File Coverage

blib/lib/Lingua/BioYaTeA.pm

Criterion	Covered	Total	%
statement	25	33	75.7
branch	4	6	66.6
condition	1	3	33.3
subroutine	6	6	100.0
pod	2	2	100.0
total	38	50	76.0

package Lingua::BioYaTeA;

use strict;
use warnings;
use utf8;

=encoding utf8

=head1 NAME

Lingua::BioYaTeA - Perl extension of Lingua::YaTeA for extracting terms from a biomedical corpus.

=head1 SYNOPSIS

use Lingua::BioYaTeA;

my %config = Lingua::YaTeA::load_config($rcfile);

$yatea = Lingua::YaTeA->new($config{"OPTIONS"}, \%config);

$corpus = Lingua::YaTeA::Corpus->new($corpus_path,$yatea->getOptionSet,$yatea->getMessageSet);

$yatea->termExtraction($corpus);


=head1 DESCRIPTION

This module is the main module of the software BioYaTeA which is an
adaptation of YaTeA (C) for biomedical text.

The module inherits from all the class and attributes of
C. The input and output files but also the
configuration files follow the same format as YaTeA.
The tuning concerns the configuration files (in the directory
C.

Default configuration is assumed to be C.

For the use of BioYaTeA, see the documentation with the script
C.

=head1 METHODS

=head2 new()

    new($command_line_options_h,$system_config_h);

The methods creates a new term extractor and sets options from the
command line (C<$commend_line_options_h>) and options defined in the
hashtable (C<$system_config_h>) given by address. The methods returns
the created object.

=head2 load_config()

    load_config($rcfile);

The method loads the configuration of the NLP Platform by reading the
configuration file given in argument. It returns the hashtable
containing the configuration.


=head1 SEE ALSO

Documentation of Lingua::YaTeA

=head1 AUTHORS

Wiktoria Golik , Zorana Ratkovic , Robert Bossy , Claire Nédellec , Thierry Hamon

=head1 LICENSE

Copyright (C) 2012 Wiktoria Golik, Zorana Ratkovic, Robert Bossy, Claire Nédellec and Thierry Hamon

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.8.6 or,
at your option, any later version of Perl 5 you may have available.


=cut

use Lingua::YaTeA;

our @ISA = qw(Lingua::YaTeA);

our $VERSION='0.11';

sub new {
    my ($class,$command_line_options_h,$system_config_h) = @_;

    if ($Lingua::YaTeA::VERSION < 0.6) {
	warn "***************************************************************************\n";
	warn "Something wrong: attempting to use a version Lingua::YaTeA greater than 0.6\n";
	warn "while found version is " . $Lingua::YaTeA::VERSION . "\n";
        warn "Please install the right version\n\n";
	warn "Exiting...\n";
	warn "***************************************************************************\n";
	exit -1;
    }
    my $this = $class->SUPER::new($command_line_options_h,$system_config_h);
    bless ($this,$class);

    return $this;
}

sub load_config {
    # my ($class, $rcfile) = @_;

    my $rcfile;
    my $class = shift;

    if (@_) {
	$rcfile = shift;
    } else {
	$rcfile = $class;
    }


    if ((! defined $rcfile) || ($rcfile eq "")) {
	$rcfile = "/etc/bioyatea/bioyatea.rc";
    }

    print STDERR "$rcfile : $class\n";

    return(Lingua::YaTeA::load_config($rcfile));
}

1;