File Coverage

blib/lib/NanoB2B/NER.pm

Criterion	Covered	Total	%
statement	26	409	6.3
branch	0	136	0.0
condition	0	24	0.0
subroutine	9	19	47.3
pod	7	9	77.7
total	42	597	7.0

#!/usr/bin/perl
# NanoB2B::NER
# (Last Updated $Id: NER.pm,v 0.09 2018/01/18 16:33:33 charityml Exp $)
#
# Perl module that turns labeled text lines into
# ARFF files based on specified features
# that are extracted using MetaMap
# and runs through WEKA to average the results
#
# Copyright (c) 2017
#
# Megan Charity, Virginia Commonwealth University
# charityml at vcu.edu
#
# Bridget T. McInnes, Virginia Commonwealth University
# btmcinnes at vcu.edu
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to
#
# The Free Software Foundation, Inc.,
# 59 Temple Place - Suite 330,
# Boston, MA  02111-1307, USA.


=head1 NAME

NanoB2B::NER - turns labeled text lines into ARFF files based on
specified features that are extracted using MetaMap and runs
through WEKA to average the results

=head1 DESCRIPTION

This package turns labeled text lines into ARFF files based on
specified features that are extracted using MetaMap and runs
through WEKA to average the results

For more information please see the NanoB2B::NER.pm documentation.

=head1 SYNOPSIS

add synopsis

=head1 ABSTRACT

There is a critical need to automatically extract and synthesize knowledge and
trends in nanotechnology research from an exponentially increasing body of
literature. Engineered nanomaterials (ENMs), such as nanomedicines, are
continuously being discovered and Natural Language Processing approaches can
semi‐automate the cataloging of ENMs and their unique physico‐chemical
properties; automatically aggregate studies on their exposure and hazards;
and link the physicochemical properties to the measured effects.
The goal of this project is to develop a nanomedicine entity extraction system
to automatically identify nanomedicine physico-characteristics,
exposure and biological effects.

=head1 INSTALL

To install the module, run the following magic commands:

  perl Makefile.PL
  make
  make test
  make install

This will install the module in the standard location. You will, most
probably, require root privileges to install in standard system
directories. To install in a non-standard directory, specify a prefix
during the 'perl Makefile.PL' stage as:

  perl Makefile.PL PREFIX=/home/milk

It is possible to modify other parameters during installation. The
details of these can be found in the ExtUtils::MakeMaker
documentation. However, it is highly recommended not messing around
with other parameters, unless you know what you're doing.

=head1 FUNCTION DESCRIPTIONS
=cut

package NanoB2B::NER;

use 5.006;
use strict;
use warnings FATAL => 'all';

use NanoB2B::UniversalRoutines;
use NanoB2B::NER::Metaman;
use NanoB2B::NER::Arffman;
use NanoB2B::NER::Wekaman;
use NanoB2B::NER::Avgman;
use NanoB2B::NER::Modelman;

#the instances of the modules (named 'boy' because they are expendable and constantly changing - like Robin, BOY Wonder to BatMAN)
my $uniSub;
my $metaboy;
my $arffboy;
my $wekaboy;
my $avgboy;
my $modelboy;

our $VERSION = '1.01';

#option variables
my $debug = 0;

#for wcs
my $wcs_found = 1;

=head1 NAME

NanoB2B-NNER-PM::NER - The main file that runs all of the processes for NER

=head1 DESCRIPTION

This package turns nanoparticle texts into ARFF
files and WEKA accuracy files based on the nanoparticle characteristics
found from pre-annotated articles

=head1 VERSION

Version 1.01

=head1 INITIALIZING THE MODULE

To create an instance of the ner module, using default values
for all configuration options:

  use NanoB2B::NER;
  my %params =  ();
  	$params{'dir'} = "my_directory";
  	$params{'features'} = "ortho morph text pos cui sem";

  my $nner = new NanoB2B::NER(\%params);

=cut


# -------------------- Class methods start here --------------------

#  method to create a new NanpB2B-NNER-PM::NER object
#  output: $self <- an NER object
sub new {
    #grab class and parameters
    my $self = {};
    my $class = shift;
    return undef if(ref $class);
    my $params = shift;

    #bless this object - amen
    bless $self, $class;
    $self->_init($params);

    #retrieve parameters for universal-routines
    my %uniParams = ();
    $uniParams{'debug'} = $debug;
	$uniSub = NanoB2B::UniversalRoutines->new(\%uniParams);

