#!/usr/local/bin/perl

###############################################################################
# $Id$
#
# SBEAMS is Copyright (C) 2000-2023 Institute for Systems Biology
# This program is governed by the terms of the GNU General Public License (GPL)
# version 2 as published by the Free Software Foundation.  It is provided
# WITHOUT ANY WARRANTY.  See the full description of GPL terms in the
# LICENSE file distributed with this software.
###############################################################################


###############################################################################
# Get the script set up with everything it will need
###############################################################################
use strict;
#use vars qw ($sbeams);

use lib "../../lib/perl";

#use CGI::Carp qw(fatalsToBrowser croak);
use vars qw($PROGRAM_FILE_NAME);

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

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


use SBEAMS::PeptideAtlas;
use SBEAMS::PeptideAtlas::Settings;
use SBEAMS::PeptideAtlas::Tables;
use SBEAMS::PeptideAtlas::Utilities;


###############################################################################
# Global Variables
###############################################################################
my $sbeams = new SBEAMS::Connection;
$sbeams->setSBEAMS_SUBDIR($SBEAMS_SUBDIR);
my $atlas = new SBEAMS::PeptideAtlas;
$atlas->setSBEAMS($sbeams);

# Read input parameters
my $params = process_params();
$|++;

our $organism;
our $organism_id;

my $show_image = 0;

{ # Main
    # Authenticate or exit
    my $username = $sbeams->Authenticate( permitted_work_groups_ref => 
                                                      ['PeptideAtlas_user',
                                                      'PeptideAtlas_admin', 
                                                      'PeptideAtlas_readonly', 'PeptideAtlas_exec'],
                                                      # connect_read_only=>1,
                                                      allow_anonymous_access=>1,
                                              ) || exit;


    ## get current settings
    my $project_id = $sbeams->getCurrent_project_id();

    my $build_help = get_table_help( table => 'build' );
    my %resultset = ();
    my $resultset_ref = \%resultset;
    my $section = $params->{section} || '';

    my $page = $sbeams->getGifSpacer( 700 ) . "<BR>\n";
  #### Get the HTML to display the tabs
    my $tabMenu = $atlas->getTabMenu(
      parameters_ref => $params,
      program_name => 'buildDetails',
    );
#		my $back = $sbeams->getBackForm();
    $page .=<<"    END";
		$tabMenu
    <P>
    <!--This shows some information about the currently selected build.
    You can view the details of other builds by selecting an 
    item in the list below.  Although this will change build whose statistics 
    are to be displayed, it will not change your currently selected build.-->
    </P>
    $build_help
    END

    # We are not forcing the user into the new build - is that correct?
    my $build_id = $params->{atlas_build_id} || $atlas->getCurrentAtlasBuildID(parameters_ref => $params);
    my $build_path = get_build_path( build_id => $build_id );

    if ( !grep /^$build_id$/, $atlas->getAccessibleBuilds() ) {
#      die( "Access to specified build is not allowed" );
       $atlas->display_page_header(init_tooltip => 1);
       $build_id = $atlas->getCurrentAtlasBuildID(parameters_ref => $params);
		   $atlas->display_page_footer();
       exit;
    }
    $organism = $atlas->getCurrentAtlasOrganism (parameters_ref => $params);
    $organism_id = $atlas->getCurrentAtlasOrganism (parameters_ref => $params, type =>'organism_id');
    my $valid_build = 1;

    if (! $params->{caching} && ! $section){
      my $page_url = 'http';
      if ($ENV{HTTPS} = "on") {
				$page_url .= "s";
      }
      $page_url .= "://$ENV{SERVER_NAME}$ENV{REQUEST_URI}";
      #my $url_mdsum = md5_hex( $page_url ); 
      $page_url =~ /(atlas_build_id=\d+)/;
      my $html_cache_name = $1; 
      my $html_cache_loc  = '';
      if ($PHYSICAL_BASE_DIR !~ /dev\w+\/sbeams/){
	$html_cache_loc = "/net/dblocal/www/html/sbeamscommon/htmlcache/buildDetails";
      }else{
	$html_cache_loc = "$PHYSICAL_BASE_DIR/htmlcache/buildDetails";
      }

      if ( -e "$html_cache_loc/$html_cache_name"){
	if (open (IN,"<$html_cache_loc/$html_cache_name")){
	  print "Content-type: text/html\n\n";
	  print $_ while (<IN>);
	  close IN; 
	  exit;
	}
      }
    }

    # Add general section 
    my $n_canonical_protein;
    my ( $header );
    if (! $section ){
      $atlas->display_page_header( init_tooltip => 1, 
                                   header_info => $header, 
                                   project_id => $project_id, 
                                   onload => 'sortables_init()', 
                                   sortable => 1 );

      if (-e "$build_path/analysis/build_detail_tables.tsv") {
	print "$page";
	generate_html_from_file (file => "$build_path/analysis/build_detail_tables.tsv",
				 build_id => $build_id,
				 build_path => $build_path);
	exit; 
      }

      my $build_overview_html;
      ($n_canonical_protein, $build_overview_html) = get_build_overview ( $build_id );
      print $build_overview_html;
    }
    if (! $section || $section =~ /what.*new/i){
      my $what_is_new = fetchResultset(atlas_build_id => $build_id,
				       rs_table => 'buildDetail-new',
				       params => $params,
				       resultset_ref => $resultset_ref,
				       module_ref => sub{ $atlas->get_what_is_new(@_)});
      print "<BR>\n$what_is_new\n" if($what_is_new);
      
