Bio::DB SeqVersion
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Summary
Bio::DB::SeqVersion - front end to querying databases for identifier
versions
Package variables
Privates (from "my" definitions)
$DEFAULTIDTYPE = 'gi'
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
newDescriptionCode
get_recentDescriptionCode
get_allDescriptionCode
_load_seqversion_moduleDescriptionCode
default_id_typeDescriptionCode
Methods description
new()code    nextTop
 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'
get_recent()codeprevnextTop
 Usage   :
Function:
Example :
Returns :
Args :
get_all()codeprevnextTop
 Usage   :
Function:
Example :
Returns :
Args :
_load_seqversion_modulecodeprevnextTop
 Title   : _load_seqversion_module
Usage : Used internally
Function: Loads up a module at run time on demand
Example :
Returns :
Args : Name of identifier type
default_id_typecodeprevnextTop
 Title   : default_id_type
Usage : my $type = $self->default_id_type
Function: Returns default identifier type for this module
Returns : string
Args : none
Methods code
newdescriptionprevnextTop
sub new {
  my($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::$type"->new(%param); }
}
get_recentdescriptionprevnextTop
sub get_recent {
  my ($self,@args) = @_;
  $self->throw_not_implemented();
}
get_alldescriptionprevnextTop
sub get_all {
	my ($self,@args) = @_;
	$self->throw_not_implemented();
}
_load_seqversion_moduledescriptionprevnextTop
sub _load_seqversion_module {
	my ($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;
}
default_id_typedescriptionprevnextTop
sub default_id_type {
    return $DEFAULTIDTYPE;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
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
of the bugs and their resolution. Bug reports can be submitted via
the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Brian OsborneTop
Email bosborne at alum.mit.edu
CONTRIBUTORSTop
Torsten Seemann - torsten.seemann AT infotech.monash.edu.au
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _