@args) = @_;
	$self->throw_not_implemented();

}

sub _load_seqversion_module {

	my ($self,$db) = @_;
	my $module = "Bio::DB::SeqVersion::" . $db;
	my $ok;

	eval { $ok = $self->_load_module($module) };
	if ( $@ ) {
		print STDERR $@;
		print STDERR <<END;
$self: $module cannot be found
Exception $@
For more information about the Bio::DB::SeqVersion system please see
the Bio::DB::SeqVersion docs.
END
		;
	}
	return $ok;

}

sub default_id_type {

    return $DEFAULTIDTYPE;
}

1;

}

General documentation

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.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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.

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:

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

Email bosborne at alum.mit.edu

Torsten Seemann - torsten.seemann AT infotech.monash.edu.au

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