#!/usr/bin/perl

use strict;

for(my $r = 200; $r<=10000; $r = $r + 200){
        my %file_list; # list of files
        my %file_gene;
        for(my $i = 1; $i <=$r; $i++){
                my $file = "$i.txt";
                open(INF, "$file");
                while(my $g=<INF>){
                        chomp $g;
                        $file_gene{$i}{$g} = ();
                }
                close INF;
                $file_list{$i} = ();
        }
        close IN;

        my %hash3; # overlapping percentage of file pairs
        my %hash4; # percentage of common items in file1
        my %hash5; # percentage of common items in file2

        my @file_list_array = keys %file_list; # list of file names
        my $file_number = $#file_list_array; # number of files - 1

        my @time = localtime(time);
        my $hr1 = $time[2];
        my $min1 = $time[1];
        my $sec1 = $time[0];

        my $x = 0;
                for(my $i = 0; $i<= $file_number - 1; $i++){
                        my $m1 = $file_list_array[$i];
                        my $value3 = 0;
                        my $value4 = 0;
                        my $value5 = 0;
                        my $pair;
                        for(my $j = $i + 1; $j <= $file_number; $j++){
                                $x = $x + 1;
                                my $m2 = $file_list_array[$j];
                                my ($Nvalue3, $Nvalue4, $Nvalue5) = find_common_items($m1, $m2, \%file_gene, 0.1);
                                if($Nvalue3 > $value3){
                                        $pair = $m1."_".$m2; # file pair name
                                        $value3 = $Nvalue3;
                                        $value4 = $Nvalue4;
                                        $value5 = $Nvalue5;
                                }
                        }
                        if($pair){
                                $hash3{"$pair"} = $value3;
                                $hash4{"$pair"} = $value4;
                                $hash5{"$pair"} = $value5;
                        }
                }

        my @time = localtime(time);

        my $hr2 = $time[2];
        my $min2 = $time[1];
        my $sec2 = $time[0];

        my $hr = $hr2 - $hr1;
        my $min = $min2 - $min1;
        my $sec = $sec2 - $sec1;

        my $time = $hr*3600 + $min*60 + $sec;

        my $unit_time = $time/$x;
        print "$r files\t$unit_time sec\n";
}

sub find_common_items{

        my ($m1, $m2, $file_gene_ref, $cutoff) = @_;

        my %file_genes = %$file_gene_ref;

        my %hash1;
        my %hash2;

        my %hash1 = %{$file_genes{$m1}}; # genes in file m1
        my %hash2 = %{$file_genes{$m2}}; # genes in file m2

        my %intersection; # intersection items
        my %union;        # union items
        my $value3 = 0;
        my $value4 = 0;
        my $value5 = 0;

        # find intersection items
        foreach(keys %hash1){
                $intersection{$_} = $hash1{$_} if exists $hash2{$_};
        }
        my $isn = scalar keys %intersection; # number of intersection items

        # find union items
        @union{keys %hash1, keys %hash2} = ();
        my $un = scalar keys %union; # number of union items

        # only store qualified file pairs
        if($isn/$un > $cutoff){ 
                my $s1 = scalar keys %hash1; # number of items in file m1, size of file m1
                my $s2 = scalar keys %hash2; # number of items in file m2, size of file m2
                $value3 = $isn/$un; # For file pair m1_m2, overlapping percentage of file pairs = intersection/union
                $value4 = $isn/$s1;  # For file pair m1_m2, percentage of common genes in file m1 = intersection/size of file m1
                $value5 = $isn/$s2;  # For file pair m1_m2, percentage of common genes in file m2 = intersection/size of file m2
        }
        return($value3, $value4, $value5);
}