    }
    if (! $section || $section =~ /ProteomeCoverage/i){
      my $proteome_cover = '';
      my $ptm_coverage = '';
      my $proteomeComponentOrder_file = "$PHYSICAL_BASE_DIR/lib/conf/PeptideAtlas/ProteomeComponentOrder.txt";
      my @patterns =();
      if (open (O, "<$proteomeComponentOrder_file")){
         while (my $line = <O>){
           chomp $line;
           next if ($line =~ /^#/ ||  $line =~ /^$/);
           my ($org_id, $str) = split(/\t/, $line);
           if ($org_id == $organism_id){
              push @patterns,$line;
           }
         }
      }
      if (@patterns){
	$proteome_cover = fetchResultset(atlas_build_id => $build_id,
                                         rs_table => 'buildDetail-ProteomeCoverage',
                                         params => $params,
                                         resultset_ref => $resultset_ref,
                                         module_ref => sub{$atlas->get_proteome_coverage_new( $build_id, \@patterns)});
	$ptm_coverage = fetchResultset(atlas_build_id => $build_id,
				       rs_table => 'buildDetail-ptmCoverage',
				       params => $params,
				       resultset_ref => $resultset_ref,
				       module_ref => sub{$atlas->get_proteome_coverage_new( $build_id, \@patterns)});
        
      }else{
	$proteome_cover = fetchResultset(atlas_build_id => $build_id,
                                         rs_table => 'buildDetail-ProteomeCoverage',
                                         params => $params,
                                         resultset_ref => $resultset_ref,
                                         module_ref => sub{$atlas->get_proteome_coverage(@_)});
      }
      
      if($proteome_cover){
	print "$proteome_cover<BR>\n";
      }
      if ($ptm_coverage){
        print "$proteome_cover<BR>\n";
      }
    }
    my ( $sample_table, $sample_array_ref ,$column_name_ref ) = get_sample_info( $build_id );
    my ($dataset_contri_table) = get_dataset_contrib_info($build_id);

    if (! $section || $section =~ /SampleContribution/i){
      if ($params->{output_mode} =~ /tsv/i && $section){
        $atlas->print_html_table_to_tsv( data_ref => $sample_array_ref,
                                         column_name_ref => $column_name_ref,
                                         filename=>'SampleContribution.tsv'); 
      }else{
	print "$sample_table\n";
	print "$dataset_contri_table\n"; 
      }
    }
    
    if (! $section){
      $page = get_dataset_protein_info( build_id => $build_id);
      print "$page";
      $page = get_dataset_spec_protein_info( build_id => $build_id);
      print "$page";
      my $mayu_data_path = "$build_path/analysis/Mayu_out.csv";
      if ( -e $mayu_data_path ) {
	$page = get_mayu_info( $mayu_data_path );
	print $page;
      }
      #  print STDERR 'showtime ' . time() . "\n";
      # Add peptide stats section
      # Add graphic
      if ( $show_image ) {
	my $plots = get_build_plots ( build_id => $build_id, 
				      sample_array_ref => $sample_array_ref, 
				      column_name_ref => $column_name_ref); 
	print $plots;
      }
      my $charge_length_data_path = "$build_path/analysis/peptide_length-charge_dist.tsv";
      if (-e $charge_length_data_path){
	$page = get_peptide_length_charge_distribution(data_path=>$charge_length_data_path);
        print $page;
      }

      if ($organism =~ /(human|Arabidopsis|Maize|Bburgdorferi)/i){ 
	my $sql = qq~
				SELECT SC.name as NAME,
							 SC.ID, 
				       COUNT (DISTINCT PI.PEPTIDE_ID) AS CNT
				FROM $TBAT_PEPTIDE_INSTANCE PI
				JOIN $TBAT_PEPTIDE_INSTANCE_SAMPLE PIS ON ( PIS.PEPTIDE_INSTANCE_ID = PI.PEPTIDE_INSTANCE_ID )
				JOIN $TBAT_SAMPLE S  ON (PIS.SAMPLE_ID = S.SAMPLE_ID)
				JOIN $TBAT_SAMPLE_CATEGORY SC ON (S.SAMPLE_CATEGORY_ID = SC.ID) 
				WHERE 1=1
				AND PI.ATLAS_BUILD_ID = $build_id 
				GROUP BY SC.NAME,SC.ID
        ORDER BY SC.NAME
			 ~;
      
	my @result = $sbeams->selectSeveralColumns($sql);
	if (@result > 1){
	  my $chart = $atlas->display_peptide_sample_category_plotly(
	    build_id=>$build_id,
	    sample_array_ref=>$sample_array_ref,
	    column_name_ref => $column_name_ref,
	    data_ref=>\@result,
	      );
	  print $chart ;
	}
      }
      ## color "Dataset Specific Protein Identification" table  
      my $col = 2;
      if ($column_name_ref->[1] eq 'Experiment Annotation'){
        $col=3;
      }

      print $atlas->tableHeatMap(table_id => 'dataset_spec_protein_info',column=>$col, total => $n_canonical_protein);
      print $atlas->tableHeatMap(table_id => 'dataset_protein_info', column=>$col, total=> $n_canonical_protein);
      $atlas->display_page_footer();
    }
} # end main

sub fetchResultset {
  my %args = @_;
  my $build_id = $args{atlas_build_id};
  my $rs_table = $args{rs_table};
  my $params = $args{params};
  my $resultset_ref = $args{resultset_ref}; 
  my $module_ref = $args{module_ref};
  #### Fetch the results from the database server
  my $result;
  $atlas->fetchResultHTMLTable(
    table_name => $rs_table,
    key_value => $build_id,	
    resultset_ref=>$resultset_ref,
    use_caching => 0
      );

  if ( $resultset_ref->{from_cache} ) {
    $log->info( "Skipping post-processing with cached RS" );
  }else{
    $resultset_ref->{data} = $module_ref->($build_id);
    my %rs_params;
    $rs_params{set_name} = 'SETME';
    my %write_params = ( rs_table => $rs_table,
			 key_field => 'atlas_build_id',
			 key_value => $build_id );

