#!/usr/local/bin/perl

use strict;
use Getopt::Long;
use FindBin;
use Data::Dumper;
use List::MoreUtils qw(uniq);
use lib "$FindBin::Bin/../../lib/perl";
use vars qw ($sbeams $sbeamsMOD $q $current_contact_id $current_username
             $PROG_NAME $USAGE %OPTIONS $QUIET $VERBOSE $DEBUG $DATABASE
             $TABLE_NAME $PROGRAM_FILE_NAME $CATEGORY $DB_TABLE_NAME
             @MENU_OPTIONS);
##use CGI::Carp qw(fatalsToBrowser croak);

use SBEAMS::Connection qw($q $log);
use SBEAMS::Connection::Settings;
use SBEAMS::Connection::Tables;
use SBEAMS::Connection::TabMenu;

use SBEAMS::PeptideAtlas;
use SBEAMS::PeptideAtlas::Settings;
use SBEAMS::PeptideAtlas::Tables;
use SBEAMS::PeptideAtlas::ConsensusSpectrum;
use SBEAMS::PeptideAtlas::ModificationHelper;
use SBEAMS::PeptideAtlas::Utilities;
use SBEAMS::PeptideAtlas::ProtInfo qw(is_uniprot_identifier);

use SBEAMS::Proteomics::Tables;
use SBEAMS::BioLink::Tables;

$sbeams = new SBEAMS::Connection;
$sbeamsMOD = new SBEAMS::PeptideAtlas;
$sbeamsMOD->setSBEAMS($sbeams);
$sbeams->setSBEAMS_SUBDIR($SBEAMS_SUBDIR);
my $htmlmode;
my $current_page = { organism => '', atlas_build_id => '' };

###############################################################################
# Set program name and usage banner for command like use
###############################################################################
$PROG_NAME = $FindBin::Script;
$USAGE = <<EOU;
Usage: $PROG_NAME [OPTIONS] key=value key=value ...
Options:
  --verbose n         Set verbosity level.  default is 0
  --quiet             Set flag to print nothing at all except errors
  --debug n           Set debug flag

 e.g.:  $PROG_NAME [OPTIONS] [keyword=value],...

EOU

#### Process options
unless (GetOptions(\%OPTIONS,"verbose:s","quiet","debug:s")) {
  print "$USAGE";
  exit;
}

$VERBOSE = $OPTIONS{"verbose"} || 0;
$QUIET = $OPTIONS{"quiet"} || 0;
$DEBUG = $OPTIONS{"debug"} || 0;

if ($DEBUG) {
  print "Options settings:\n";
  print "  VERBOSE = $VERBOSE\n";
  print "  QUIET = $QUIET\n";
  print "  DEBUG = $DEBUG\n";
}


###############################################################################
# Set Global Variables and execute main()
###############################################################################
main();
exit(0);
###############################################################################
# Main Program:
#
# Call $sbeams->Authenticate() and exit if it fails or continue if it works.
###############################################################################
sub main {

  #### Do the SBEAMS authentication and exit if a username is not returned
  exit unless ($current_username = $sbeams->Authenticate(
    #permitted_work_groups_ref=>['PeptideAtlas_user','PeptideAtlas_admin'],
    # connect_read_only=>1,
    allow_anonymous_access=>1,
  ));


  #### Read in the default input parameters
  my %parameters;

  $parameters{uploaded_file_not_saved} = 1;

  my $n_params_found = $sbeams->parse_input_parameters(
    q=>$q,parameters_ref=>\%parameters);
     #$sbeams->printDebuggingInfo($q);

  #### Process generic "state" parameters before we start
  $sbeams->processStandardParameters(parameters_ref=>\%parameters);

  #### Decide what action to take based on information so far
  if ($parameters{action} eq "???") {

    # Some action

  } else {

    my $project_id = $sbeamsMOD->getProjectID(
        atlas_build_id => $parameters{atlas_build_id}
        );

