diff lib/hr.pm @ 0:86296c048e46 draft

Init repository for [hr2]

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/hr.pm	Wed Jun 05 09:40:20 2019 -0400
@@ -0,0 +1,775 @@
+package lib::hr ;
+
+use strict;
+no strict "refs" ;
+use warnings ;
+use Exporter ;
+use threads ;
+use HTML::Template ;
+use Carp ;
+
+use Data::Dumper ;
+
+use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS);
+
+our $VERSION = "1.0";
+our @ISA = qw(Exporter);
+our @EXPORT = qw( manage_atoms_and_ranges manage_atoms check_hr_exe manage_atom_and_range manage_tolerance manage_mode config_hr_exe );
+our %EXPORT_TAGS = ( ALL => [qw(manage_atoms_and_ranges manage_atoms check_hr_exe manage_atom_and_range manage_tolerance manage_mode config_hr_exe )] );
+
+=head1 NAME
+
+lib::hr - A module for managing / launching hr binary (structure elucidation c++ progr)
+
+=head1 SYNOPSIS
+
+    use lib::hr;
+    my $object = lib::hr->new();
+    print $object->as_string;
+
+=head1 DESCRIPTION
+
+This module does not really exist, it
+was made for the sole purpose of
+demonstrating how POD works.
+
+=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 manage_atoms_and_ranges
+
+	## Description : allow from an initial config to add or delete atoms and their range
+	## Input : $atomsconfig, $atombasic, $atomsupp
+	## Output : $atomcleanconfig
+	## Usage : my ( $atomcleanconfig ) = manage_atoms_and_ranges ( $atomsconfig, $atombasic, $atomsupp ) ;
+	
+=cut
+## START of SUB
+sub manage_atoms_and_ranges {
+    ## Retrieve Values
+    my $self = shift ;
+    my ( $atomsconfig, $CONF, $atombasic, $atomsupp ) = @_;
+    my ( $atomcleanconfig ) = ( undef ) ;
+    
+    # basic atoms case:
+    foreach my $atom ( (split(",", $atombasic )) ) {
+    	if ( exists $CONF->{$atom} ) 	{ $atomsconfig->{$atom}{'max'} = $CONF->{$atom} ; }
+    }
+    
+    # suppl. atoms case
+    foreach my $atom ( (split(",", $atomsupp )) ) {
+    	print "*** $atom***\n" ;
+    	if ( exists $atomsconfig->{$atom} ) 	{ $atomsconfig->{$atom} = $CONF->{'DEFAULT_MAX'} ; }
+    }
+    
+    # Create atoms and range parameters:    
+    foreach my $selectedAtom ( keys %{$atomsconfig} ) {
+    	$atomcleanconfig .= ' -'.$selectedAtom.' '.$atomsconfig->{$selectedAtom}{'min'}.'-'.$atomsconfig->{$selectedAtom}{'max'} ;
+    }
+    
+    return ($atomcleanconfig) ;
+}
+### END of SUB
+
+
+     
+=head2 METHOD manage_atoms ### DEPRECATED
+
+	## Description : controles atoms input list and prepare it like hr binary parameter 
+	## Input : $input_atoms, $conf_atoms
+	## Output : $hr_atoms_param
+	## Usage : my ( $hr_atoms_param ) = manage_atoms( $input_atoms, $conf_atoms ) ;
+	### DEPRECATED
+	
+=cut
+## START of SUB
+sub manage_atoms { ### DEPRECATED
+	## Retrieve Values
+    my $self = shift ;
+    my ( $input_atoms, $conf_atoms ) = @_ ;
+    my $hr_atoms_param = undef ;
+    
+    if ( ( defined $$input_atoms ) and ( defined $$conf_atoms )  ) {
+    	if ( ( $$input_atoms eq 'None' ) or ( $$input_atoms eq '' ) or ( $$input_atoms eq ' ' ) )	{  $hr_atoms_param =  $$conf_atoms ; 	}