    $sbeams->writeResultSet(
      resultset_file_ref=>\$rs_params{set_name},
      resultset_ref=>$resultset_ref,
      query_parameters_ref=>$params,
      resultset_params_ref=>\%rs_params,
      query_name=>"$SBEAMS_SUBDIR/$PROGRAM_FILE_NAME",
      %write_params
	);
  }
  return $resultset_ref->{data};
}
 
sub get_table_help {
  my %args = @_;
  my $name = $args{table};
  return '' unless $name;
  $args{mode} ||= 'section';
  my @entries;
  my $hidetext;
  my $showtext;
  my $heading;
  my $description;

  if ( $name eq 'build' ) {  
    @entries = ( { key => 'Build Name', value => 'The simple name for this build, usually contains organism, prophet cutoff, and other information. ' },
                 { key => 'Build Description', value => 'More detailed information about build. ' },
                 { key => 'Reference Database', value => 'Database to which peptides were mapped, generally different than search database.  This mapping is done by running BLAST, and allows the peptides to be mapped the the organism\'s genomic sequence. ' },
                 { key => 'Build Date', value => 'Date upon which build was finished. ' },
                 { key => 'Probability threshold', value => 'iProphet probability threshold applied to each experiment in this build' },
                 { key => 'PSM FDR threshold', value => 'PSM (peptide-spectrum match) level FDR threshold applied to each experiment in this build' },
                 { key => 'Build PSM FDR', value=>'MAYU PSM level FDR'},
                 { key => 'Build peptide FDR', value=>'MAYU peptide level FDR'},
                 { key => 'Build protein FDR', value=>'MAYU protein level FDR'},
                 { key => '# Datasets', value => 'The number of individual datasets which comprise this build.' } ,
                 { key => '# Experiments', value => 'The number of individual experiments which comprise this build.  Each experiment contains one or more LCMS/MS runs, and generally corresponds to a single scientific experiment.' } ,
                 { key => '# MS Runs', value => 'The total number of MS runs for the build.' } ,
                 { key => '# Searched Spectra', value => 'The total number of spectra that were searched for the build.' },
                 { key => '# Identified Spectra', value => 'The total number of spectra that yeilded identifications above the build threshold.  Observations of the same base peptide sequences multiple times or in <br>various charge states/modifications, whould each contribute to the total' },
                 { key => 'Distinct Modified Peptides', value => 'This shows the number of distinct modified peptide sequences that were seen in this build.  Observations of the peptide in different charge states or with different modifications are not coalesced.' } ,
                 { key => 'Distinct Stripped Peptides', value => 'This shows the number of distinct peptide sequences that were seen in this build.  Observations of the peptide in different charge states or with different modifications are coalesced.' } ,
                 { key => 'Unique Stripped Peptides From Respect', value => 'This shows the number of distinct peptide sequences that were only identified by the Respect search.  Observations of the peptide in different charge states or with different modifications are coalesced.' } ,
                 { key => 'Canonical Proteins', value => 'Minimally redundant set of proteins required to explain (virtually) all non-decoy peptides observed in build (<a target=_termdefs href="http://www.peptideatlas.org/docs/protein_ident_terms.php">more info</a>)' },
                 { key => 'Noncore-Canonical', value => 'Noncore canonical means that there are uniquely mapping peptides to this protein that do not map to a protein that is considered part of the core proteome <br>of a species. A non-core canonical protein might be an isoform, contaminant, or protein missing from the core reference proteome.  Contaminants are not included in the count.'},
                 { key => 'Indistinguishable Representative Protein', value=>'Indistinguishable representative means that there are peptides that map uniquely to a set of non-canonical proteins, thereby indicating that at least<br> one of the proteins in the set must be present, but it cannot be determined which it is. Contaminants are not included in the count.'},
                 { key => 'Marginally Distinguished Proteins', value=>'Marginally distinguished means that this protein has peptides that are shared with a canonical peptide, but it also has a small number of <br>peptides that appear to distinguish it from the canonical identification.  Contaminants are not included in the count.'},
                 { key => 'Representative Proteins', value=>'Representative means that there are peptides that map uniquely to a set of non-canonical proteins, thereby indicating that at least one of the <br>proteins in the set must be present, but it cannot be determined which it is.  Contaminants are not included in the count.'},
                 { key => 'Insufficient evidence', value=>'Protein has one or more apparently uniquely mapping peptides but none are 9AA or greater. Contaminants are not included in the count.'},
                 { key => 'weak', value=>'Protein has one peptide that is uniquely mapping and at least 9 AA long, but is missing a second peptide that meets HPP guidelines. <br>Contaminants are not included in the count.'},
        );

    $showtext = 'show row descriptions';
    $hidetext = 'hide row descriptions';
    $heading = 'Build Overview';
    $description= 'These values pertain to the atlas build as a whole';
  } 

  return unless @entries;
  return \@entries if $args{mode} eq 'entries_only';

  my $help = $atlas->get_table_help_section( name => $name,
                                             description => $description,
                                             heading => $heading,
                                             entries => \@entries,
                                             showtext => $showtext,
                                             hidetext => $hidetext  );
  return $help;

} # end get_table_help
sub get_mayu_info {
  my $mayu_data_path = shift;
  open (mayu, $mayu_data_path);
  my $line = <mayu>;
  my @headings = split(",",$line);
  my @sortable;
  for my $col ( @headings ) {
    push @sortable, $col, $col;
  }

  my @records = ();
  for $line (<mayu>) {
    chomp ($line);
    my @fields = split(",",$line);
    for my $field (@fields) {
      if ($field =~ /^\d+$/) {
	$field = $sbeams->commifyNumber($field);
      }
    }
    push @records, \@fields;
  }
  my @align = qw(center center left
right center center right right center center left center left center center
center left center left center center center center left center center center
center left);
  my $html = $atlas->create_table (data => \@records,
				   column_names=> \@headings,
				   table_name => "Mayu Decoy-based FDR Analysis",
				   table_id => "mayu",
				   align => \@align,
				   sortable => 0);
  return ($html);
}

sub get_dataset_spec_protein_info {
  my %args = @_;
  my $build_id = $args{build_id};

