--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ACF/lib/IonFiltration.pm	Fri Oct 18 04:59:51 2019 -0400
@@ -0,0 +1,181 @@
+#!usr/bin/perl
+package IonFiltration;
+
+### Perl modules
+use strict;
+use warnings;
+
+
+
+
+
+
+########################################################################
+### Création of a hash containing all adduits and fragments possible ###
+########################################################################
+
+
+sub MassCollecting{
+	
+	my $mass_file = $_[0];
+	my %hmass;
+
+	open (F1, $mass_file);
+	
+	while(my $line = <F1>){
+		chomp $line;
+		my @tline = split(/[\t;]/, $line);
+		if(defined($hmass{$tline[2]})){
+			print "The mass difference already exists : $tline[2] !\n";
+		}
+		$hmass{$tline[1]}{$tline[2]}=$tline[0];
+	}
+	
+	close F1;
+	return %hmass;
+	
+}
+
+
+
+
+
+
+
+########################################################
+### Creation of a sif table + correlation filtration ###
+########################################################
+
+
+sub sifTableCreation{
+	
+	my $file = $_[0];
+	my $output_sif = $_[1];
+#	my $opt = $_[2];
+#	my $rt_threshold = $_[3];
+#	my $mass_threshold = $_[4];
+	my $correl_threshold = $_[5];
+#	my $dataMatrix = $_[6];
+#	my $output_tabular = $_[7];
+	my $combined_DMVM = $_[8];
+#	my $repres_opt = $_[9];
+#	my $intensity_threshold = $_[10];
+#	my $intensity_pourc = $_[11];
+#	my $refhmass = $_[12];
+	
+	
+	
+	
+	my %hheader_file;
+	my %hduplicate;
+	
+	my %hcorrelgroup;
+	my $groupct=1;
+
+	
+	my $linenb3=0;
+	my %hheader_line;
+	my %hrtmz;
+	
+	open (F5, $combined_DMVM);
+	while(my $line = <F5>){
+		chomp $line;
+		my @tline = split(/\t/, $line);
+		
+		if($linenb3 == 0){
+			for(my $i=0; $i<scalar(@tline);$i++){
+				my $a = $tline[$i];
+				$hheader_line{$a}=$i;
+			}
+		}
+		else{
+			if(defined($hheader_line{mzmed})){
+				my $b = $tline[$hheader_line{mzmed}];
+				$hrtmz{$tline[0]}{mz}=$b;
+			}
+			else{
+				my $b = $tline[$hheader_line{mz}];
+				$hrtmz{$tline[0]}{mz}=$b;
+			}
+			if(defined($hheader_line{rtmed})){
+				my $d = $tline[$hheader_line{rtmed}];
+				$hrtmz{$tline[0]}{rt}=$d;
+			}
+			else{
+				my $d = $tline[$hheader_line{rt}];
+				$hrtmz{$tline[0]}{rt}=$d;
+			}
+		}
+		
+		$linenb3 ++;
+	}
+	close F5;
+	
+	
+	my $linenb=0;
+	
+	open (F1, $file) or die "Impossible to open $file\n";
+	open(F2, ">$output_sif") or die "Impossible to open $output_sif\n";
+	
+	
+	while(my $line = <F1>){
+		chomp $line;
+		my @tline = split(/\t/, $line);
+		
+		###############################
+		### Création of a sif table ###
+		###############################
+		
+		if($linenb == 0){
+			for(my $i=0; $i<scalar(@tline);$i++){
+				my $a = $tline[$i];
+				$hheader_file{$i}=$a;
+			}
+		}
+		else{
+			for(my $i=1; $i<scalar(@tline);$i++){
+				my $a=$tline[0];
+				my $b=$hheader_file{$i};
+				my $coef=$tline[$i];
+								
+				if($a eq $b){
+	#				print "This is a correlation between A ($a) and A ($b) !\n"
+				}
+				else{
+					
+					#########################
+					### Remove duplicates ###
+					#########################
+					
+					my $y = $a."/".$b;
+					my $z = $b."/".$a;
+					
+					if((!(defined($hduplicate{$y}))) && (!(defined($hduplicate{$z})))){
+						
+						$hduplicate{$y}=1;
+#						my $abcoef=abs($coef); # Only when you want to consider negative correlations
+						
+#						if($abcoef > $correl_threshold){ # Only when you want to consider negative correlations
+						if($coef > $correl_threshold){
+						
+							print F2 "$a\t$coef\t$b\n";
+							
+							my $count=0;
+							
+						}
+					}
+				}
+			}
+		}
+		$linenb ++;
+	}
+	close F1;
+	close F2;
+	return ($output_sif, %hrtmz);
+}			
+							
+							
+							
+							
+
+1;
\ No newline at end of file