    $sbeamsMOD->display_page_header( project_id => $project_id,
                                     use_tabbed_panes => 1
                                   );
    handle_request(ref_parameters=>\%parameters);

    $sbeamsMOD->display_page_footer( use_tabbed_panes => 1 );

  }


} # end main


###############################################################################
# Handle Request
###############################################################################
sub handle_request {

  my %args = @_;

  #### Process the arguments list
  my $ref_parameters = $args{'ref_parameters'}
    || die "ref_parameters not passed";
  my %parameters = %{$ref_parameters};


  #### Show current user context information
  #$sbeams->printUserContext();

  #### Get the HTML to display the tabs
  my $tabMenu = $sbeamsMOD->getTabMenu(
    parameters_ref => \%parameters,
    program_name => $PROG_NAME,
  );
  if ($sbeams->output_mode() eq 'html') {
    print $tabMenu->asHTML();
    print "<script>document.title = 'PeptideAtlas: Get PTM Spectra';</script>";
  }

  #### Get the current atlas_build_id based on parameters or session
  my $atlas_build_id = $sbeamsMOD->getCurrentAtlasBuildID(
    parameters_ref => \%parameters,
  );
  if (defined($atlas_build_id) && $atlas_build_id < 0) {
    return;
  }
  $parameters{atlas_build_id} = $atlas_build_id;

  #### Define some generic variables
  my ($i,$element,$key,$value,$line,$result,$sql);


  #### Define some variables for a query and resultset
  my %resultset = ();
  my $resultset_ref = \%resultset;
  my (%url_cols,%hidden_cols,%max_widths,$show_sql);

  #### Read in the standard form values
  my $apply_action  = $parameters{'action'} || $parameters{'apply_action'};
  my $TABLE_NAME = $parameters{'QUERY_NAME'};

  #### Set some specific settings for this program
  my $CATEGORY="Get PTM Spectra";
  my $PROGRAM_FILE_NAME = $PROG_NAME;
  my $base_url = "$CGI_BASE_DIR/$SBEAMS_SUBDIR/$PROGRAM_FILE_NAME";
  my $help_url = "$CGI_BASE_DIR/help_popup.cgi";


  #### If the apply action was to recall a previous resultset, do it
  my %rs_params = $sbeams->parseResultSetParams(q=>$q);
  if ($apply_action =~ /VIEWRESULTSET|VIEWPLOT/ ) {
    $sbeams->readResultSet(
        resultset_file=>$rs_params{set_name},
        resultset_ref=>$resultset_ref,
        query_parameters_ref=>\%parameters
    );
  }

  #### Build ATLAS_BUILD constraint
  my $atlas_build_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"AB.atlas_build_id",
    constraint_type=>"int_list",
    constraint_name=>"Atlas Build",
    constraint_value=>$parameters{atlas_build_id} );
  return if ($atlas_build_clause eq '-1');

  my $chimera_clause = '';
  if ($parameters{ptm_type} =~ /\_respect/){
    $chimera_clause = 'AND S.chimera_level > 1';
    $parameters{ptm_type} =~ s/_respect//;
  }

  my $ptm_type_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"SPI.ptm_type",
    constraint_type=>"plain_text",
    constraint_name=>"PTM Type",
    constraint_value=>$parameters{ptm_type} );
  return if ($ptm_type_clause eq '-1');

  my $protein_site_clause = ''; 
  if ($parameters{site}){
    $parameters{site} =~ s/\s//g;
    if ($parameters{site} =~ /\D/){
      $sbeams->reportException(
        state => 'ERROR',
        type => 'CONSTRAINT ERROR',
        message => 'protein site should be numbers',
      );
      return; 
    }
    $protein_site_clause = qq~
      AND PM.start_in_biosequence <= $parameters{site}
      AND PM.end_in_biosequence >= $parameters{site}
    ~;
  }