  my $sql = qq~
   SELECT A.repository_id , A.NAME, count (distinct A.ID) as cnt
   FROM (
     SELECT PID.dataset_specific_id as repository_id,
            PRL.LEVEL_NAME AS NAME,
            PID.biosequence_id as ID
     FROM $TBAT_PROTEIN_IDENTIFICATION PID 
     JOIN  $TBAT_PROTEIN_PRESENCE_LEVEL PRL
     ON (PID.PRESENCE_LEVEL_ID = PRL.PROTEIN_PRESENCE_LEVEL_ID)
     WHERE 1 = 1
           AND atlas_build_id IN ($build_id)
           AND dataset_specific_id IS NOT NULL
           AND dataset_specific_id != ''
           AND dataset_specific_id != 'OTHERS'
     UNION
     SELECT BR.DATASET_SPECIFIC_ID AS  repository_id, 
            BRT.RELATIONSHIP_NAME AS NAME, 
            BR.RELATED_BIOSEQUENCE_ID as ID 
     FROM $TBAT_BIOSEQUENCE_RELATIONSHIP BR
     JOIN $TBAT_BIOSEQUENCE_RELATIONSHIP_TYPE BRT
     ON (BR.RELATIONSHIP_TYPE_ID = BRT.BIOSEQUENCE_RELATIONSHIP_TYPE_ID)
     WHERE 1 = 1
           AND atlas_build_id IN ($build_id)
           AND dataset_specific_id IS NOT NULL
           AND dataset_specific_id != '' 
           AND dataset_specific_id != 'OTHERS'
   ) AS A
   GROUP BY A.repository_id, A.NAME
   order by cnt DESC  
  ~;
  my @rows = $sbeams->selectSeveralColumns($sql);
  return '' if (@rows < 1);
  my %unique_prot2dataset_cnt;
  my $possibly_distinguished = 0; 
  foreach my $row(@rows){
    my ($repository_id, $name,$cnt) =@$row;
    $unique_prot2dataset_cnt{$repository_id}{$name} = $cnt;
    if ($name =~ /(possibly_distinguished|ntt-subsumed)/i){
      $possibly_distinguished++;
    }
  } 
  ## older builds
  return '' if ($possibly_distinguished > 0);

  my @level_names = ('canonical','noncore-canonical','indistinguishable representative'  ,'representative'
                     ,'marginally distinguished','weak','insufficient evidence','indistinguishable','subsumed');
  $sql =qq~;
    SELECT LEVEL_NAME AS NAME, PROTEIN_PRESENCE_LEVEL_ID AS ID
    FROM $TBAT_PROTEIN_PRESENCE_LEVEL
    UNION 
    SELECT RELATIONSHIP_NAME AS NAME, BIOSEQUENCE_RELATIONSHIP_TYPE_ID AS ID
    FROM $TBAT_BIOSEQUENCE_RELATIONSHIP_TYPE 
  ~;
  my %protein_level_ids = $sbeams->selectTwoColumnHash($sql);

  my @headings =('Dataset', @level_names);
  my @sortable=();
  my @align=();
  for my $col ( @headings ) {
    $col =~ s/(\w+)/\u$1/g;
    push @sortable, $col,$col;
    push @align, 'center';
  }
  $align[0] = 'left';
  my @records = ();
  my @annotation_urls;
  my $anno = 0;
  foreach my $repository_id (sort {$a cmp $b } keys %unique_prot2dataset_cnt){ 
    my @row =();
    my ($repository_id_w_links, $annotation_url) = $atlas->get_dataset_url($repository_id);
    push @row , $repository_id_w_links;
    push @annotation_urls, $annotation_url; 
    $anno =1 if ($annotation_url ne '');
    foreach my $level_name (@level_names){
      my $cnt = $unique_prot2dataset_cnt{$repository_id}{$level_name} || '';
      if (defined $unique_prot2dataset_cnt{$repository_id}{$level_name}){
         my $cnt = $unique_prot2dataset_cnt{$repository_id}{$level_name};
         my $level_id = $protein_level_ids{$level_name};
         my $constraint = '';
         if($level_name =~ /^indistinguishable$/i){
            $constraint = "redundancy_constraint=1";
         }elsif ($level_name =~ /(subsumbed_by|identical)/i){
            $constraint = "redundancy_constraint=$level_id";
         }else{
           $constraint = "presence_level_constraint=$level_id&redundancy_constraint=4";
        }
         my $str  = $atlas->make_pa_tooltip( tip_text => $cnt,
           link_text => "<a href='$CGI_BASE_DIR/PeptideAtlas/GetProteins?atlas_build_id=$build_id&biosequence_name_constraint=!DECOY%&dataset_specific_id=$repository_id&$constraint&apply_action=QUERY' target='_blank'>$cnt</a>" );
         push @row , $str;
      }else{
         push @row ,'';
      }
    }
    push @records, \@row;
  }
  ## insert annotation column to second column
  if ($anno){
    for (my $i=0; $i<=$#records; $i++){
      splice @{$records[$i]}, 1, 0, $annotation_urls[$i];
    }
    splice @headings, 1, 0, 'Experiment Annotation';
    splice @align, 1, 0, 'center';
  }
  my $html = $atlas->create_table (data => \@records,
                          column_names=> \@headings,
                          table_name => "Dataset Specific Protein Identification",
                          table_id => "dataset_spec_protein_info",
                          align => \@align,
                          sortable => 1);

  return $html; 
}

# General build info, date, name, organism, specialty, default
sub get_build_overview {
  my $build_id = shift;
  
  # Get a list of accessible project_ids
  my @project_ids = $sbeams->getAccessibleProjects();
  my $project_ids = join( ",", @project_ids ) || '0';

  my $build_info = $sbeams->selectrow_hashref( <<"  BUILD" );
  SELECT atlas_build_name, probability_threshold, atlas_build_description, 
  build_date, set_name, protpro_PSM_FDR_per_expt
  FROM $TBAT_ATLAS_BUILD AB 
  JOIN $TBAT_BIOSEQUENCE_SET BS ON AB.biosequence_set_id = BS.biosequence_set_id
  WHERE atlas_build_id = $build_id 
  AND AB.record_status <> 'D'
  BUILD

