#!/usr/bin/perl
######### Sequest ###########################################
#                                                           # 
#       **************************************************  #    
#       **** Deisotope program for MS2		          ****  #    
#       ****					                      ****  #    
#       ****Copyright (C) 20212 - Xusheng Wang	      ****  #    
#       ****all rights reserved.		              ****  #    
#       ****xusheng.wang@stjude.org		              ****  #    
#       ****					                      ****  #    
#       ****					                      ****  #    
#       **************************************************  #   
#############################################################
package Spiders::Params;

use strict;
use vars qw($VERSION @ISA @EXPORT);

$VERSION     = 1.00;
@ISA	 = qw(Exporter);
@EXPORT = qw(error  path  parse_param  get_adducts parameter_check get_full_text  write_text  reconstruct  rewrite  update  get  set_default_dir  get_defaults); 

my $ERROR;

#################################################################
#CLASS METHODS
#################################################################
sub new {
  my ($class,%args) = @_;
  my $self = {};
  $self->{PATH} = $args{-path};
  bless $self;
  
  if($args{CREATE_DEFAULT}){
    Spiders::Params->make_default($args{path});
  }
  
  eval {
    $self->parse_param();
  };
  $ERROR = $@ if($@);
  return $self;
}


#################################################################
#PUBLIC OBJECT METHODS
#################################################################
sub error {
  return $ERROR;
}

sub path {
  my $self = shift;
  $self->{PATH} = shift if(@_);
  return $self->{PATH};
}


	
sub parse_param {
	my($self) = @_;
  
	my ($paramhash, $paramfile) = @_;
	
	my %parameters;
	$parameters{'labeled_data'} = 1;
	$parameters{'labeled_ID_method'} = 1;
	$parameters{'mode'} = 1;	
	$parameters{'unlabel_scan'} = 1;
	$parameters{'unlabel_min_mass'} = 1;
	$parameters{'unlabel_max_mass'} = 1;
	$parameters{'database'} = 1;
	$parameters{'mass_formula_database'} = 1;
	$parameters{'structure_database'} = 1;
	$parameters{'formula_mass_tolerance_searching'} = 1;
	$parameters{'formula_mass_tolerance_pairing'} = 1;
	$parameters{'c12_c13_tolerance'} = 1;
	$parameters{'c12_n15_tolerance'} = 1;
	$parameters{'relative_isotopes_intensity'} = 1;
	$parameters{'min_pair_correlation'} = 1;
	$parameters{'cluster_tolerance'} = 1;
	$parameters{'first_scan_extraction'} = 1;
	$parameters{'last_scan_extraction'} = 1;
	$parameters{'tolerance_unit'} = 1;	
	$parameters{'isolation_window'} = 1;
	$parameters{'mass_correction'} = 1;
	$parameters{'loading_normalization'}=1;
	$parameters{'decharge_ppm'}=1;
	$parameters{'deisotope_ppm'}=1;

	$parameters{'percentage_ms2_peaks'}=1;
	$parameters{'frag_mass_tolerance'}=1;		
	$parameters{'frag_mass_tolerance_unit'}=1;
	$parameters{'matched_scan_dist'}=1;		
	
	$parameters{'mass_shift'}=1;
	$parameters{'data_acquisition_mode'}=1;
	$parameters{'intensity_threshold'}=1;
	$parameters{'intensityThresholdScale2D'}=1;
	$parameters{'noise_detection_method'}=1;	
	$parameters{'noisePercentage2D'}=1;
	$parameters{'noisePercentage3D'}=1;
	$parameters{'processor_number'}=1;
	$parameters{'fragment_method'}=1;
	$parameters{'cluster'}=1;		
	$parameters{'job_management_system'} = 1;
	$parameters{'signal_noise_ratio'}=1;
	$parameters{'adduct'} = 1;
	$parameters{'library_search'} = 1;
	$parameters{'decoy_strategy'} = 1;
	my $path = $self->{PATH};

	if(open(P,"< $path"))
	{
		my($line);
		my $phash = {};
    
		while($line = <P>)
		{
			my $linehash = {};
			my $comments = "";
      
			if( $line =~ s/\s*([;\#].*)$// ) {$comments = $1;}
      
			$linehash->{Comments} = $comments;
      
			if($line =~ /^(.+?)\s*=\s*(.+)$/)
			{
				my ($key,$data) = ($1,$2);
		
				$data =~ s/\s+$//o;
				$phash->{$key} = $data;

				#if((!defined($parameters{$key})) and ($key !~/adduct/))
				#{
				#	print "  You put a wrong parameter: $key\n";
				#	exit(1);
				#}					
			}      
		}
     
		close P;
		$self->{PARAMETERS} = $phash;
		return $phash;
	}
	return 0;
  