+    	elsif ( $$input_atoms =~ /[P|S|F|L|K|B|A|1|,]+/ ) { $hr_atoms_param =  $$conf_atoms.','.$$input_atoms ;  }
+    	else 							{  $hr_atoms_param =  $$conf_atoms ;  	}
+    } ## END IF
+    elsif ( !defined $$input_atoms ) { 	$hr_atoms_param =  $$conf_atoms ; }
+    elsif ( !defined $$conf_atoms )  { 	warn "hr module can't manage any atom list (undef values in conf)\n" ; }
+    else {						    	warn "hr module musn't manage any atom list\n" ; }
+    
+    return(\$hr_atoms_param) ;
+}
+## END of SUB
+
+=head2 METHOD manage_atom_and_range ### DEPRECATED
+
+	## Description : build atom range with defined value in conf file
+	## Input : $atom, $min, $max
+	## Output : $hr_range
+	## Usage : my (  ) = manage_atom_and_range( $atom, $min, $max ) ;
+	### DEPRECATED
+	
+=cut
+## START of SUB
+sub manage_atom_and_range { ### DEPRECATED
+	## Retrieve Values
+    my $self = shift ;
+    my ( $atom, $min, $max ) = @_ ;
+    my $hr_range = undef ;
+    
+    if ( ( defined $$atom ) and ( defined $$min ) and ( defined $$max )  ) {
+    	## manage ragne like "-C 0-200"
+    	$hr_range = ' -'.$$atom.' '.$$min.'-'.$$max ;
+    } ## END IF
+    else {
+    	warn "Some argvts are missing to build the current atom range line\n" ;
+    }    
+    return(\$hr_range) ;
+}
+## END of SUB
+
+=head2 METHOD manage_tolerance
+
+	## Description : check range and format of tolerance
+	## Input : $tolerance, $default_value
+	## Output : $set_tol
+	## Usage : my ( $set_tol ) = manage_tolerance( $tolerance, $default_value ) ;
+	
+=cut
+## START of SUB
+sub manage_tolerance {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $tolerance, $default_value ) = @_ ;
+    my ($set_tol, $tmp_tol ) = (undef, undef) ;
+        
+    if ( ( defined $$tolerance ) and ( defined $$default_value )) {
+    	$tmp_tol = $$tolerance ;
+    	$tmp_tol =~ tr/,/./;
+		## tolerance doit etre >0 et <10
+		if ( $tmp_tol <= 0 || $tmp_tol >= 10 ){
+			$set_tol = $$default_value ;
+			warn "The used tolerance is set to $$default_value (out of authorized range)\n" ;
+		}
+		else{ $set_tol = $tmp_tol ; }
+    }
+    else { 	warn "Your tolerance or the default tol are not defined\n" ;   }
+    
+    return(\$set_tol) ;
+}
+## END of SUB
+
+=head2 METHOD manage_mode
+
+	## Description : manage mode and apply mass correction (positive/negative/neutral)
+	## Input : $mode, $charge, $electron, $proton, $mass
+	## Output : $exact_mass
+	## Usage : my ( $exact_mass ) = manage_mode( $mode, $charge, $electron, $proton, $mass ) ;
+	
+=cut
+## START of SUB
+sub manage_mode {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $mode, $charge, $electron, $proton, $mass ) = @_ ;
+    my ($exact_mass, $tmp_mass) = ( undef, undef ) ;
+    
+    ## some explanations :
+    	# MS in + mode = adds H+ (proton) and molecule is positive : el+ => $charge = "positive"
+		# For HR, need to subtrack proton mz and to add electron mz (1 electron per charge) to the input mass which comes neutral!
+    
+    if ( ( defined $$electron ) and ( defined $$proton ) ) {
+    	# check mass
+    	if ( defined $$mass ) {  $tmp_mass = $$mass ;   $tmp_mass =~ tr/,/./ ; } # manage . and , in case of...