#  for my $k ( keys( %$build_info ) ) { print STDERR "$k => $build_info->{$k}\n"; }
  my $build_name = $build_info->{atlas_build_name};
  my $phospho_info;
  if ($build_name =~ /phospho/i){
    my ($id_col_name, $protein_name_contraint);
    if ($build_name =~ /human/i){
      $id_col_name = '#_neXtProt_(PE=1-4)';
      $protein_name_contraint = 'AND B.dbxref_id = 65 and BSS.organism_id = 2'; 
    }else{
      $id_col_name = '#_protein';
      $protein_name_contraint ="AND B.biosequence_name not like 'CONTAM%' AND B.biosequence_name not like 'DECOY%'";  
    }
    $phospho_info =  $sbeams->selectrow_hashref( <<"  PHOS" );
  SELECT PS.atlas_build_id, 
         count(distinct PS.biosequence_id) as '$id_col_name', 
         count(offset) as #_observed_phosphorylation_sites, 
         sum(case when residue = 'S'  then 1 else 0 end) as S_sites,
         sum(case when residue = 'T'  then 1 else 0 end) as T_sites,
         sum(case when residue = 'Y'  then 1 else 0 end) as Y_sites
  FROM $TBAT_PTM_SUMMARY PS 
  JOIN $TBAT_BIOSEQUENCE B ON PS.BIOSEQUENCE_ID = B.BIOSEQUENCE_ID
  JOIN $TBAT_BIOSEQUENCE_SET BSS ON B.BIOSEQUENCE_SET_ID = BSS.BIOSEQUENCE_SET_ID
  WHERE PS.atlas_build_id = $build_id
  $protein_name_contraint
  GROUP BY PS.atlas_build_id
  PHOS

     my $sql = qq~
       SELECT mp.modified_peptide_sequence
       FROM $TBAT_PEPTIDE_INSTANCE PI
       JOIN $TBAT_MODIFIED_PEPTIDE_INSTANCE MP ON (PI.PEPTIDE_INSTANCE_ID = MP.PEPTIDE_INSTANCE_ID)
       JOIN $TBAT_PEPTIDE_MAPPING PM ON (PI.PEPTIDE_INSTANCE_ID = PM.PEPTIDE_INSTANCE_ID)
       JOIN $TBAT_BIOSEQUENCE B ON (B.BIOSEQUENCE_ID = PM.MATCHED_BIOSEQUENCE_ID)
       JOIN $TBAT_BIOSEQUENCE_SET BSS ON B.BIOSEQUENCE_SET_ID = BSS.BIOSEQUENCE_SET_ID
       WHERE PI.ATLAS_BUILD_ID = $build_id
       $protein_name_contraint
     ~;

     my @rows = $sbeams->selectSeveralColumns($sql);
     my %result =();
     foreach my $row(@rows){
       my ($mod_pep) = @$row;
       $mod_pep =~ s/([^STY])\[\d+\]/$1/g;
       $mod_pep =~ s/[nc]//g;
       my @m = $mod_pep =~ /[STY]\[/g;
       if (@m == 1){
         $result{'singly_phosphorylated'}{$mod_pep} =1;
       }elsif(@m == 2){
          $result{'doubly_phosphorylated'}{$mod_pep} =1;
       }else{
          $result{'over_2_phosphorylated'}{$mod_pep} =1;
       }
     }
     foreach my $type(keys %result){
       $phospho_info->{$type} = scalar keys %{$result{$type}};
     }
  }

  my $pep_count = $sbeams->selectrow_hashref( <<"  PEP" );
  SELECT COUNT(*) cnt,  SUM(n_observations) obs
  FROM $TBAT_PEPTIDE_INSTANCE 
  WHERE atlas_build_id = $build_id 
  PEP

  my $pep_count = $sbeams->selectrow_hashref( <<"  PEP" );
  SELECT COUNT(*) cnt,  SUM(n_observations) obs
	FROM (
		SELECT DISTINCT PI.PEPTIDE_INSTANCE_ID, PI.N_OBSERVATIONS
		FROM $TBAT_PEPTIDE_INSTANCE PI
		JOIN $TBAT_PEPTIDE_MAPPING PM ON (PI.PEPTIDE_INSTANCE_ID = PM.PEPTIDE_INSTANCE_ID)
		JOIN $TBAT_BIOSEQUENCE B ON (PM.MATCHED_BIOSEQUENCE_ID = B.BIOSEQUENCE_ID)
		WHERE  ATLAS_BUILD_ID= $build_id AND B.BIOSEQUENCE_NAME NOT LIKE 'DECOY%'
          AND B.BIOSEQUENCE_NAME NOT LIKE 'CONTAM%'
	) A
  PEP

  my $smpl_count = $sbeams->selectrow_hashref( <<"  SMPL" );
  SELECT COUNT(*) cnt FROM $TBAT_ATLAS_BUILD_SAMPLE 
  WHERE atlas_build_id = $build_id
  SMPL

  my %prot_count = $sbeams->selectTwoColumnHash( <<"  PROT" );
  SELECT PPL.level_name, COUNT(BS.biosequence_name) cnt
  FROM $TBAT_PROTEIN_IDENTIFICATION PID
  JOIN $TBAT_PROTEIN_PRESENCE_LEVEL PPL
  ON PPL.protein_presence_level_id = PID.presence_level_id
  JOIN $TBAT_BIOSEQUENCE BS
  ON BS.biosequence_id = PID.biosequence_id
  WHERE PID.atlas_build_id = $build_id
  AND PPL.level_name in 
      ('canonical', 'indistinguishable representative', 
       'marginally distinguished', 'representative',
       'possibly_distinguished','weak', 'insufficient evidence')
  AND BS.biosequence_name NOT LIKE 'DECOY%'
  AND BS.biosequence_name NOT LIKE '%UNMAPPED%'
  AND BS.biosequence_name NOT LIKE '%CONTAM%'
  AND BS.biosequence_desc NOT LIKE '%common contaminant%'
  GROUP BY PPL.level_name 
  PROT