  my $biosequence_name_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"BS.biosequence_name",
    constraint_type=>"plain_text",
    constraint_name=>"biosequence_name",
    constraint_value=>$parameters{biosequence_name} );

  return if ($biosequence_name_clause eq '-1');
  
	my %colnameidx = ();
	my @column_titles = ();
	my @column_array = (
    ["biosequence_name", "BS.biosequence_name","Biosequence Name"],
    ["site", "''", "site"],
    ["residue", "''", "residue"],
		["Spectrum", "SI.spectrum_identification_id","Spectrum"],
    ["start_in_biosequence", "PM.start_in_biosequence", "Peptide Mapping Start"], 
		["modpep", "modified_peptide_sequence", "Modified Sequence"],
		["chg", "MPI.peptide_charge","Charge"],
		#["instrument_name", "I.instrument_name","Instr"],
		["probability", "SI.probability","Prob"],
    ["site_ptm_score", "''", "PTM Score"],
		["ptm_sequence", "SPI.ptm_sequence","PTM Sequence"],
		["ptm_lability","SPI.ptm_lability", "PTM Lability"],
    ["ptm_norm_info_gain", "SPI.ptm_norm_info_gain", "PTM Normalized Information Content"],
		["frg_type", "FRG.FRAGMENTATION_TYPE","Fragmentation Type"],
		["precursor_intensity", "S.precursor_intensity", "Precursor Intensity (x10^6)"],
		["total_ion_current", "S.total_ion_current", "TIC (x10^6)"],
		["signal_to_noise", "S.signal_to_noise", "S/N"],
		["scan_time", "scan_time", "RT"],
		["collision_energy","collision_energy", "CE"],
		["spectrum_name", "S.spectrum_name","Spectrum Name"],
		["ptm_type", "SPI.ptm_type","PTM Type"],
		["sample_tag", "SMP.sample_tag", "Experiment Tag"],
		["sample_id", "SMP.sample_id","Expt"],
	);
	my $columns_clause = $sbeams->build_SQL_columns_list(
		column_array_ref=>\@column_array,
		colnameidx_ref=>\%colnameidx,
		column_titles_ref=>\@column_titles
	);

  my $sql = qq~
    select distinct $columns_clause 
		FROM $TBAT_PEPTIDE_INSTANCE PI
    JOIN $TBAT_PEPTIDE_MAPPING PM ON (PM.peptide_instance_id = PI.peptide_instance_id)
		JOIN $TBAT_MODIFIED_PEPTIDE_INSTANCE MPI ON ( PI.peptide_instance_id = MPI.peptide_instance_id )
	  JOIN $TBAT_ATLAS_BUILD AB ON ( PI.atlas_build_id = AB.atlas_build_id )
	  JOIN $TBAT_SPECTRUM_IDENTIFICATION SI ON ( MPI.modified_peptide_instance_id = SI.modified_peptide_instance_id )
		JOIN $TBAT_SPECTRUM_PTM_IDENTIFICATION SPI ON ( SI.spectrum_identification_id = SPI.spectrum_identification_id)
		JOIN $TBAT_SPECTRUM S ON ( SI.spectrum_id = S.spectrum_id )
		LEFT JOIN $TBAT_FRAGMENTATION_TYPE FRG ON (FRG.FRAGMENTATION_TYPE_ID = S.FRAGMENTATION_TYPE_ID)
		JOIN $TBAT_SAMPLE SMP ON ( S.sample_id = SMP.sample_id )
    JOIN $TBAT_BIOSEQUENCE BS ON  (BS.BIOSEQUENCE_ID = PM.MATCHED_BIOSEQUENCE_ID)
    WHERE 1=1
    $atlas_build_clause 
    $protein_site_clause
    $ptm_type_clause
    $biosequence_name_clause
    $chimera_clause
  ~;
  my $show_sql = 0;
  #### Apply any parameter adjustment logic
  if ( $parameters{display_options} =~ /ShowSQL/ ) {
    $show_sql = 1;
  }