	#return the object
    return $self;
}

#  method to initialize the NanoB2B::NER::Arffman object.
#  input : $parameters <- reference to a hash
#  output: (module variables to use in other parameters)
sub _init {
    my $self = shift;
    my $params = shift;

    $params = {} if(!defined $params);

    #get the parameters
    my $opt_dir 		= $params->{'dir'};
    my $opt_file 		= $params->{'file'};
    my $opt_sortbysize 	= $params->{'sortBySize'};
    my $opt_index 		= $params->{'index'};
    my $opt_debug 		= $params->{'debug'};
    my $opt_importmeta 	= $params->{'import_meta'};
    my $opt_features 	= $params->{'features'};
    my $opt_buckets 	= $params->{'buckets'};
    my $opt_stopwords 	= $params->{'stopwords'};
    my $opt_is_cui 		= $params->{'is_cui'};
    my $opt_sparse 		= $params->{'sparse_matrix'};
    my $opt_prefix 		= $params->{'prefix'};
    my $opt_suffix 		= $params->{'suffix'};
    my $opt_wcs 		= $params->{'wcs'};
    my $opt_wekatype 	= $params->{'weka_type'};
    my $opt_wekasize 	= $params->{'weka_size'};
	my $opt_metamaparguments = $params->{'metamap_arguments'};
	my $opt_model	    = $params->{'model'};


    #set the global variables

    #required variables
    if(defined $opt_dir){										#if using the entire directory
		$self->{program_dir} = $opt_dir;
	}else{
		print ("***ERROR: DIRECTORY NOT DEFINED!!***\n");
		exit(-1);
	}
	if(defined $opt_features){									#grab the features you want to use
		$self->{features} = $opt_features;
	}else{
		print("***ERROR: FEATURE SET NOT DEFINED!!***\n");
		exit(-1);
	}


	#not required variables
	if(defined $opt_file){										#if using one file
		$self->{program_file} = $opt_file;
	}

	if(defined $opt_debug){										#run the programs with debug mode on
		$self->{debug} = $opt_debug;
		$debug = $opt_debug;
	}else{
		$debug = 0;
	}

	if(defined $opt_stopwords){									#exclude stop words from arff vectors
		$self->{stopwords} = $opt_stopwords;
	}

	if(defined $opt_is_cui){									#if a word doesn't have a cui - don't make a vector
		$self->{is_cui} = $opt_is_cui;
	}else{
		$self->{is_cui} = 0;
	}

	if(defined $opt_sparse){									#decide to turn vector's into sparse format
		$self->{sparse_matrix} = $opt_sparse;
	}else{
		$self->{sparse_matrix} = 0;
	}

	if(defined $opt_importmeta){								#decide to import metamap or not
		$self->{import_meta} = $opt_importmeta;
	}else{
		$self->{import_meta} = 0;
	}

	if(defined $opt_prefix){									#get the word prefix character count
		$self->{prefix} = $opt_prefix;
	}else{
		$self->{prefix} = 3;
	}
	if(defined $opt_suffix){									#get the word suffix character count
		$self->{suffix} = $opt_suffix;
	}else{
		$self->{suffix} = 3;
	}

	if(defined $opt_wcs){										#check if to do worst-case-scenario backup
		$self->{wcs} = $opt_wcs;
		$wcs_found = 0;
	}

	if(defined $opt_wekatype){									#get the type of weka algorithm to run
		$self->{weka_type} = $opt_wekatype;
	}else{
		$self->{weka_type} = "weka.classifiers.bayes.NaiveBayes";
	}

	if(defined $opt_wekasize){									#set the memory allocation size for weka to run
		$self->{weka_size} = $opt_wekasize;
	}else{
		$self->{weka_size} = "-Xmx2G";
	}

	if(defined $opt_buckets){									#set the number of buckets to run for k-fold cross validation
		$self->{bucketsNum} = $opt_buckets;
	}else{
		$self->{bucketsNum} = 10;
	}

	if(defined $opt_index){										#start at a certain file given an index
		$self->{fileIndex} = $opt_index;
	}else{
		$self->{fileIndex} = 1;
	}

	if(defined $opt_sortbysize){								#start at a certain file given an index
		$self->{sortSize} = $opt_sortbysize;
	}else{
		$self->{sortSize} = 0;
	}
	if(defined $opt_metamaparguments){							#run metamap with specific arguments
		$self->{metamap_arguments} = $opt_metamaparguments;
	} else {
		$self->{metamap_arguments} = "-q";
	}

	if(defined $opt_model){
		$self->{model} = $opt_model;
	}else{
		$self->{model} = 0;
	}