  $build_info->{pep_count}{obs} = $pep_count->{obs};
  $build_info->{pep_count}{cnt} = $pep_count->{cnt}; 
  $build_info->{smpl_count} = $smpl_count->{cnt}; 
  $build_info->{phospho_info} = $phospho_info;
  $build_info->{prot_count} = \%prot_count;
 
  my $table =  build_overview_html (build_info => $build_info);
  return ($prot_count{canonical},  $table);

}
sub build_overview_html { 
  my %args =@_;
  my $build_info = $args{build_info};
                     
  my $build_name = $build_info->{atlas_build_name};

  my $table = "<table style='margin-left:15px;'>\n";
  my ( $tr, $link ) = $sbeams->make_table_toggle( name    => 'build_overview',
                                                  visible => 1,
                                                  tooltip => 'Show/Hide Section',
                                                  imglink => 1,
                                                  sticky  => 1 );

  $table .= $atlas->encodeSectionHeader(
      LMTABS => 1,
      no_toggle => 1,
      divname => 'build_overview_div',
      text => 'Build Overview',
      span => 4,
      link => $link
  );

  $tr = 'class="hoverable"';
  $build_info->{build_date} =~ s/^([0-9-]+).*$/$1/;

  if ($build_info->{protpro_PSM_FDR_per_expt} <= 0) {
    $build_info->{protpro_PSM_FDR_per_expt} =  $sbeams->makeInactiveText( 'n/a' );
  } else {
    $build_info->{protpro_PSM_FDR_per_expt} = sprintf( "%0.7f", $build_info->{protpro_PSM_FDR_per_expt} );
    $build_info->{protpro_PSM_FDR_per_expt} =~ s/ /&nbsp;/g;
  }
  if ($build_info->{probability_threshold} <= 0) {
    $build_info->{probability_threshold} = $sbeams->makeInactiveText( 'n/a' );
  } else {
    $build_info->{probability_threshold} = sprintf( "%0.4f", $build_info->{probability_threshold} );
    $build_info->{probability_threshold} =~ s/ /&nbsp;/g;
  }

  $table .= $atlas->encodeSectionItem( key   => 'Build Name', tr_info => $tr,
				       value => $build_info->{atlas_build_name}, vspan => 3 ) . "\n";
  $table .= $atlas->encodeSectionItem( key   => 'Build Description', tr_info => $tr,
				       value => $build_info->{atlas_build_description}, vspan => 3 ) . "\n";
  $table .= $atlas->encodeSectionItem( key   => 'Reference Database', tr_info => $tr,
				       value => $build_info->{set_name}, vspan => 3 ) . "\n";
  $table .= $atlas->encodeSectionItem( key   => 'Build Date', tr_info => $tr,
				       value => $build_info->{build_date} ) . "\n";
  if ($build_info->{dataset_count}){
    $table .= $atlas->encodeSectionItem( key   => '# Datasets', tr_info => $tr,
               value => $build_info->{dataset_count}, align => 'right' ) . "\n" 
  }
  $table .= $atlas->encodeSectionItem( key   => '# Experiments', tr_info => $tr,
				       value => $build_info->{smpl_count}, align => 'right' ) . "\n";
  if ($build_info->{n_runs}){
    $table .= $atlas->encodeSectionItem( key   => '# MS Runs', tr_info => $tr,
               value => $build_info->{n_runs}, align => 'right' ) . "\n"
  }

  $table .= $atlas->encodeSectionItem( key   => 'PSM FDR threshold', tr_info => $tr,
				       value => $build_info->{protpro_PSM_FDR_per_expt}, align => 'right' ) . "\n";
  $table .= $atlas->encodeSectionItem( key   => 'Probability threshold', tr_info => $tr,
				       value => $build_info->{probability_threshold}, align => 'right' ) . "\n" 
                if ($build_info->{probability_threshold} ne 'na');
  if ($build_info->{'Build PSM FDR'}){
    $table .= $atlas->encodeSectionItem( key   => 'Build PSM FDR', tr_info => $tr,
               value => $build_info->{'Build PSM FDR'}, align => 'right' ) . "\n";
    $table .= $atlas->encodeSectionItem( key   => 'Build peptide FDR', tr_info => $tr,
               value => $build_info->{'Build peptide FDR'}, align => 'right' ) . "\n";
    $table .= $atlas->encodeSectionItem( key   => 'Build protein FDR', tr_info => $tr,
               value => $build_info->{'Build protein FDR'}, align => 'right' ) . "\n";

	}
  if ($build_info->{n_searched_spectra}){
    $table .= $atlas->encodeSectionItem( key   => '# Searched Spectra', tr_info => $tr,
               value => $build_info->{n_searched_spectra}, align => 'right' ) . "\n"
  }

  $table .= $atlas->encodeSectionItem( key   => '# Identified Spectra', tr_info => $tr,
				       value => $sbeams->commifyNumber($build_info->{pep_count}->{obs}), align => 'right' ) . "\n";

  if ($build_info->{modpep_count}){
    $table .= $atlas->encodeSectionItem( key   => 'Distinct Modified Peptides', tr_info => $tr,
               value => $sbeams->commifyNumber($build_info->{modpep_count}), align => 'right' ) . "\n";
  }

  my $url = "<a href='$CGI_BASE_DIR/PeptideAtlas/GetPeptides?atlas_build_id=$build_info->{atlas_build_id}\&".
              'biosequence_name_constraint=%21CONTAM%25%3B%21DECOY%25&QUERY_NAME=AT_GetPeptides&apply_action=QUERY'.
              "\&row_limit=1500000'>".
              $sbeams->commifyNumber($build_info->{pep_count}{cnt}) .
              '</a>';
    