+    	else {	warn "No mass is defined\n"  	}
+    	
+    	# manage charge
+    	if ( ( !defined $$charge ) || ($$charge < 0) ){ warn "Charge is not defined or value is less than zero\n" ; }
+    	
+    	# set neutral mass in function of ms mode
+    	if($$mode eq 'positive')	{	$exact_mass = (	$tmp_mass - $$proton + $$electron) * $$charge ; }
+    	elsif($$mode eq 'negative')	{ 	$exact_mass = (	$tmp_mass + $$proton - $$electron) * $$charge ; }
+    	elsif($$mode eq "neutral")	{	$exact_mass = 	$tmp_mass ;  }
+	    else { 	warn "This mode doesn't exist : please select positive/negative or neutral mode\n" ; 	    }
+    }
+    else {
+    	warn "Missing some parameter values (electron, neutron masses), please check your conf file\n" ;
+    } 
+    return(\$exact_mass) ;
+}
+## END of SUB
+
+=head2 METHOD check_hr_exe
+
+	## Description : permit to check the path of hr.exe and its full availability
+	## Input : $hr_path, $hr_version
+	## Output : true/false
+	## Usage : my ( $res ) = check_hr_exe( $hr_path, $hr_version ) ;
+	
+=cut
+## START of SUB
+sub check_hr_exe {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $hr_path, $hr_version ) = @_ ;
+    my $success = undef ;
+    my $check_res = undef ;
+    
+    ## test path :
+    if ( ( defined $$hr_path ) and ( defined $$hr_version ) ) {
+   		if ( defined $$hr_path ) {
+   			$success = `$$hr_path -version`;
+   			print "$success\n" ;
+   			if ($success !~/^$$hr_version/) { 	warn "You do not use the expected version of hr2 ($$hr_version)\n" ;  }
+   			else { 								$check_res = 1 ; }
+   		}
+    	else { warn "Can't use HR because the binary file doesn't exist at the specified path ($$hr_path)\n" ; }
+    	
+    } ## END IF
+    else { 	warn "No HR path or Hr version defined\n" ;   }
+    
+    return($check_res) ;
+}
+## END of SUB
+
+=head2 METHOD config_hr_exe
+
+	## Description : builds hr execute line with needed params
+	## Input : $hr_path, $hr_delta, $mass, $has_goldenrules, $atoms_and_ranks
+	## Output : var2
+	## Usage : my ( var2 ) = config_hr_exe( $hr_path, $hr_delta, $mass, $has_goldenrules, $atoms_and_ranks ) ;
+	
+=cut
+## START of SUB
+sub config_hr_exe {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $hr_path, $hr_delta, $mass, $has_goldenrules, $atoms_and_ranks ) = @_ ;
+    my $hr_cmd = undef ;
+    
+    if ( ( defined $$hr_path ) and ( defined $$hr_delta ) and ( defined $$mass ) and ( defined $$atoms_and_ranks )  ) {
+    	$hr_cmd = $$hr_path.' -t '.$$hr_delta.' -m '.$$mass.' '.$$atoms_and_ranks ;
+    	if ( defined $$has_goldenrules ) { 	$$hr_cmd .= ' -g ' ;   	}
+    } ## END IF
+    else { 	warn "Some argvts are missing to build the current hr exec line\n" ; }
+    
+    return(\$hr_cmd) ;
+}
+## END of SUB
+
+=head2 METHOD threading_hr_exe
+
+	## Description : prepare 5 threads for hr executing
+	## Input : $method, $list
+	## Output : $results
+	## Usage : my ( $results ) = threading_hr_exe( $method, $list ) ;
+	
+=cut
+## START of SUB
+sub threading_hr_exe {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $method, $list ) = @_ ;