	#error handling?
	if(defined $opt_file and $self->{fileIndex} > 1){
		print("***ERROR: Cannot have an index value for a single file!***\n");
		exit;
	}

	#check for out of bounds index
	opendir (my $DIR, $self->{program_dir}) or die $!;
	my @files = grep { $_ ne '.' and $_ ne '..' and substr($_, 0, 1) ne '_'} readdir $DIR;
	my $totFiles = @files;
	if($self->{fileIndex} > $totFiles){
		print("***ERROR: Index cannot be greater than the number of files in the directory!***\n");
		exit;
	}

}




#########################			THE MEATY STUFF			##########################

=head3 nerByFile

description:

  Runs the files specified in the parameters program_dir metamaps all the files, arffs all the files, wekas all the files, and averages all the files
  This NER method doesn't move on to the next file until all the methods have been used

input:

 None

output:

 Metamap files, ARFF file sets, Weka file sets, and Averaged Accuracy files

example:

  use NanoB2B::NER;
  my %params =  ();
  	$params{'dir'} = "my_directory";
  	$params{'features'} = "ortho morph text pos cui sem";

  my $nner = new NanoB2B::NER(\%params);
  $nner->nerByFile();

=cut

sub nerByFile{
	my $self = shift;

	#open the directory
	opendir (my $DIR, $self->{program_dir}) or die $!;

	#if not doing a single file
	if(!defined $self->{program_file}){
		my @files = grep { $_ ne '.' and $_ ne '..' and substr($_, 0, 1) ne '_'} readdir $DIR;	#get each file from the directory

		#sort by size?
		if($self->{sortSize}){
			@files = sortBySize($self, \@files);
		}
		#ner the files individually
		my $totalTags = @files;
		for(my $a = $self->{fileIndex}; $a <= $totalTags; $a++){
			$uniSub->printColorDebug("on_blue", "FILE #$a / $totalTags");
			my $tag = $files[$a - 1];

			#metamap the files if needed
			if(!$self->{import_meta}){
				$uniSub->printColorDebug("bold cyan", "---  METAMAP  ---\n");
				my %paramsm = ();
				$paramsm{'directory'} = $self->{program_dir};
				$paramsm{'index'} = $self->{index};
				$paramsm{'metamap_arguments'} = $self->{metamap_arguments};
				$paramsm{'debug'} = $debug;
				$metaboy = NanoB2B::NER::Metaman->new(\%paramsm);
				$metaboy->meta_file($tag);
			}

			#arff the file
			$uniSub->printColorDebug("bold magenta", "---    ARFF    ---\n");
				#define arffboy with the parameters
				my %paramsr = ();
				$paramsr{'directory'} = $self->{program_dir};
				$paramsr{'features'} = $self->{features};
				$paramsr{'bucketsNum'} = $self->{bucketsNum};
			    $paramsr{'debug'} = $debug;
				$paramsr{'prefix'} = $self->{prefix};
				$paramsr{'suffix'} = $self->{suffix};
			    $paramsr{'index'} = $self->{index};
			    $paramsr{'stopwords'} = $self->{stopwords};
			    $paramsr{'is_cui'} = $self->{is_cui};
			    $paramsr{'sparse_matrix'} = $self->{sparse_matrix};
			    if(!$wcs_found){
			   		$paramsr{'wcs'} = $self->{wcs};
			   		$wcs_found = 1;
			    }
				$arffboy = NanoB2B::NER::Arffman->new(\%paramsr);
			$arffboy->arff_file($tag);

			#weka the file
			if($self->{bucketsNum} > 1){
				$uniSub->printColorDebug("bold yellow", "---    WEKA    ---\n");
					#define wekaboy with the parameters
					my %paramsw = ();
					$paramsw{'directory'} = $self->{program_dir};
					$paramsw{'type'} = $self->{weka_type};
					$paramsw{'weka_size'} = $self->{weka_size};
					$paramsw{'features'} = $self->{features};
					$paramsw{'buckets'} = $self->{bucketsNum};
					$paramsw{'debug'} = $debug;
					$wekaboy = NanoB2B::NER::Wekaman->new(\%paramsw);
				$wekaboy->weka_file($tag);
			}