	$hidden_cols{'RT'} =1;
	$hidden_cols{'CE'} =1;
  #$hidden_cols{'ptm_type'} =1;
  $hidden_cols{'Expt'} = 1;
  
  $sbeams->display_sql( sql => $sql,use_tabbed_panes => 0 ) if ($show_sql);

 #########################################################################
  #### If QUERY or VIEWRESULTSET was selected, display the data
  if ($apply_action =~ /QUERY|VIEWRESULTSET|VIEWPLOT/i ) {
    if ($apply_action =~ /QUERY/){
      $sbeams->fetchResultSet(
        sql_query=>$sql,
        resultset_ref=>$resultset_ref,
        use_caching => 0 
      );
      postProcessResultset(
				rs_params_ref=>\%rs_params,
				resultset_ref=>$resultset_ref,
				query_parameters_ref=>\%parameters,
				column_titles_ref=>\@column_titles,
        colnameidx_ref => \%colnameidx,
				hidden_cols => \%hidden_cols);

      $rs_params{set_name} = "SETME";
      my %write_params = ( rs_table => $TBAT_ATLAS_BUILD,
                           key_field => 'atlas_build_id',
                           key_value => $parameters{atlas_build_id} );
      $sbeams->writeResultSet(
        resultset_file_ref=>\$rs_params{set_name},
        resultset_ref=>$resultset_ref,
        query_parameters_ref=>\%parameters,
        resultset_params_ref=>\%rs_params,
        query_name=>"$SBEAMS_SUBDIR/$PROGRAM_FILE_NAME",
        column_titles_ref=>\@column_titles,
#        %write_params
      );
    }
    #### Construct table help
    my $obs_help = ''; # get_table_help( 'spectra' );
    #### Display the resultset
    $sbeams->displayResultSet(
      resultset_ref=>$resultset_ref,
      query_parameters_ref=>\%parameters,
      rs_params_ref=>\%rs_params,
      url_cols_ref=>\%url_cols,
      hidden_cols_ref=>\%hidden_cols,
      max_widths=>\%max_widths,
      use_tabbed_panes => 1,
      column_titles_ref=>\@column_titles,
      column_help=>$obs_help,
      base_url=>$base_url,
    );

    #### Display the resultset controls
    $sbeams->displayResultSetControls(
      resultset_ref=>$resultset_ref,
      query_parameters_ref=>\%parameters,
      rs_params_ref=>\%rs_params,
      use_tabbed_panes => 1,
      base_url=>$base_url,
    );

#    #### Display a plot of data from the resultset
#    $sbeams->displayResultSetPlot_plotly(
#      rs_params_ref=>\%rs_params,
#      resultset_ref=>$resultset_ref,
#      query_parameters_ref=>\%parameters,
#      column_titles_ref=>\@column_titles,
#      use_tabbed_panes => 1,
#      mouseover_column => 'peptide_sequence',
#      mouseover_url => $url_cols{'Peptide Sequence'},
#      mouseover_tag => '%1V',
#      base_url=>$base_url,
#    );
    print qq~
    <script src="../../usr/javascript/ptm/ptm.js"></script>
    <script>
			const tempSpan = document.createElement('span');
			tempSpan.textContent = 'A';
			tempSpan.className = 'char';
			tempSpan.style.visibility = 'hidden'; // Make the element invisible
			document.body.appendChild(tempSpan); // Append to the body to get the correct width
			const letterheight = tempSpan.getBoundingClientRect().height;
			const letterwidth = tempSpan.getBoundingClientRect().width;
			document.body.removeChild(tempSpan); // Remove the temporary element

			function ptm_pep_html() {
				const table = document.getElementById('TBL');
				const rows = table.getElementsByTagName('tbody')[0].getElementsByTagName('tr');
				const columnIndex = 9;
				const tempSpan = document.createElement('span');
				for (let k = 1; k < rows.length; k++) {
					const cell = rows[k].getElementsByTagName('td')[columnIndex];
					const ptm_sequence = cell.innerText;
					cell.innerText = '';
					var pep_with_bars = show_prob_bars(ptm_sequence,barcolor='#ff5f00',label='ptmprob=',letterheight,letterwidth);
					cell.appendChild(pep_with_bars);
				}
			}
			// Call the function when the document is loaded
			document.addEventListener('DOMContentLoaded', ptm_pep_html);
		 </script> 
   ~;

