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

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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 # do not instantiate this class directly

DESCRIPTION

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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.

new()

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.

Accessors

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.

Custom classes

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.

FEEDBACK

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Mailing Lists

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

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 Bugs

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

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Martin Senger (senger@ebi.ac.uk)

COPYRIGHT

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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.

DISCLAIMER

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

BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Biblio::BiblioBase
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Martin Senger <senger@ebi.ac.uk>
# For copyright and disclaimer see below.

# POD documentation - main docs before the code



# Let the code begin...


package Bio::Biblio::BiblioBase;
use strict;
use vars qw($AUTOLOAD);


use base qw(Bio::Root::Root);

# these methods should not be called here;
# they should be implemented by a subclass
sub _accessible { shift->throw_not_implemented(); }
sub _attr_type { shift->throw_not_implemented(); }

#
# deal with 'set_' and 'get_' methods
#
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 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 _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 print_me {
    my ($self) = @_;
    require Data::Dumper;
    return Data::Dumper->Dump ( [$self], ['Citation']);
}

1;
__END__