			#model the file
			if($self->{model}){
				$uniSub->printColorDebug("bold red", "---  MODEL  ---\n");
					my %paramsmo = ();
					$paramsmo{'directory'} = $self->{program_dir};
					$paramsmo{'type'} = $self->{weka_type};
					$paramsmo{'weka_size'} = $self->{weka_size};
					$paramsmo{'features'} = $self->{features};
					$paramsmo{'buckets'} = $self->{bucketsNum};
					$paramsmo{'debug'} = $debug;
					$modelboy = NanoB2B::NER::Modelman->new(\%paramsmo);
				$modelboy->make_model_file($tag);
			}

			#average the file
			if($self->{bucketsNum} > 1){
				$uniSub->printColorDebug("bold green", "---    AVG    ---\n");
					#define avgboy with the parameters
					my %paramsa = ();
					$paramsa{'directory'} = $self->{program_dir};
						my @a = split(/\./, $self->{weka_type});
					$paramsa{'weka_dir'} = $a[$#a];
					$paramsa{'features'} = $self->{features};
					$paramsa{'buckets'} = $self->{bucketsNum};
					$paramsa{'debug'} = $debug;
					$avgboy = NanoB2B::NER::Avgman->new(\%paramsa);
				$avgboy->avg_file($tag);
			}


			$uniSub->printColorDebug("on_blue", "##         FINISHED #$a - $tag!        ##");
		}
	}else{
		my $tag = $self->{program_file};
		$uniSub->printColorDebug("on_blue", "FILE #$tag");

		#metamap the files if needed
		if(!$self->{import_meta}){
			$uniSub->printColorDebug("bold cyan", "---  METAMAP  ---\n");
			my %paramsm = ();
			$paramsm{'directory'} = $self->{program_dir};
			$paramsm{'index'} = $self->{index};
			$paramsm{'metamap_arguments'} = $self->{metamap_arguments};
			$paramsm{'debug'} = $debug;
			$metaboy = NanoB2B::NER::Metaman->new(\%paramsm);
			$metaboy->meta_file($tag);
		}

		#arff the file
		$uniSub->printColorDebug("bold magenta", "---    ARFF    ---\n");
			#define arffboy with the parameters
			my %paramsr = ();
			$paramsr{'directory'} = $self->{program_dir};
			$paramsr{'features'} = $self->{features};
			$paramsr{'bucketsNum'} = $self->{bucketsNum};
		    $paramsr{'debug'} = $debug;
			$paramsr{'prefix'} = $self->{prefix};
			$paramsr{'suffix'} = $self->{suffix};
		    $paramsr{'index'} = $self->{index};
		    $paramsr{'stopwords'} = $self->{stopwords};
		    $paramsr{'is_cui'} = $self->{is_cui};
		    $paramsr{'sparse_matrix'} = $self->{sparse_matrix};
		    if(!$wcs_found){
			   	$paramsr{'wcs'} = $self->{wcs};
			   	$wcs_found = 1;
			}
			$arffboy = NanoB2B::NER::Arffman->new(\%paramsr);
		$arffboy->arff_file($tag);

		#weka the file
		if($self->{bucketsNum} > 1){
			$uniSub->printColorDebug("bold yellow", "---    WEKA    ---\n");
				#define wekaboy with the parameters
				my %paramsw = ();
				$paramsw{'directory'} = $self->{program_dir};
				$paramsw{'type'} = $self->{weka_type};
				$paramsw{'weka_size'} = $self->{weka_size};
				$paramsw{'features'} = $self->{features};
				$paramsw{'buckets'} = $self->{bucketsNum};
				$paramsw{'debug'} = $debug;
				$wekaboy = NanoB2B::NER::Wekaman->new(\%paramsw);
			$wekaboy->weka_file($tag);
		}

		#model the file
		if($self->{model}){
			$uniSub->printColorDebug("bold red", "---  MODEL  ---\n");
				my %paramsmo = ();
				$paramsmo{'directory'} = $self->{program_dir};
				$paramsmo{'type'} = $self->{weka_type};
				$paramsmo{'weka_size'} = $self->{weka_size};
				$paramsmo{'features'} = $self->{features};
				$paramsmo{'buckets'} = $self->{bucketsNum};
				$paramsmo{'debug'} = $debug;
				$modelboy = NanoB2B::NER::Modelman->new(\%paramsmo);
			$modelboy->make_model_file($tag);
		}