+    
+    my @results = () ;
+    
+    if ( ( defined $list ) and ( defined $method )) {
+    	
+    	for (my $i = 0; $i < (scalar @{$list}); $i+=6 ) {
+			my $thr1 = threads->create($method, $self, $list->[$i]) if $list->[$i] ;
+			my $thr2 = threads->create($method, $self, $list->[$i+1]) if $list->[$i+1] ;
+			my $thr3 = threads->create($method, $self, $list->[$i+2]) if $list->[$i+2] ;
+			my $thr4 = threads->create($method, $self, $list->[$i+3]) if $list->[$i+3] ;
+			my $thr5 = threads->create($method, $self, $list->[$i+4]) if $list->[$i+4] ;
+			my $thr6 = threads->create($method, $self, $list->[$i+5]) if $list->[$i+5] ;
+			push ( @results, $thr1->join )  if $list->[$i] ;
+			push ( @results, $thr2->join ) if $list->[$i+1] ;
+			push ( @results, $thr3->join ) if $list->[$i+2] ;
+			push ( @results, $thr4->join ) if $list->[$i+3] ;
+			push ( @results, $thr5->join ) if $list->[$i+4] ;
+			push ( @results, $thr6->join ) if $list->[$i+5] ;
+		}
+    }
+    else {
+    	warn "Your input list or your method is undefined\n" ;
+    }
+    
+    return(\@results) ;
+}
+## END of SUB
+
+=head2 METHOD hr_exe
+
+	## Description : hr_exe launches hr and catches result
+	## Input : $cmd
+	## Output : $res
+	## Usage : my ( $res ) = hr_exe( $cmd ) ;
+	
+=cut
+## START of SUB
+sub hr_exe {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $cmd ) = @_ ;
+    my $res = undef ;
+	
+	if (defined $cmd){
+		#print "\n--CMD used : $cmd\n" ;
+		$res = `$cmd` ;
+		sleep(0.5) ;
+		#print "Results : $res\n" ;
+	}
+
+	return (\$res) ;
+}
+## END of SUB
+
+
+=head2 METHOD hr_out_parser
+
+	## Description : parse output of hr and return a hash of features
+	## Input : $res
+	## Output : $parsed_res
+	## Usage : my ( $parsed_res ) = hr_out_parser( $res ) ;
+	
+=cut
+## START of SUB
+sub hr_out_parser {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $res ) = @_ ;
+    
+    my %parsed_res = () ;
+    my ( @formula, @rings_and_double_bond_equivalents, @formula_mz, @mmus ) = ( (), (), (), () ) ;
+    my ( $formula_nb, $formula_total, $time ) = ( undef, undef, undef ) ;
+    
+    if ( defined $$res ) {
+    	# foreach line
+    	foreach my $line (split(/\n/,$$res)){
+    		## v1.02 - parse result line "C7.H17.N5.		2.0	171.1484	+17.2 mmu"
+    		## v1.03 - parse result line "C10.H25.N5.O5.P2.S2.    C10H25N5O5P2S2  8.00    421.0772333     0       0       +0.40"
+    		## $1 = "C10.H25.N5.O5.P2.S2. " 	$2 = "C10H25N5O5P2S2" 	$3 = "8.00"		$4="421.0772333"	$5="0"	$6="0"	$7="+0.40"
+    		## if ( $line =~ /([\w|\.]+)\s+(\d+.?\d*)\s+(\d+.?\d*)\s+([+|-]\d+.?\d*)\s+(.*)/ ) { ## for hr2 1.02
+    		
+    		if ( $line =~ /([\w|\.]+)\s+(\w+)\s+(\d+.?\d*)\s+(\d+.?\d*)\s+(\d+.?\d*)\s+(\d+.?\d*)\s+([+|-]\d+.?\d*)/ ) { # for hr2 1.03
+    			my ( $formula, $cleanformula, $rings_and_double_bond_equivalent, $formula_mz, $abscharge, $nadd, $mmu_value  ) = ( $1, $2, $3, $4, $5, $6, $7 ) ;
+     			
+    			if (defined $formula ) 		{ $formula =~ s/\.//g ; 	push (@formula, $formula) ;	} # clean \.