  $table .= $atlas->encodeSectionItem( key   => 'Distinct Stripped Peptides', tr_info => $tr,
				       value => $url, align => 'right' ) . "\n";

  if ($build_info->{pep_count_respect}){
    $table .= $atlas->encodeSectionItem( key   => 'Unique Stripped Peptides From Respect', tr_info => $tr,
               value => $sbeams->commifyNumber($build_info->{pep_count_respect}), align => 'right' ) . "\n";
  }


  foreach my $proteome (sort {$a cmp $b} keys %{$build_info->{prot_count}}){
    $table .= $atlas->encodeSectionItem( key   => "$proteome Protein Presence Levels", tr_info => $tr, value => '', align => 'right' ) . "\n";
    my @levels = keys %{$build_info->{prot_count}{$proteome}};
    my @sorted_levels = sort custom_sort @levels;

		foreach my $key (@sorted_levels){
			 my $level = $key;
			 $level =~ s/\_/ /g;
			 $level =~ s/(\w+)/\u$1/g; 
			 $table .= $atlas->encodeSectionItem( key   => "&#8195;$level", tr_info => $tr, value => $sbeams->commifyNumber($build_info->{prot_count}{$proteome}{$key}), align => 'right' ) . "\n";
		}
  }
  if ($build_name =~ /phospho/i){
    $table .= $atlas->encodeSectionItem( key   => 'PhosphoProteome Summary', tr_info => $tr, value => '', align => 'right' ) . "\n";
    $table .= $atlas->encodeSectionItem( key   => "&#8195;# of Phosphorylated Sites in Modified Peptides", tr_info => $tr, value =>'', align => 'right' ) . "\n";
    foreach my $key (qw (singly_phosphorylated doubly_phosphorylated over_2_phosphorylated)){
      my $level = $key;
      $level =~ s/\_/ /g;
      $level =~ s/(\w+)/\u$1/g;
      $table .= $atlas->encodeSectionItem( key   => "&#8195;&#8195;$level", tr_info => $tr, value => $build_info->{phospho_info}->{$key}, align => 'right' ) . "\n";
    }

  }
 
  $table .= "</table>\n";
  $table .= "<script>document.title = 'PeptideAtlas Build Details: $build_info->{atlas_build_name}';</script>\n";
  return $table; 
}
### 
# Custom sort function
sub custom_sort {
    my ($a_val, $b_val) = ($a, $b);
    # Check if $a or $b is equal to the top element
    if ($a =~ /canonical/) {
        return -1; # $a comes before $b
    } elsif ($b eq 'noncore-canonical') {
        return 1;  # $b comes before $a
    }
    # Otherwise, use default string comparison
    return $a_val cmp $b_val;
}
# Peptide build stats
sub get_sample_info {
  my $build_id = shift;

  # Get a list of accessible project_ids
  my @project_ids = $sbeams->getAccessibleProjects();
  my $project_ids = join( ",", @project_ids ) || '0';
  #### Define some variables needed to build the query
  my @column_array = (
      ["repository_identifiers","S.repository_identifiers","Dataset"],
      ["sample_id", "S.sample_id","Experiment ID"],
      ["sample_tag", "sample_tag", "Experiment Tag"],
      ["n_runs","SBS.n_runs", "MS Runs"],
      ["n_searched_spectra", "SBS.n_searched_spectra", "Spectra Searched"],
      ["n_good_spectra", "n_good_spectra", "Spectra ID'd"],
      ["per_id", "CASE WHEN SBS.n_searched_spectra > 0 THEN FORMAT((n_good_spectra*1.00)/(SBS.n_searched_spectra/1.00), 'P2') ELSE '' END", "%Spectra ID'd"],
      ["n_distinct_peptides", "n_distinct_peptides","Distinct Peptides"],
      ["n_uniq_contributed_peptides", "n_uniq_contributed_peptides", "Unique Peptides"],
      ["n_progressive_peptides", "n_progressive_peptides", "Added Peptides"],
      ["cumulative_n_peptides", "cumulative_n_peptides", "Cumulative Peptides"],
      ["n_canonical_proteins", "n_canonical_proteins", "Distinct Canonical Proteins"],
      ["n_unique_canonical_prots", "''", "Unique Canonical Proteins"],
      ["n_unique_prots", "''", "Unique All Proteins"],
      ["n_added_canonical_prots", "''", "Added Canonical Proteins"],
      ["cumulative_n_proteins", "cumulative_n_proteins", "Cumulative Canonical Proteins"],
      ["date_created", "CONVERT(VARCHAR(10), PE.date_created, 126)", "Date Added"],
      ["pubmed_id", "pubmed_id", "Pubmed Id or DOI"],
      ["instrument_name","instrument_name","Instrument Name"],
      ["sample_category", "SC.name", "Sample Category"],
      ["sample_category_id", "S.sample_category_id", "sample_category_id"]
    );