  }else{
    if ($sbeams->invocation_mode() eq 'http') {
      print "<H4>Select parameters above and press QUERY</H4>\n";
    } else {
      print "You need to supply some parameters to contrain the query\n";
    }
  }
 }
#
#			my $spectra_display = $sbeamsMOD->get_individual_spectra_display( 
#				column_titles_ref=>\@column_titles,
#				colnameidx_ref => \%colnameidx,
#				resultset_ref=> $resultset_ref,
#				hidden_cols_ref=>\%hidden_cols );
#
#
#      #############################################################################
#      #### PTM Spectra
#      #############################################################################
#      if (%ptm_peps && $htmlmode){
#         $sbeamsMOD->display_spectra_ptm_table (
#           ptm_identification_ref => \%ptm_peps,
#           column_titles_ref=>\@column_titles,
#           colnameidx_ref => \%colnameidx,
#           resultset_ref=> $resultset_ref,
#           hidden_cols_ref=>\%hidden_cols,
#           ptm_score_summary_ref => \%ptm_score_summary );
#			}
#
#   } 
#}# end handle_request

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

sub postProcessResultset {
  my %args = @_;
  my ($i,$element,$key,$value,$line,$result,$sql);

  #### Process the arguments list
  my $resultset_ref = $args{'resultset_ref'};
  my $rs_params_ref = $args{'rs_params_ref'};
  my $query_parameters_ref = $args{'query_parameters_ref'};
  my $column_titles_ref = $args{'column_titles_ref'};
  my $colnameidx_ref = $args{'colnameidx_ref'};
  my $min_ptm_score = $query_parameters_ref->{min} || 0;
  my $max_ptm_score = $query_parameters_ref->{max} || 1.1;
  my $nochoice_id = $query_parameters_ref->{nochoice} || 0;
  my $query_site = $query_parameters_ref->{site};
  my $residue = $query_parameters_ref->{residue};

	#--------------------------------------------------
#   ["biosequence_name", "BS.biosequence_name","Biosequence Name"],
#    ["site", "''", "site"],
#    ["residue", "''", "residue"],
#    ["spectrum_name", "S.spectrum_name","Spectrum Name"],
#    ["Spectrum", "SI.spectrum_identification_id","Spectrum"],
#    ["start_in_biosequence", "PM.start_in_biosequence", "Peptide Mapping Start"],
#    ["modpep", "modified_peptide_sequence", "Modified Sequence"],
#    ["chg", "MPI.peptide_charge","Charge"],
#    ["probability", "SI.probability","Prob"],
#    ["ptm_sequence", "SPI.ptm_sequence","PTM Sequence"],
#    ["ptm_lability","SPI.ptm_lability", "PTM Lability"],
#    ["frg_type", "FRG.FRAGMENTATION_TYPE","Fragmentation Type"],
#    ["precursor_intensity", "S.precursor_intensity", "Precursor Intensity (x10^6)"],
#    ["total_ion_current", "S.total_ion_current", "TIC (x10^6)"],
#    ["signal_to_noise", "S.signal_to_noise", "S/N"],
#    ["scan_time", "scan_time", "RT"],
#    ["collision_energy","collision_energy", "CE"],
#    ["ptm_type", "SPI.ptm_type","PTM Type"],
#    ["sample_tag", "SMP.sample_tag", "Experiment Tag"],
#    ["sample_id", "SMP.sample_id","Expt"],

