--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/parser.pm	Tue Apr 11 03:47:06 2017 -0400
@@ -0,0 +1,250 @@
+package lib::parser ;
+
+use strict;
+use warnings;
+
+use Data::Dumper;
+use Carp ;
+
+use Exporter;
+use vars qw($VERSION @ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
+
+$VERSION     = "1.0";
+@ISA         = qw(Exporter);
+@EXPORT      = ();
+@EXPORT_OK   = qw( get_oxidation_ref get_neutral_loss_ref set_category set_class set_subclass );
+%EXPORT_TAGS = ( ALL => [qw( get_oxidation_ref get_neutral_loss_ref set_category set_class set_subclass )] ) ;
+
+=head1 NAME
+
+My::operations - An example module
+
+=head1 SYNOPSIS
+
+    use My::operations;
+    my $object = My::Module->new();
+    print $object->as_string;
+
+=head1 DESCRIPTION
+
+This module clusters several more used maths functions like factorial...
+
+=head1 METHODS
+
+Methods are :
+
+=head2 METHOD new
+
+	## Description : new
+	## Input : $self
+	## Ouput : bless $self ;
+	## Usage : new() ;
+
+=cut
+
+sub new {
+    ## Variables
+    my $self={};
+    bless($self) ;
+    return $self ;
+}
+### END of SUB
+
+=head2 METHOD get_oxidation_ref
+
+	## Description : get oxidation type and oxidation modification from conf file
+	## Input : $CONF
+	## Output : $list_oxidations, $list_ox_values
+	## Usage : my ( $list_oxidations, $list_ox_values ) = get_oxidation_ref( $CONF, $selected_ox ) ;
+	
+=cut
+## START of SUB
+sub get_oxidation_ref {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $CONF, $selected_ox ) = @_ ;
+    
+    my @list_oxidations = () ;
+    my @clean_list_oxidations = () ;
+	my @list_ox_values = () ;
+	
+    if ( defined $selected_ox ) {
+    	
+	    @list_oxidations = split( /,/, $selected_ox ) ;
+	    my $pos = 0 ; ## manage the splice
+	    
+	    foreach my $ox ( @list_oxidations  ) {
+			if ($ox !~/NA$/ ) { ## case of ox
+				push(@clean_list_oxidations, $ox) ;
+				if		( $ox =~/^loss_(.*)/ ) 	{ push ( @list_ox_values, ($CONF->{$1}) ) ; }
+				elsif	( $ox =~/^add_(.*)/ )  	{ push ( @list_ox_values, -($CONF->{$1}) ) ; } ### carefull of the number sign
+				else { 								warn "This oxidation ($ox) is unknown in conf and menu\n" ; }
+			}
+			else { # if atoms eq NA, splice it
+				next ;
+			}
+			$pos++ ;
+		}
+    }
+    return(\@clean_list_oxidations, \@list_ox_values) ;
+}
+## END of SUB
+
+=head2 METHOD get_neutral_loss_ref
+
+	## Description : get neutral loss type and neutral loss modifications from conf file
+	## Input : $CONF
+	## Output : $list_neutral_losses, $list_nloss_values
+	## Usage : my ( $list_neutral_losses, $list_nloss_values ) = get_neutral_loss_ref( $CONF, $selected_nloss ) ;
+	
+=cut
+## START of SUB
+sub get_neutral_loss_ref {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $CONF, $selected_nloss ) = @_ ;
+    
+    my @list_neutral_losses = () ; ## complete list
+    my @clean_list_neutral_losses = () ; # list without NA
+	my @list_nloss_values = () ; # values
+    
+    if ( defined $selected_nloss ) {
+	    @list_neutral_losses = split( /,/, $selected_nloss ) ;
+
+	    foreach my $nloss ( @list_neutral_losses  ) {
+	    	
+			if ($nloss !~/NA$/ ) { ## case of neutral loss
+				push(@clean_list_neutral_losses, $nloss) ;
+				if		( $nloss =~/^loss_(.*)/ ) 	{ push ( @list_nloss_values, ($CONF->{$1}) ) ; }
+				elsif	( $nloss =~/^add_(.*)/ )  	{ push ( @list_nloss_values, -($CONF->{$1}) ) ; } ### carefull of the number sign
+				else { 									warn "This neutral loss ($nloss) is unknown in conf and menu\n" ; }
+			}
+			else { # if atoms eq NA, splice it
+				next ;
+			}
+		}
+    }
+    return(\@clean_list_neutral_losses, \@list_nloss_values) ;
+}
+## END of SUB
+
+=head2 METHOD set_category
+
+	## Description : set the category id from any types of ids
+	## Input : $unknown_id
+	## Output : $cat_id
+	## Usage : my ( $cat_id ) = set_category( $unknown_id ) ;
+	
+=cut
+## START of SUB
+sub set_category {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $unknown_id ) = @_ ;
+    my $cat_id = undef ;
+    
+    if ( defined $unknown_id ) {
+    	if ( $unknown_id > 0 ) {
+    		if ( (length $unknown_id) == 1 )  { $cat_id = $unknown_id }
+    		elsif ( (length $unknown_id) == 3 )  { $cat_id = substr($unknown_id, 0, 1) }
+    		elsif ( (length $unknown_id) == 5 )  { $cat_id = substr($unknown_id, 0, 1) }
+    	}
+    }
+    else {
+    	warn "Can't find any id to substr\n" ;
+    }
+    return( \$cat_id ) ;
+}
+## END of SUB
+
+=head2 METHOD set_class
+
+	## Description : set the class id from any types of ids
+	## Input : $unknown_id
+	## Output : $class_id
+	## Usage : my ( $class_id ) = set_category( $unknown_id ) ;
+	
+=cut
+## START of SUB
+sub set_class {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $unknown_id ) = @_ ;
+    my $class_id = undef ;
+    
+    if ( defined $unknown_id ) {
+    	if ( $unknown_id > 0 ) {
+    		if ( (length $unknown_id) == 3 )  { $class_id = $unknown_id }
+    		elsif ( (length $unknown_id) == 5 )  { $class_id = substr($unknown_id, 0, 3) }
+    	}
+    }
+    else {
+    	warn "Can't find any id to substr\n" ;
+    }
+    return( \$class_id ) ;
+}
+## END of SUB
+
+=head2 METHOD set_subclass
+
+	## Description : set the subclass id from any types of ids
+	## Input : $unknown_id
+	## Output : $subclass_id
+	## Usage : my ( $subclass_id ) = set_subclass( $unknown_id ) ;
+	
+=cut
+## START of SUB
+sub set_subclass {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $unknown_id ) = @_ ;
+    my $subclass_id = undef ;
+    
+    if ( defined $unknown_id ) {
+    	if ( $unknown_id > 0 ) {
+    		if ( (length $unknown_id) == 5 )  { $subclass_id = $unknown_id }
+    	}
+    }
+    else {
+    	warn "Can't find any id to substr\n" ;
+    } 
+    return( \$subclass_id ) ;
+}
+## END of SUB
+
+
+
+1 ;
+
+
+__END__
+
+=head1 SUPPORT
+
+You can find documentation for this module with the perldoc command.
+
+ perldoc XXX.pm
+
+=head1 Exports
+
+=over 4
+
+=item :ALL is ...
+
+=back
+
+=head1 AUTHOR
+
+Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt>
+
+=head1 LICENSE
+
+This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
+
+=head1 VERSION
+
+version 1 : xx / xx / 201x
+
+version 2 : ??
+
+=cut
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