+    			if (defined $rings_and_double_bond_equivalent ) {		push (@rings_and_double_bond_equivalents, $rings_and_double_bond_equivalent) ;	} # 
+    			if (defined $formula_mz ) 	{ 						 	push (@formula_mz, $formula_mz) ;	}
+    			if (defined $mmu_value ) 	{ $mmu_value =~ s/\+// ; 	push (@mmus, $mmu_value) ;	} # clean (+)
+    		}
+    		elsif (  $line =~ /(\d+)\s+formulas.+\s+(\d+)\s+seconds.+\s+(\d+)\s+formulae/ ) {
+    			( $formula_nb, $time, $formula_total  ) = ( $1, $2, $3 ) ;
+    		}
+    		else {	next;	}
+    	}
+    	# build parser
+    	if ( scalar(@formula) > 0 ){
+    		$parsed_res{'ENTRY_FORMULA'} = \@formula ; 
+	    	$parsed_res{'rings_and_double_bond_equivalents'} = \@rings_and_double_bond_equivalents ; 
+	    	$parsed_res{'ENTRY_CPD_MZ'} = \@formula_mz ; 
+	    	$parsed_res{'ENTRY_DELTA'} = \@mmus ; 
+	    	$parsed_res{'MASSES_TOTAL'} = \$formula_nb ; 
+	    	$parsed_res{'time'} = \$time ;
+    	}
+    }
+    return(\%parsed_res) ;
+}
+## END of SUB
+
+
+=head2 METHOD set_html_tbody_object
+
+	## Description : initializes and build the tbody object (perl array) need to html template
+	## Input : $nb_pages, $nb_items_per_page
+	## Output : $tbody_object
+	## Usage : my ( $tbody_object ) = set_html_tbody_object($nb_pages, $nb_items_per_page) ;
+	
+=cut
+## START of SUB
+sub set_html_tbody_object {
+	my $self = shift ;
+    my ( $nb_pages, $nb_items_per_page ) = @_ ;
+
+	my ( @tbody_object ) = ( ) ;
+	
+	for ( my $i = 1 ; $i <= $nb_pages ; $i++ ) {
+	    
+	    my %pages = ( 
+	    	# tbody feature
+	    	PAGE_NB => $i,
+	    	MASSES => [], ## end MASSES
+	    ) ; ## end TBODY N
+	    push (@tbody_object, \%pages) ;
+	}
+    return(\@tbody_object) ;
+}
+## END of SUB
+
+=head2 METHOD add_mz_to_tbody_object
+
+	## Description : initializes and build the mz object (perl array) need to html template
+	## Input : $tbody_object, $nb_items_per_page, $mz_list
+	## Output : $tbody_object
+	## Usage : my ( $tbody_object ) = add_mz_to_tbody_object( $tbody_object, $nb_items_per_page, $mz_list ) ;
+	
+=cut
+## START of SUB
+sub add_mz_to_tbody_object {
+	my $self = shift ;
+    my ( $tbody_object, $nb_items_per_page, $mz_list, $ids_list, $totals ) = @_ ;
+
+	my ( $current_page, $mz_index ) = ( 0, 0 ) ;
+	
+	foreach my $page ( @{$tbody_object} ) {
+		
+		my @colors = ('white', 'green') ;
+		my ( $current_index, , $icolor ) = ( 0, 0 ) ;
+		
+		for ( my $i = 1 ; $i <= $nb_items_per_page ; $i++ ) {
+			# 
+			if ( $current_index > $nb_items_per_page ) { ## manage exact mz per html page
+				$current_index = 0 ; 
+				last ; ##
+			}
+			else {
+				$current_index++ ;
+				if ( $icolor > 1 ) { $icolor = 0 ; }
+				
+				if ( exists $mz_list->[$mz_index]  ) {
+					my $total = \0 ;
+					if ( $totals->[$mz_index]{'MASSES_TOTAL'} ) { $total = $totals->[$mz_index]{'MASSES_TOTAL'} }					
+					
+					my %mz = (
+						# mass feature
+						MASSES_ID_QUERY => $ids_list->[$mz_index],