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

  my $protein_idx =$colnameidx_ref->{biosequence_name};
  my $offset_idx = $colnameidx_ref->{site};
  my $residue_idx = $colnameidx_ref->{residue};
  my $name_idx = $colnameidx_ref->{spectrum_name};
  my $spec_idx = $colnameidx_ref->{"Spectrum"};
  my $mseq_idx = $colnameidx_ref->{"modpep"};  
  my $chrg_idx = $colnameidx_ref->{"chg"};      
  my $smpl_idx = $colnameidx_ref->{"sample_id"};   
  my $prob_idx = $colnameidx_ref->{"probability"};
  my $ptm_idx = $colnameidx_ref->{"ptm_sequence"}; 
  my $ptm_lability_idx = $colnameidx_ref->{"ptm_lability"};
  my $frag_idx = $colnameidx_ref->{"frg_type"}; 
  my $it_idx = $colnameidx_ref->{"precursor_intensity"};
  my $tic_idx = $colnameidx_ref->{"total_ion_current"};
  my $sn_idx = $colnameidx_ref->{"signal_to_noise"}; 
  my $rt_idx = $colnameidx_ref->{"scan_time"}; 
  my $ce_idx = $colnameidx_ref->{"collision_energy"}; 
  my $ptm_type_idx = $colnameidx_ref->{"ptm_type"};
  my $start_idx = $colnameidx_ref->{"start_in_biosequence"};
  my $sample_tag_idx = $colnameidx_ref->{"sample_tag"};  
  my $site_ptm_score_idx = $colnameidx_ref->{"site_ptm_score"}; 

  my $has_ptm_score = 0;
  my $n_rows = scalar(@{$resultset_ref->{data_ref}});
  my %processed_spec=();
  my @processed_data;
 for (my $i=0; $i<$n_rows; $i++) {
    #### Loops through resultset and do formatting
    my $pep = $resultset_ref->{data_ref}->[$i];
    $pep->[$offset_idx]  = $query_site;
    $pep->[$residue_idx] = $residue;
		$pep->[$name_idx] =~ /(\S+)\.(\d+?)\.(\d+?)\.(\d)/;
		$processed_spec{$pep->[$name_idx] . '-'. $pep->[$smpl_idx] }++;
		my $mzml_basename = $1;
		my $precursor_charge = $4;
		$mzml_basename =~ s/\.mzML$//;    #remove .mzML if it's there
		my $mzml_fname = "$mzml_basename.mzML";
		my $rt;
		$pep->[$prob_idx] = sprintf("%0.3f", $pep->[$prob_idx]) unless $pep->[$prob_idx] == 1;
		$pep->[$prob_idx] = 1 if $pep->[$prob_idx] == 1;
		my $build_id = $query_parameters_ref->{atlas_build_id};
		my $img = "<IMG BORDER=0 SRC='$HTML_BASE_DIR/images/spectrum.gif' TITLE='View spectrum for $pep->[$mseq_idx] (+$pep->[$chrg_idx])'>";
 $pep->[$spec_idx] = qq~<A HREF="$CGI_BASE_DIR/PeptideAtlas/ShowObservedSpectrum?atlas_build_id=$build_id&spectrum_identification_id=$pep->[$spec_idx]&peptide=$pep->[$mseq_idx]&assumed_charge=$pep->[$chrg_idx]&sample_id=$pep->[$smpl_idx]&spectrum_name=$pep->[$name_idx]" TARGET=blank>$img</A>~;

		my $modified_pepseq = $pep->[$mseq_idx];
    my $start_in_biosequence = $pep->[$start_idx];
#      $pep->[$mseq_idx] =   $sbeamsMOD->formatMassMods($pep->[$mseq_idx]);
    ## filter using offset and min_score
    my $pass = 0;

		if ($pep->[$ptm_idx]){
      $pep->[$ptm_type_idx] =~ /^(.*):(.*)$/;
      my $ptm_residues=$1;
      my $ptm_name = $2;
      my $ptm_sequence = $pep->[$ptm_idx];
      my @elms = split(/\)/, $ptm_sequence);
      
