#!/usr/bin/perl -w

package runnetcglyc;

use strict;

use base 'Exporter';
our @EXPORT = qw/netcglyc_extract_results/;

use IO::File;


sub netcglyc_extract_results($$$$){
	
	my ($delta, $netcglyc_result_file, $name_encoding_file, $output_file) = @_;
	#~ my ($delta, $path, $date) = @_;
	
	my $tmpfile = $output_file.".tmp";
	print "$tmpfile\n";
	
	#Construct the hash table
	my $sav = new IO::File $name_encoding_file || die "Can not open $name_encoding_file : $! \n";
	my %id;#Hash with all name / id
	while(<$sav>){
		if($_ =~ m/^>(\S*)\s*(.*)/){
			$id{$2} .= $1;
		}
	}
	$sav->close();
	
	#Open and extract name, position and score of C manosylation.
	my $res = new IO::File $netcglyc_result_file || die "Can not open file $netcglyc_result_file : $! \n";
	my $tmp = new IO::File ">$tmpfile" || die "Can not create netcglyc temp file $tmpfile: $! \n";
	while(<$res>){
		if($_ =~ m/^_(\d*)\s*\S*\s*\S*\s*(\d*)\s*(\d*)\s*(\S*)\s*\S*\s*(\S*)/){
			print $tmp "$1\t$2\t$4\t$5\n";
		}
	}
	$tmp->close();
	$res->close();
	
	#Find variations
	$tmp = new IO::File "$tmpfile" || die "Can not open netcglyc temp file $tmpfile: $! \n";
	my $netcglyc = new IO::File ">$output_file" || die "Can not create final results of netcglyc $output_file: $! \n";
	my %a1;
	my %a2;
	my %check;
	my $allele = "";
	my $name = "";
	my $c = 2;
	while(<$tmp>){
		my $line = $_;
		if($line =~ s/^(\d*)/$id{$1}/){#Substitute the ID by his coresponding name
			if($line =~ m/^(\S*)_allele(\d)\s*(\d*)\s(\S*)\s(\S*)/){
				if($2 eq $allele){
					if($c == 0){#Same allele1
						$allele = $2;
						if($5 eq "W"){
							my $position = $3;
							my $score = $4;
							$a1{$position}.=$score;
							$check{$position}.="1";
						}
					}
					elsif($c == 1){#Same allele2
						$allele = $2;
						if($5 eq "W"){
							my $position = $3;
							my $score = $4;
							$a2{$position}.= $score;
							$check{$position}.="2";
						}
					}
				}
				else{
					if($c == 0){#Other allele
						$c++;
						$allele = $2;
						if($5 eq "W"){
							my $position = $3;
							my $score = $4;
							$a2{$position}.=$score;
							$check{$position}.="2";
						}
					}
					elsif($c == 1){#Other transcript
						compare($netcglyc,$delta,\%a1,\%a2,\%check,$name);
						%a1=();
						%a2=();
						%check=();
						$allele = $2;
						$name = $1;
						if($5 eq "W"){
							my $position = $3;
							my $score = $4;
							$a1{$position}.=$score;
							$check{$position}.="1";
						}
						$c = 0;
					}
					elsif($c == 2){#Initialisation
						$name = $1;
						$allele = $2;
						if($5 eq "W"){
							my $position = $3;
							my $score = $4;
							$a1{$position}.=$score;
							$check{$position}.="1";
						}
						$c = 0;
					}
				}
			}
		}
	}
	compare_netcglyc_alleles($netcglyc,$delta,\%a1,\%a2,\%check,$name);#For the last transcript
	$tmp->close();
	$netcglyc->close();
}

sub compare_netcglyc_alleles($$$$$$){

	my ($netcglyc,$delta,$ref1,$ref2,$ref3,$name) = @_;
	my %a1=%$ref1;
	my %a2=%$ref2;
	my %check=%$ref3;
	foreach my $k (keys(%check)){
		
		print "ok\n";
		
		my $v = $check{$k};
		if($v eq "12"){
			my $diffscore = $a1{$k}-$a2{$k};
			if($diffscore >= $delta){
				print $netcglyc "$name : Signal lost at position $k. Score allele 1 = $a1{$k} - Score allele 2 = $a2{$k}\n";
			}
			elsif($diffscore <= -$delta){
				print $netcglyc "$name : Signal gain at position $k. Score allele 1 = $a1{$k} - Score allele 2 = $a2{$k}\n";
			}
		}
		elsif($v eq "1"){
			print $netcglyc "$name : Signal lost at position $k . Score : $a1{$k}\n";
		}
		elsif($v eq "2"){
			print $netcglyc "$name : Signal gain at position $k. Score : $a2{$k}\n";
		}
	}
}

1;