+						MASSES_MZ_QUERY => $mz_list->[$mz_index],
+						MZ_COLOR => $colors[$icolor],
+						MASSES_NB => $mz_index+1,
+						MASSES_TOTAL => $$total ,
+						ENTRIES => [] ,
+					) ;
+					push ( @{ $tbody_object->[$current_page]{MASSES} }, \%mz ) ;
+					# Html attr for mass
+					$icolor++ ;
+				}
+			}
+			$mz_index++ ;
+		} ## foreach mz
+
+		$current_page++ ;
+	}
+    return($tbody_object) ;
+}
+## END of SUB
+
+=head2 METHOD add_entries_to_tbody_object
+
+	## Description : initializes and build the mz object (perl array) need to html template
+	## Input : $tbody_object, $nb_items_per_page, $mz_list, $entries
+	## Output : $tbody_object
+	## Usage : my ( $tbody_object ) = add_entries_to_tbody_object( $tbody_object, $nb_items_per_page, $mz_list, $entries ) ;
+	
+=cut
+## START of SUB
+sub add_entries_to_tbody_object {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $tbody_object, $results ) = @_ ;
+    
+    my $index_page = 0 ;
+    my $index_mz_continous = 0 ;
+    
+    foreach my $page (@{$tbody_object}) {
+    	
+    	my $index_mz = 0 ;
+    	
+    	foreach my $mz (@{ $tbody_object->[$index_page]{MASSES} }) {
+    		
+    		my $index_res = 0 ;
+    		if ( $results->[$index_mz_continous]{ENTRY_FORMULA} ){
+	    			
+    			my $entry_nb = scalar( @{ $results->[$index_mz_continous]{ENTRY_FORMULA} } ) ;
+    			for( my $i = 0 ; $i<$entry_nb; $i++ ) {
+    				my %entry = (
+			    		ENTRY_COLOR 	=> $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR},
+			   			ENTRY_FORMULA 	=> $results->[$index_mz_continous]->{ENTRY_FORMULA}[$i],
+						ENTRY_CPD_MZ 	=> $results->[$index_mz_continous]->{ENTRY_CPD_MZ}[$i],
+						ENTRY_DELTA 	=> $results->[$index_mz_continous]->{ENTRY_DELTA}[$i]			
+			    	) ;
+		    		push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ;
+    			}
+    			$index_res++ ;	
+    		}
+    		$index_mz ++ ;
+    		$index_mz_continous ++ ;
+    	}
+    	$index_page++ ;
+    }
+    return($tbody_object) ;
+}
+## END of SUB
+
+=head2 METHOD write_html_skel
+
+	## Description : prepare and write the html output file
+	## Input : $html_file_name, $html_object, $html_template
+	## Output : $html_file_name
+	## Usage : my ( $html_file_name ) = write_html_skel( $html_file_name, $html_object ) ;
+	
+=cut
+## START of SUB
+sub write_html_skel {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $html_file_name,  $html_object, $pages , $search_condition, $html_template, $js_path, $css_path ) = @_ ;
+    
+    my $html_file = $$html_file_name ;
+    
+    if ( defined $html_file ) {
+		open ( HTML, ">$html_file" ) or die "Can't create the output file $html_file " ;
+		
+		if (-e $html_template) {
+			my $ohtml = HTML::Template->new(filename => $html_template);
+			$ohtml->param(  JS_GALAXY_PATH => $js_path, CSS_GALAXY_PATH => $css_path  ) ;
+			$ohtml->param(  CONDITIONS => $search_condition  ) ;
+			$ohtml->param(  PAGES_NB => $pages  ) ;