		#average the file
		if($self->{bucketsNum} > 1){
			$uniSub->printColorDebug("bold green", "---    AVG    ---\n");
				#define avgboy with the parameters
				my %paramsa = ();
				$paramsa{'directory'} = $self->{program_dir};
					my @a = split(/\./, $self->{weka_type});
				$paramsa{'weka_dir'} = $a[$#a];
				$paramsa{'features'} = $self->{features};
				$paramsa{'buckets'} = $self->{bucketsNum};
				$paramsa{'debug'} = $debug;
				$avgboy = NanoB2B::NER::Avgman->new(\%paramsa);
			$avgboy->avg_file($tag);
		}


		$uniSub->printColorDebug("on_blue", "##         FINISHED #$tag!        ##");
	}

}


=head3 nerByMethod

description:

  Runs the files specified in the parameters program_dir metamaps all the files, arffs all the files, wekas all the files, and averages all the files
  This NER method doesn't move on to the next method until all the files have been processed

input:

 None

output:

 Metamap files, ARFF file sets, Weka file sets, and Averaged Accuracy files

example:

  use NanoB2B::NER;
  my %params =  ();
  	$params{'dir'} = "my_directory";
  	$params{'features'} = "ortho morph text pos cui sem";

  my $nner = new NanoB2B::NER(\%params);
  $nner->nerByMethod();

=cut

sub nerByMethod{
	my $self = shift;

	#meta the files if needed
	if(!$self->{import_meta}){
		$self->metaSet();
	}

	#arff the files
	$self->arffSet();

	#weka the files
	if($self->{bucketsNum} > 1){
		$self->wekaSet();
	}


	if($self->{model}){
		$self->modelSet();
	}

	#average the files
	if($self->{bucketsNum} > 1){
		$self->avgSet();
	}
}

=head3 metaSet

description:

  Runs a set of files through metamap

input:

 None

output:

 Metamap files for every file found in the directory specified in the constructor parameters

example:

  use NanoB2B::NER;
  my %params =  ();
  	$params{'dir'} = "my_directory";
  	$params{'features'} = "ortho morph text pos cui sem";

  my $nner = new NanoB2B::NER(\%params);
  $nner->metaSet();

=cut
sub metaSet{
	my $self = shift;

	print "\tDIR: " .  $self->{'program_dir'} . "\n";

	#open the directory
	opendir (my $DIR, $self->{program_dir}) or die $!;
	my @tags = grep { $_ ne '.' and $_ ne '..' and substr($_, 0, 1) ne '_'} readdir $DIR;	#get each file from the directory
	my $totalTags = @tags;

	#if only file
	if($self->{program_file}){
		$totalTags = 1;
	}

	#sort by size?
	if($self->{sortSize}){
		@tags = sortBySize($self, \@tags);
	}

	#if only one file reduce it to the one
	if(defined $self->{program_file}){
		@tags = ($self->{program_file});
	}

	#define metaboy with the parameters
	my %params = ();
	$params{'directory'} = $self->{program_dir};
	$params{'index'} = $self->{index};
	$params{'metamap_arguments'} = $self->{metamap_arguments};
	$params{'debug'} = $debug;
	$metaboy = NanoB2B::NER::Metaman->new(\%params);

	#run set through metamap
	for(my $a = $self->{fileIndex}; $a <= $totalTags; $a++){
		$uniSub->printColorDebug("bold cyan", "META FILE #$a / $totalTags\n");
		my $tag = $tags[$a - 1];
		$metaboy->meta_file($tag);
		$uniSub->printColorDebug("bold cyan", "##         FINISHED METAMAP #$a - $tag!        ##\n");
	}
}

=head3 arffSet

description:

  Turns a set of files into ARFF files based on the features specificied in the constructor parameters

input:

 None

output:

 ARFF file sets for every file found in the directory specified in the constructor parameters

example:

  use NanoB2B::NER;
  my %params =  ();
  	$params{'dir'} = "my_directory";
  	$params{'features'} = "ortho morph text pos cui sem";

  my $nner = new NanoB2B::NER(\%params);
  $nner->arffSet();

=cut
sub arffSet{
	my $self = shift;