      ### filter no choice ids
      my $modified_pepseq_w_n = $modified_pepseq;
      next if ($residue eq 'n' && $modified_pepseq !~ /^\[/);

      if ($ptm_residues =~ /n/ && $modified_pepseq !~ /^n/){
        $modified_pepseq_w_n = 'n'. $modified_pepseq_w_n;
      }
          
      my @m = $ptm_sequence =~ /([${ptm_residues}])/g;
      my @n = $modified_pepseq_w_n =~ /([${ptm_residues}]\[${ptm_name}\])/g;
      ## for human phospho 2022-04 build
      if ($modified_pepseq_w_n =~ /[${ptm_residues}]\[/ && $modified_pepseq_w_n !~ /${ptm_name}/){
        @n = $modified_pepseq_w_n =~ /([${ptm_residues}]\[)/g;
      }
 
      my $m = scalar @m;
      my $n = scalar @n;
      my $nochoice = 0;
      if ($n == $m){
        if (! $nochoice_id){
          next; 
        }
        $nochoice = 1;
      }

      if($ptm_sequence =~ /^n/ && $ptm_sequence !~ /n\(/){
        $ptm_sequence=~ s/n//;
      }
 
      my $cur_pos = $pep->[$start_idx]-1;
      foreach my $str (@elms){
				if ($str =~ /(.*)\((.*)/){
           my $aas = $1;
					 my $ptm_score = $2;
					 $cur_pos = $cur_pos + length($aas);
           #print "$ptm_sequence $query_site $aas $pep->[$start_idx] $cur_pos min_score=$min_ptm_score $ptm_score<BR>";
           if ($query_site && $cur_pos == $query_site){
              if ($nochoice ){
                if ($nochoice_id ){
									$pass = 1 ;
									$pep->[$site_ptm_score_idx] = $ptm_score;
                }
              }else{
                next if ($nochoice_id);
                if ($ptm_score >= $min_ptm_score && $ptm_score < $max_ptm_score){
									$pep->[$site_ptm_score_idx] = $ptm_score;
									$pass =1;
                }
              }
              last;
           }
           $cur_pos-- if ($aas eq 'n'); 
				} else {
					  $cur_pos = $cur_pos + length($str);
				}
      }
    }
    next if(! $pass);
    
    $pep->[$it_idx] = ( $pep->[$it_idx] ) ?  sprintf("%.2f", $pep->[$it_idx]/1000000) : $sbeams->makeInactiveText('n/a'); 
    $pep->[$tic_idx] = ( $pep->[$tic_idx] ) ?  sprintf("%.2f", $pep->[$tic_idx]/1000000): $sbeams->makeInactiveText('n/a');
    $pep->[$sn_idx] = ( $pep->[$sn_idx] ) ? sprintf("%.0f", $pep->[$sn_idx]) : $sbeams->makeInactiveText('n/a');

      $pep->[$rt_idx] = ( $pep->[$rt_idx] ) ? sprintf( "%0.1f", $pep->[$rt_idx]/60 ) : $sbeams->makeInactiveText('n/a'); 
      $pep->[$ce_idx] = ( $pep->[$ce_idx] ) ? sprintf( "%0.1f", $pep->[$ce_idx] ) : $sbeams->makeInactiveText('n/a'); 
    #if ($processed_spec{$pep->[$name_idx]. '-'. $pep->[$smpl_idx]} == 1){
      push @processed_data,  $resultset_ref->{data_ref}->[$i];
    #}
  } # end for each pep
  
  $resultset_ref->{data_ref} = \@processed_data;
  
  if ($has_ptm_score){
    #sort_ptm_peps($ptm_peps_ref);
  }
}