+			$ohtml->param(  PAGES => $html_object  ) ;
+			print HTML $ohtml->output ;
+		}
+		else {
+			croak "Can't fill any html output : No template available ($html_template)\n" ;
+		}
+		
+		close (HTML) ;
+    }
+    else {
+    	croak "No output file name available to write HTML file\n" ;
+    }
+    return(\$html_file) ;
+}
+## END of SUB
+
+=head2 METHOD write_csv_one_mass
+
+	## Description :  print a csv file
+	## Input : $masses, $ids, $results, $file
+	## Output : N/A
+	## Usage : write_csv_one_mass( $ids, $results, $file ) ;
+	
+=cut
+## START of SUB
+sub write_csv_one_mass {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $masses, $ids, $results, $file,  ) = @_ ;
+    
+    open(CSV, '>:utf8', "$file") or die "Cant' create the file $file\n" ;
+    print CSV "ID\tMASS_SUBMIT\tCPD_FORMULA\tCPD_MW\tDELTA\n" ;
+    	
+    my $i = 0 ;
+    	
+    foreach my $id (@{$ids}) {
+    	my $mass = $masses->[$i] ;
+    	
+    	if ( $results->[$i] ) { ## an requested id has a result in the list of hashes $results.
+    		
+    		my $entry_nb = 0 ;
+    		
+    		## in case of no results -- Hr_parsed Results : $VAR1 = [ { 'ENTRY_FORMULA' => [] } ];
+    		if ( !$results->[$i]{'ENTRY_FORMULA'} ) { 	print CSV "$id\t$mass\tN/A\t0.0\t0.0\n" ; 	}
+    		
+    		foreach (@{$results->[$i]{'ENTRY_FORMULA'}}) {
+
+    			print CSV "$id\t$mass\t" ;
+    			## print cpd formula
+    			if ( $results->[$i]{'ENTRY_FORMULA'}[$entry_nb] ) 	{	print CSV "$results->[$i]{'ENTRY_FORMULA'}[$entry_nb]\t" ; }
+    			else { 							print CSV "N/A\t" ; }
+    			## print cpd name
+    			if ( $results->[$i]{'ENTRY_CPD_MZ'}[$entry_nb] ) 	{ 	print CSV "$results->[$i]{'ENTRY_CPD_MZ'}[$entry_nb]\t" ; }
+    			else { 							print CSV "0.0\t" ; }
+    			## print delta
+    			if ( $results->[$i]{'ENTRY_DELTA'}[$entry_nb] ) 	{ print CSV "$results->[$i]{'ENTRY_DELTA'}[$entry_nb]\n" ; }
+    			else { 							print CSV "0.0\n" ; }
+    			$entry_nb++ ;
+    		}
+    	}
+    	else {
+    		print CSV "$id\t$mass\tN/A\t0.0\t0.0\n" ;
+    	}
+    	$i++ ;
+    }
+   	close(CSV) ;
+    return() ;
+}
+## END of SUB
+
+=head2 METHOD add_hr_matrix_to_input_matrix
+
+	## Description : build a full matrix (input + lm column)
+	## Input : $input_matrix_object, $lm_matrix_object
+	## Output : $output_matrix_object
+	## Usage : my ( $output_matrix_object ) = add_hr_matrix_to_input_matrix( $input_matrix_object, $hr_matrix_object ) ;
+	
+=cut
+## START of SUB
+sub add_hr_matrix_to_input_matrix {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $input_matrix_object, $hr_matrix_object ) = @_ ;
+    
+    my @output_matrix_object = () ;
+    my $index_row = 0 ;
+    
+    foreach my $row ( @{$input_matrix_object} ) {
+    	my @init_row = @{$row} ;
+    	
+    	if ( $hr_matrix_object->[$index_row] ) {
+    		my $dim = scalar(@{$hr_matrix_object->[$index_row]}) ;
+    		
+    		if ($dim > 1) { warn "the add method can't manage more than one column\n" ;}