	#open the directory
	opendir (my $DIR, $self->{program_dir}) or die $!;
	my @tags = grep { $_ ne '.' and $_ ne '..' and substr($_, 0, 1) ne '_'} readdir $DIR;	#get each file from the directory
	my $totalTags = @tags;

	#if only one file
	if($self->{program_file}){
		$totalTags = 1;
	}

	#sort by size?
	if($self->{sortSize}){
		@tags = sortBySize($self, \@tags);
	}

	#if only one file reduce it to the one
	if(defined $self->{program_file}){
		@tags = ($self->{program_file});
	}

	#define arffboy with the parameters
	my %params = ();
	$params{'directory'} = $self->{'program_dir'};
	$params{'features'} = $self->{'features'};
	$params{'bucketsNum'} = $self->{'bucketsNum'};
    $params{'debug'} = $debug;
	$params{'prefix'} = $self->{'prefix'};
	$params{'suffix'} = $self->{'suffix'};
    $params{'index'} = $self->{'index'};
    $params{'stopwords'} = $self->{'stopwords'};
    $params{'is_cui'} = $self->{'is_cui'};
    $params{'sparse_matrix'} = $self->{'sparse_matrix'};
    $params{'wcs'} = $self->{'wcs'};
	$arffboy = NanoB2B::NER::Arffman->new(\%params);

	for(my $a = $self->{fileIndex}; $a <= $totalTags; $a++){
		$uniSub->printColorDebug("bold magenta", "ARFF FILE #$a / $totalTags\n");
		my $tag = $tags[$a - 1];
		if($wcs_found){
			$params{'wcs'} = "";
			$arffboy = NanoB2B::NER::Arffman->new(\%params);
		}else{
			$wcs_found = 1;
		}
		$arffboy->arff_file($tag);
		$uniSub->printColorDebug("bold magenta", "##         FINISHED ARFF #$a - $tag!        ##\n");
	}
}

=head3 wekaSet

description:

  Runs a set of ARFF files through WEKA

input:

 None

output:

 WEKA files for every file found in the directory specified in the constructor parameters

example:

  use NanoB2B::NER;
  my %params =  ();
  	$params{'dir'} = "my_directory";
  	$params{'features'} = "ortho morph text pos cui sem";

  my $nner = new NanoB2B::NER(\%params);
  $nner->wekaSet();

=cut
sub wekaSet{
	my $self = shift;

	#open the directory
	opendir (my $DIR, $self->{program_dir}) or die $!;
	my @tags = grep { $_ ne '.' and $_ ne '..' and substr($_, 0, 1) ne '_'} readdir $DIR;	#get each file from the directory
	my $totalTags = @tags;

	#if only one file
	if($self->{program_file}){
		$totalTags = 1;
	}

	#sort by size?
	if($self->{sortSize}){
		@tags = sortBySize($self, \@tags);
	}

	#if only one file reduce it to the one
	if(defined $self->{program_file}){
		@tags = ($self->{program_file});
	}

	#define wekaboy with the parameters
	my %params = ();
	$params{'directory'} = $self->{program_dir};
	$params{'type'} = $self->{weka_type};
	$params{'weka_size'} = $self->{weka_size};
	$params{'features'} = $self->{features};
	$params{'buckets'} = $self->{bucketsNum};
	$params{'debug'} = $debug;
	$wekaboy = NanoB2B::NER::Wekaman->new(\%params);

	for(my $a = $self->{fileIndex}; $a <= $totalTags; $a++){
		$uniSub->printColorDebug("bold yellow", "##         WEKA FILE #$a / $totalTags         ##\n");
		my $tag = $tags[$a - 1];
		$wekaboy->weka_file($tag);
		$uniSub->printColorDebug("bold yellow", "##         FINISHED WEKA #$a - $tag!        ##\n");
		sleep(1);
	}
}

=head3 modelSet

description:

  Creates WEKA models from the training ARFF files

input:

 None

output:

 WEKA model files for every file with training ARFF files

example:

  use NanoB2B::NER;
  my %params =  ();
  	$params{'dir'} = "my_directory";
  	$params{'features'} = "ortho morph text pos cui sem";

  my $nner = new NanoB2B::NER(\%params);
  $nner->modelSet();

=cut
sub modelSet{
	my $self = shift;

	#open the directory
	opendir (my $DIR, $self->{program_dir}) or die $!;
	my @tags = grep { $_ ne '.' and $_ ne '..' and substr($_, 0, 1) ne '_'} readdir $DIR;	#get each file from the directory
	my $totalTags = @tags;

