Toolbar

Summary

Bio::Biblio::BiblioBase - An abstract base for other biblio classes

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

 # do not instantiate this class directly

Description

It is a base class where all other biblio data storage classes inherit
from. It does not reflect any real-world object, it exists only for
convenience, in order to have a place for shared code. The new() class method constructs a new biblio storage object. It
accepts list of named arguments - the same names as attribute names
prefixed with a minus sign. Available attribute names are listed in
the documentation of the individual biblio storage objects. All attribute names can be used as method names. When used without any
parameter the method returns current value of the attribute (or
undef), when used with a value the method sets the attribute to this
value and also returns it back. The set method also checks if the type
of the new value is correct. If there is a need for new attributes, create your own class which
usually inherits from Bio::Biblio::Ref. For new types of providers
and journals, let your class inherit directly from this
Bio::Biblio::BiblioBase class.

Methods

Methods description

None available.

Methods code

sub AUTOLOAD {

    my ($self, $newval) = @_;

    if ($AUTOLOAD =~ /.*::(\w+)/ && $self->_accessible ("_$1")) {
	my $attr_name = "_$1";
	my $attr_type = $self->_attr_type ($attr_name);
	my $ref_sub =
	    sub {
		my ($this, $new_value) = @_;
		return $this->{$attr_name} unless defined $new_value;

		# here we continue with 'set' method
		my ($newval_type) = ref ($new_value) || 'string';
		my ($expected_type) = $attr_type || 'string';
#		$this->throw ("In method $AUTOLOAD, trying to set a value of type '$newval_type' but '$expected_type' is expected.")
		$this->throw ($this->_wrong_type_msg ($newval_type, $expected_type, $AUTOLOAD))
		    unless ($newval_type eq $expected_type) or
		      UNIVERSAL::isa ($new_value, $expected_type);
                       
		$this->{$attr_name} = $new_value;
		return $new_value;
	    };

        no strict 'refs'; 
        *{$AUTOLOAD} = $ref_sub;
        use strict 'refs'; 
        return $ref_sub->($self, $newval);
    }

    $self->throw ("No such method: $AUTOLOAD");
}

# 

}

sub _accessible {

 shift->throw_not_implemented();

}

sub _attr_type {

 shift->throw_not_implemented();

}

sub _wrong_type_msg {

    my ($self, $given_type, $expected_type, $method) = @_;
    my $msg = 'In method ';
    if (defined $method) {
	$msg .= $method;
    } else {
	$msg .= (caller(1))[3];
    }
    return ("$msg: Trying to set a value of type '$given_type' but '$expected_type' is expected.");
}

#
# probably just for debugging
# TBD: to decide...
#

}

sub new {

    my ($caller, @args) = @_;
    my $class = ref ($caller) || $caller;

    # create and bless a new instance    
    my ($self) = $class->SUPER::new (@args);	

    # make a hashtable from @args
    my %param = @args;
    @param { map { lc $_ } keys %param } = values %param; # lowercase keys

    # set all @args into this object with 'set' values;
    # change '-key' into '_key', and making keys lowercase
    my $new_key;
    foreach my $key (keys %param) {
	($new_key = $key) =~ s/-/_/og;   # change it everywhere, why not
        my $method = lc (substr ($new_key, 1));   # omitting the first '_'
        no strict 'refs'; 
        $method->($self, $param { $key });
    }

    # done
    return $self;
}

#
# set methods test whether incoming value is of a correct type;
# here we return message explaining it
#

}

sub print_me {

    my ($self) = @_;
    require Data::Dumper;
    return Data::Dumper->Dump ( [$self], ['Citation']);
}

1;
__END__

}

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/MailList.shtml  - About the mailing lists

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
email or the web:

  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/

Martin Senger (senger@ebi.ac.uk)

Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
This module is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.

This software is provided "as is" without warranty of any kind.