}

sub get_adducts
{
	my ($self,$parameter) = @_;
	my $adducts;
	foreach my $param (keys %$parameter)
	{
		if($param =~/adduct\_(\w+)/)
		{
			$adducts->{$1} = $parameter->{$param};
		}
	}
	return $adducts;
}

sub parameter_check
{
	my($self,$params) = @_;
	if(($params->{last_scan_extraction} - $params->{first_scan_extraction})<50)
	{
		print "  Please set a larger scan region (e.g. >100) for peak dection\n";
		print "  For unlabeled data, the searched scan is defined by a parameter of unlabel_scan instead of these two parameters\n";
		print "  The scan region has to cover unlabel_scan\n\n";		
		exit;
	}

	if(!-e($params->{mass_formula_database}))
	{
		print "  The specified mass formula database can not be found\n";
		exit;
	}
	if(!-e($params->{structure_database}))
	{
		print "  The specified structure database can not be found\n";
		exit;
	}
=head	
	unless(($params->{database} eq "PUBCHEM") or ($params->{database} eq "pubchem") or ($params->{database} eq "HMDB") or ($params->{database} eq "hmdb"))
	{
		print "  You set a wrong database name\n";
		exit;
	}
=cut	
=head	
	if(($params->{c12_c13_tolerance})>0.01)
	{
		print "  The tolerance between C12 and C13 (i.e. c12_c13_tolerance) is too large\n";
		exit;
	}
	if(($params->{c12_n15_tolerance})>0.01)
	{
		print "  The tolerance between C12 and N15 (i.e. c12_n15_tolerance) is too large\n";
		exit;
	}
=cut	
}

sub get_full_text {
  my($self) = @_;
  local $/ = undef;
  my $path = $self->{PATH} || return;
  open(P,"< $path") || return;
  my $p = <P>;
  close P;
  return $p;
}

sub write_text {
  my ($self) = @_;
  #figure out something safe;
}

##################################################################

sub reconstruct {
  my ($self,$newpath) = @_;
  my $path = $self->{PATH};
  open(P,"< $path") || die "Couldn't open $path: $!";
  my @lines = <P>;
  close P;
  
  my $mask = "%-40s";
  
  open(NEW,"> $newpath") || die "Couldnt't open $newpath: $!";
  my $line;
  my @newlines = ();
  my $parameters = $self->{PARAMETERS};
  
  foreach $line (@lines){
    if($line =~ /^(.+?)\s*=\s*(.+)$/ && exists $parameters->{$1}){
      printf(NEW $mask,"$1 = $parameters->{$1}->{data}");
      print NEW $parameters->{$1}->{Comments}."\n";
    }
    else{
      print NEW $line;
    }
  }
  close NEW;
  
}


sub reconstruct_new {
  my ($self,$newpath) = @_;
  my $path = $self->{PATH};
  open(P,"< $path") || die "Couldn't open $path: $!";
  my @lines = <P>;
  close P;

  my $mask = "%-40s";

  open(NEW,"> $newpath") || die "Couldnt't open $newpath: $!";
  my $line;
  my @newlines = ();
  my $parameters = $self->{PARAMETERS};

  foreach $line (@lines){
        next if($line =~/duc/);
        if($line=~/SEQUEST_ENZYME_INFO/)
        {
                @lines=();
        }
    if($line =~ /^(.+?)\s*=\s*(.+)$/ && exists $parameters->{$1}){
      printf(NEW $mask,"$1 = $parameters->{$1}->{data}");
      print NEW $parameters->{$1}->{Comments}."\n";
    }
    else{
      print NEW $line;
    }
  }
  close NEW;

}



#-----------------------------------------------------------------

sub rewrite {
  my($self) = @_;
  return $self->reconstruct($self->{PATH});
}

#################################################################

sub update {
  my($self,$key,$newval) = @_;
  my $parameters = $self->{PARAMETERS};
  
  if(exists $parameters->{$key}){
    $parameters->{$key}->{data} = $newval;
  }
}

sub get {
  my($self,$key) = @_;
  
  my $parameters = $self->{PARAMETERS};
  if($key eq 'current_enzyme'){return $self->current_enzyme();}
  if(my $p  = $parameters->{$key}){return $p->{data}}
  
  return 'Unknown';
}

#################################################################

sub set_default_dir {
  my ($self,$defaultdir) = @_;
  if(opendir(DIR,$defaultdir)){
    $defaultdir =~ s/\/$//o;
    $defaultdir .= '/';
    $self->{defaultdir} = $defaultdir;
    
    my @defaults = map {"$defaultdir".$_}
    grep {/\.params/} readdir(DIR);
    
    $self->{defaults} = \@defaults;
  }
}

sub get_defaults {
  my($self) = @_;
  return $self->{defaults};
}



1;