#!/usr/bin/perl -w

package runnetoglyc;

use strict;
use IO::File;

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

use formatAlleleSeq;


sub netoglyc_extract_results($$$$$){
	
	my ($delta, $netoglyc_result_file, $name_encoding_file, $output_file, $BASE_SEQ_NAME) = @_;

	my ($fh_in,$fh_out,$fh_tmp,$allele,$name,$line,$seq_name,$pos,$Gscore,$Iscore,$signal);
	my ($nameA1,$nameA2,$score_diff,$score,$basis_name);
	
	my %score_allele1 = (); # key : initial complete name => score value (for the alléle 1 position)
	my %score_allele2 = (); # key : initial complete name => signal value (for the alléle 1 position : ++)
	my %signal_allele1 = (); # key : initial complete name => score value (for the alléle 2 position)
	my %signal_allele2 = (); # key : initial complete name => signal value (for the alléle 2 position : ++)
	
	my ($h_encodingName,$h_encodingID,$h_name_allele,$h_name_position) = getEncoding($name_encoding_file);
	
	my $prog = "netoglyc";
	
	my $outpath = $output_file;
	$outpath =~ s/\/([^\/]+)$//;
	
	my $fh_title = new IO::File ">$outpath/$prog\_title.txt" || die "Can not open $outpath/$prog\_title.txt : $! \n";
	print $fh_title ("Sequence Name\tCase\tscore allele1\tscore allele2\tsignal allele1\tsignal allele2\n");	
	$fh_title->close();
	
	#Find variations	
	$fh_in = new IO::File "$netoglyc_result_file" || die "Can not opennetoglyc_result_file $netoglyc_result_file : $! \n";
	$fh_out = new IO::File ">$output_file" || die "Can not create final results of netoglyc $output_file: $! \n";

	while($line = <$fh_in>){

		#~ print "$line\n";
		
		if($line =~ m/^$BASE_SEQ_NAME\d+\s*\S*\s*(\d*)\s*(\S*)\s*(\S*)\s*(\S*)/){
			
			($seq_name,$pos,$Gscore,$Iscore,$signal) = $line =~ /^($BASE_SEQ_NAME\d+)\s*\S*\s*(\d*)\s*(\S*)\s*(\S*)\s*(\S*)/;
			
			#~ print "$seq_name,$pos,$Gscore,$Iscore,$signal\n";
					
			
			if($line =~ s/^($BASE_SEQ_NAME\d+)/$h_encodingID->{$seq_name}/){#Substitute the ID by his coresponding name
			
				my $a = $h_name_position->{$seq_name};
				my $b = $h_name_allele->{$seq_name} ;
				print "hash_pos:$a\nhash_allele:$b\n";
				
				print ">>seq_name:*$seq_name*, pred_pos:$pos, pred_score:$Gscore,$Iscore, $signal\n\n";
				
				if($pos eq $h_name_position->{$seq_name}){
					
					if($h_name_allele->{$seq_name} eq "allele1"){
						
						$signal_allele1{$seq_name} = $signal;
						$score_allele1{$seq_name} = $Gscore;
						
					}
					elsif($h_name_allele->{$seq_name} eq "allele2"){
						
						$signal_allele2{$seq_name} = $signal;
						$score_allele2{$seq_name} = $Gscore;
					}
					else{
					
						print "PB: $seq_name :$h_name_allele->{$seq_name}\n";	
						exit(12);
					}				
				}												
			}
			else{
				
				print "PB: NON existing sequence name for id:$1\n";
			}
		}		
		elsif($line =~ /netOglyc: surface prediction failed in entry/){
			
			print "Error: NETOGLYC FAILED:\n$line\n";
			exit(11);
		}
	}
	
	
	foreach $seq_name (keys %signal_allele1){
									
		($basis_name) = $h_encodingID->{$seq_name} =~ /(.*)_allele\d$/;		
		
		$nameA1 = $seq_name;
		$name = $h_encodingID->{$seq_name};
		$name =~ s/allele1/allele2/;		
		$nameA2 = $h_encodingName->{$name};				
		
		if(not defined $signal_allele2{$nameA2}){
		
			print $fh_out ("$basis_name\tloss\t$score_allele1{$nameA1}\t\t$signal_allele1{$nameA1}\t\n");
			#~ print ("$name\tloss\t$score_allele1{$nameA1}\t$signal_allele1{$nameA1}\n");
		}
		else{
			
			$score_allele1{$nameA1} =~ s /\,/\./;
			$score_allele2{$nameA2} =~ s /\,/\./;
			
			$score_diff = $score_allele1{$nameA1} - $score_allele2{$nameA2};
			$score_diff =~ s/-//;
			
			if($score_diff >= $delta && $score_allele1{$nameA1} > $score_allele2{$nameA2}){
								
				print $fh_out ("$basis_name\tloss?\t$score_allele1{$nameA1}\t$score_allele2{$nameA2}\t$signal_allele1{$nameA1}\t$signal_allele2{$nameA2}\n");
			}
			elsif($score_diff >= $delta && $score_allele1{$nameA1} < $score_allele2{$nameA2}){
				
				print $fh_out ("$basis_name\tgain?\t$score_allele1{$nameA1}\t$score_allele2{$nameA2}\t$signal_allele1{$nameA1}\t$signal_allele2{$nameA2}\n");
			}
		}
		
		delete $signal_allele2{$nameA2};
	}
	
	foreach $seq_name (keys %signal_allele2){
		
		($basis_name) = $h_encodingID->{$seq_name} =~ /(.*)_allele\d$/;		
		
		$nameA2 = $seq_name;
		$name = $h_encodingID->{$seq_name};
		$name =~ s/allele2/allele1/;
		$nameA1 = $h_encodingName->{$name};
						
		if(not defined $signal_allele1{$nameA1}){
		
			print $fh_out ("$basis_name\tgain\t\t$score_allele2{$nameA2}\t\t$signal_allele2{$nameA2}\n");
		}
		else{
			
			$score_allele1{$nameA1} =~ s /\,/\./;
			$score_allele2{$nameA2} =~ s /\,/\./;
			
			$score_diff = $score_allele1{$nameA1} - $score_allele2{$nameA2};
			$score_diff =~ s/-//;
			
			if($score_diff >= $delta && $score_allele1{$nameA1} > $score_allele2{$nameA2}){
								
				print $fh_out ("$basis_name\tloss?\t$score_allele1{$nameA1}\t$score_allele2{$nameA2}\t$signal_allele1{$nameA1}\t$signal_allele2{$nameA2}\n");
			}
			elsif($score_diff >= $delta && $score_allele1{$nameA1} < $score_allele2{$nameA2}){
				
				print $fh_out ("$basis_name\tgain?\t$score_allele1{$nameA1}\t$score_allele2{$nameA2}\t$signal_allele1{$nameA1}\t$signal_allele2{$nameA2}\n");
			}
		}		
	}
	
	$fh_out->close;
	$fh_in->close;
}

1;