#!/usr/bin/env perl
use strict;
use warnings;

use MCE::Signal qw($tmp_dir);
use MCE::Flow;

my $proteinFile = shift;

mce_flow_f {
   RS => "\n>", chunk_size => 100, max_workers => 20, use_slurpio => 1
},
sub {
   my ($mce, $slurp_ref, $chunk_id) = @_;

   # pad with zeros -- 4 digits; e.g. 0001, 0002, ...
   $chunk_id = sprintf "%04d", $chunk_id;

   # create input file for java
   open my $out_fh, ">", "$tmp_dir/$chunk_id.in";
   print $out_fh $$slurp_ref;
   close $out_fh;

   # launch java
   system("java -Xmx300m java_code/ALPHAtest -a tables/A.TRAINED -e tables/E.TRAINED -c tables/conf.tat -f $tmp_dir/$chunk_id.in > $tmp_dir/$chunk_id.out");

   # unlink input file after running
   unlink "$tmp_dir/$chunk_id.in";

}, $proteinFile;

# the tmp_dir is removed automatically when the script terminates
system("cd $tmp_dir; cat *.out");