	#if only one file
	if($self->{program_file}){
		$totalTags = 1;
	}

	#sort by size?
	if($self->{sortSize}){
		@tags = sortBySize($self, \@tags);
	}

	#if only one file reduce it to the one
	if(defined $self->{program_file}){
		@tags = ($self->{program_file});
	}

	#define wekaboy with the parameters
	my %params = ();
	$params{'directory'} = $self->{program_dir};
	$params{'type'} = $self->{weka_type};
	$params{'weka_size'} = $self->{weka_size};
	$params{'features'} = $self->{features};
	$params{'buckets'} = $self->{bucketsNum};
	$params{'debug'} = $debug;
	$modelboy = NanoB2B::NER::Modelman->new(\%params);

	for(my $a = $self->{fileIndex}; $a <= $totalTags; $a++){
		$uniSub->printColorDebug("bold red", "##         MODEL FILE #$a / $totalTags         ##\n");
		my $tag = $tags[$a - 1];
		$modelboy->make_model_file($tag);
		$uniSub->printColorDebug("bold red", "##         FINISHED MODEL #$a - $tag!        ##\n");
		sleep(1);
	}
}


=head3 avgSet

description:

  Averages together a set of WEKA files

input:

 None

output:

 Average accuracy files for every file found in the directory specified in the constructor parameters

example:

  use NanoB2B::NER;
  my %params =  ();
  	$params{'dir'} = "my_directory";
  	$params{'features'} = "ortho morph text pos cui sem";

  my $nner = new NanoB2B::NER(\%params);
  $nner->avgSet();

=cut
sub avgSet{
	my $self = shift;

	#open the directory
	opendir (my $DIR, $self->{program_dir}) or die $!;
	my @tags = grep { $_ ne '.' and $_ ne '..' and substr($_, 0, 1) ne '_'} readdir $DIR;	#get each file from the directory
	my $totalTags = @tags;

	#if only one file
	if($self->{program_file}){
		$totalTags = 1;
	}

	#sort by size?
	if($self->{sortSize}){
		@tags = sortBySize($self, \@tags);
	}

	#if only one file reduce it to the one
	if(defined $self->{program_file}){
		@tags = ($self->{program_file});
	}

	#define avgboy with the parameters
	my %params = ();
	$params{'directory'} = $self->{program_dir};
		my @a = split(/\./, $self->{weka_type});
	$params{'weka_dir'} = $a[$#a];
	$params{'features'} = $self->{features};
	$params{'buckets'} = $self->{bucketsNum};
	$params{'debug'} = $debug;
	$avgboy = NanoB2B::NER::Avgman->new(\%params);

	for(my $a = $self->{fileIndex}; $a <= $totalTags; $a++){
		$uniSub->printColorDebug("bold green", "AVG FILE #$a / $totalTags\n");
		my $tag = $tags[$a - 1];
		$avgboy->avg_file($tag);
		$uniSub->printColorDebug("bold green", "##         FINISHED AVERAGING #$a - $tag!        ##\n");
	}
}


#sorts a directory by the file size
# input  : @files  <-- get the list of files in the folder
# output : @newset <-- the set of files ordered by size from smallest to largest
sub sortBySize{
	my $self = shift;
	my $files_ref = shift;
	my @files = @$files_ref;

	my %hash = ();
	my @newSet = ();

	my $dir = $self->{program_dir};

	#create hashmap
	foreach my $file (@files){
		my $s = -s "$dir/$file";
		$hash{$s} = $file;
	}

	#add sorted sizes to array
	foreach my $key (sort { $a <=> $b } keys %hash){
		my $name = $hash{$key};
		#printColorDebug("cyan", "$name - $key\n");
		push @newSet, $name;
	}

	return @newSet;
}

1;

=head1 SEE ALSO

=head1 AUTHOR

Megan Charity
Bridget T McInnes

=head1 COPYRIGHT

 Copyright (c) 2017
 Megan Charity, Virginia Commonwealth University
 charityml at vcu.edu

 Bridget T. McInnes, Virginia Commonwealth University
 btmcinnes at vcu.edu

This program is free software; you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation; either version 2 of the License, or (at your option) any later
version.

This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with
this program; if not, write to

 The Free Software Foundation, Inc.,
 59 Temple Place - Suite 330,
 Boston, MA  02111-1307, USA.

=cut