+    		my $lm_col =  $hr_matrix_object->[$index_row][$dim-1] ;
+
+   		 	push (@init_row, $lm_col) ;
+	    	$index_row++ ;
+    	}
+    	push (@output_matrix_object, \@init_row) ;
+    }
+    return(\@output_matrix_object) ;
+}
+## END of SUB
+
+=head2 METHOD write_csv_skel
+
+	## Description : prepare and write csv output file
+	## Input : $csv_file, $rows
+	## Output : $csv_file
+	## Usage : my ( $csv_file ) = write_csv_skel( $csv_file, $rows ) ;
+	
+=cut
+## START of SUB
+sub write_csv_skel {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $csv_file, $rows ) = @_ ;
+    
+    my $ocsv = lib::csv::new() ;
+	my $csv = $ocsv->get_csv_object("\t") ;
+	$ocsv->write_csv_from_arrays($csv, $$csv_file, $rows) ;
+    
+    return($csv_file) ;
+}
+## END of SUB
+
+=head2 METHOD set_hr_matrix_object
+
+	## Description : build the hr_row under its ref form
+	## Input : $header, $init_mzs, $entries
+	## Output : $hr_matrix
+	## Usage : my ( $hmdb_matrix ) = set_hr_matrix_object( $header, $init_mzs, $entries ) ;
+	
+=cut
+## START of SUB
+sub set_hr_matrix_object {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $header, $init_mzs, $entries ) = @_ ;
+    
+    my @hr_matrix = () ;
+    
+    if ( defined $header ) {
+    	my @headers = () ;
+    	push @headers, $header ;
+    	push @hr_matrix, \@headers ;
+    }
+    
+    my $index_mz = 0 ;
+    
+    foreach my $mz ( @{$init_mzs} ) {
+    	
+    	my $index_entries = 0 ;
+    	my @clusters = () ;
+    	my $cluster_col = undef ;
+    	
+    	my $nb_entries = $entries->[$index_mz]{MASSES_TOTAL} ;
+    	
+    	foreach (@{$entries->[$index_mz]{'ENTRY_FORMULA'}}) {
+    				
+    		my $delta = $entries->[$index_mz]{'ENTRY_DELTA'}[$index_entries] ;
+	    	my $hr_formula = $entries->[$index_mz]{'ENTRY_FORMULA'}[$index_entries] ;
+	    	my $hr_mz = $entries->[$index_mz]{'ENTRY_CPD_MZ'}[$index_entries] ;
+    		
+	    	
+	    	## METLIN data display model 
+	   		## entry1=VAR1::VAR2::VAR3::VAR4|entry2=VAR1::VAR2::VAR3::VAR4|...
+	   		# manage final pipe
+	   		if ($index_entries < $$nb_entries-1 ) { 	$cluster_col .= $delta.'::('.$hr_formula.')::'.$hr_mz.'|' ; }
+	   		else { 						   			$cluster_col .= $delta.'::('.$hr_formula.')::'.$hr_mz ; 	}
+	    		
+	    	$index_entries++ ;
+	    } ## end foreach
+	    if ( !defined $cluster_col ) { $cluster_col = 'No_result_found_with HR' ; }
+    	push (@clusters, $cluster_col) ;
+    	push (@hr_matrix, \@clusters) ;
+    	$index_mz++ ;
+    }
+    return(\@hr_matrix) ;
+}
+## END of SUB
+
+
+
+1 ;
+
+
+__END__
+
+=head1 SUPPORT
+
+You can find documentation for this module with the perldoc command.
+
+ perldoc hr.pm
+
+=head1 Exports
+
+=over 4
+
+=item :ALL is manage_atoms, check_hr_exe, manage_tolerance
+
+=back
+
+=head1 AUTHOR
+
+Franck Giacomoni E<lt>[e-mail]<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 : 02 / 20 / 2014
+
+version 2 : ??
+
+=cut
\ No newline at end of file