  #### Build the columns part of the SQL statement
  my %colnameidx = ();
  my @column_titles = ();
  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 $columns_clause
  FROM $TBAT_SEARCH_BATCH_STATISTICS SBS 
  JOIN $TBAT_ATLAS_BUILD_SEARCH_BATCH ABSB ON ABSB.atlas_build_search_batch_id = SBS.atlas_build_search_batch_id
  JOIN $TBAT_ATLAS_SEARCH_BATCH ASB ON ( ASB.atlas_search_batch_id = ABSB.atlas_search_batch_id )
  JOIN $TBAT_SAMPLE S ON (S.sample_id = ASB.sample_id)
  LEFT JOIN $TBAT_SAMPLE_CATEGORY SC ON (S.sample_category_id = SC.id)
  LEFT JOIN (
		SELECT DISTINCT SAMPLE_ID, 
		STUFF(
			(SELECT DISTINCT ',' + CONVERT (VARCHAR , P.PUBMED_ID )
			FROM $TBAT_SAMPLE_PUBLICATION F2
			JOIN $TBAT_PUBLICATION P ON (P.PUBLICATION_ID = F2.PUBLICATION_ID AND F2.record_status != 'D')
      AND F1.SAMPLE_ID = F2.SAMPLE_ID
			FOR XML PATH ('')),1, 1, '' 
      ) AS Pubmed_ID
		FROM $TBAT_SAMPLE_PUBLICATION F1
  ) AS A ON (A.SAMPLE_ID = S.SAMPLE_ID) 
  JOIN $TBPR_SEARCH_BATCH PSB  ON (PSB.SEARCH_BATCH_ID = ASB.PROTEOMICS_SEARCH_BATCH_ID)
  JOIN $TBPR_PROTEOMICS_EXPERIMENT PE ON (PE.EXPERIMENT_ID = PSB.EXPERIMENT_ID)
  JOIN $TBPR_INSTRUMENT I ON (I.INSTRUMENT_ID = PE.INSTRUMENT_ID) 
  WHERE ABSB.atlas_build_id = $build_id
  ORDER BY rownum, cumulative_n_peptides, ABSB.atlas_build_search_batch_id ASC
  ~;

  my @sample_info = $sbeams->selectSeveralColumns ( $sql );
  #$log->debug( "build table SQL: $td" );

  my (%unique_prot2sample_cnt, %unique_canprot2sample_cnt);
  $sql = qq~
   SELECT A.sample_id , count (distinct A.id)
   FROM (
		 SELECT sample_specific_id as sample_id, biosequence_id as id 
		 FROM $TBAT_PROTEIN_IDENTIFICATION 
		 WHERE 1 = 1
					 AND atlas_build_id IN ($build_id)
					 AND sample_specific_id is not null
		 UNION 
		 SELECT sample_specific_id as sample_id, related_biosequence_id as id 
		 FROM $TBAT_BIOSEQUENCE_RELATIONSHIP
		 WHERE 1 = 1
					 AND atlas_build_id IN ($build_id)
					 AND sample_specific_id is not null
   ) AS A
   GROUP BY A.sample_id
	~;
  %unique_prot2sample_cnt = $sbeams->selectTwoColumnHash($sql);
  $sql = qq~
     SELECT sample_specific_id , count(biosequence_id) 
     FROM $TBAT_PROTEIN_IDENTIFICATION
     WHERE 1 = 1
           AND atlas_build_id IN ($build_id)
           AND sample_specific_id is not null
           AND presence_level_id = 1
     GROUP BY sample_specific_id
  ~;
  %unique_canprot2sample_cnt = $sbeams->selectTwoColumnHash($sql);

  # Massage/format some of the columns in the sample info just retrieved
  my %hidden_cols = ();

  if ($organism !~ /(human|Arabidopsis|Maize|Bburgdorferi)/i){
    $hidden_cols{'sample_category'} = 1;
  }
  #$hidden_cols{'sample_id'} = 1;
  my @samples;
  ## rows without second and last column
  my @samples2;
  my $rownum =0;
  my @column_names;
  my @annotation_urls;
  my $anno = 0;

  for my $batch ( @sample_info ) {
    $show_image++;
    # if these aren't defined, set to zero
    for my $col_name (qw(n_uniq_contributed_peptides 
                    n_progressive_peptides 
                    cumulative_n_peptides
                    n_canonical_proteins
                    cumulative_n_proteins)){
        $batch->[$colnameidx{$col_name}] ||=0;
    }
    if ($rownum == 0){
      $batch->[$colnameidx{n_added_canonical_prots}] = $batch->[$colnameidx{n_canonical_proteins}];
    }else{
      $batch->[$colnameidx{n_added_canonical_prots}] = $batch->[$colnameidx{cumulative_n_proteins}] 
                                                       - $sample_info[$rownum-1]->[$colnameidx{cumulative_n_proteins}];
    } 
    for my $idx ( $colnameidx{'n_unique_prots'}) {
      if (defined $unique_prot2sample_cnt{$batch->[$colnameidx{sample_id}]}){
         $batch->[$idx] = $unique_prot2sample_cnt{$batch->[$colnameidx{sample_id}]};
         $batch->[$idx] = $atlas->make_pa_tooltip( tip_text => $batch->[$idx],
           link_text => "<a href='$CGI_BASE_DIR/PeptideAtlas/GetProteins?atlas_build_id=$build_id&".
                        "sample_specific_id=$batch->[$colnameidx{sample_id}]&apply_action=QUERY' target='_blank'>$batch->[$idx]</a>" );
      }else{
        $batch->[$idx] = '';
      }
    }
    for my $idx ( $colnameidx{'n_unique_canonical_prots'}) {
      if (defined $unique_canprot2sample_cnt{$batch->[$colnameidx{sample_id}]}){
         $batch->[$idx] = $unique_canprot2sample_cnt{$batch->[$colnameidx{sample_id}]};
         $batch->[$idx] = $atlas->make_pa_tooltip( tip_text => $batch->[$idx],
           link_text => "<a href='$CGI_BASE_DIR/PeptideAtlas/GetProteins?atlas_build_id=$build_id&presence_level_constraint=1&".
                        "redundancy_constraint=4&sample_specific_id=$batch->[$colnameidx{sample_id}]&apply_action=QUERY' target='_blank'>$batch->[$idx]</a>" );
      }else{
        $batch->[$idx] = '';
      }
    }

    for my $idx ($colnameidx{'sample_tag'}) {
      $batch->[$idx] = $atlas->make_pa_tooltip( tip_text => $batch->[$idx],
          link_text => "<a href='$CGI_BASE_DIR/$SBEAMS_PART/ManageTable.cgi?TABLE_NAME=AT_SAMPLE&sample_id=$batch->[1]' target='_blank'>$batch->[$idx]</a>" );
    }
    for my $idx ($colnameidx{pubmed_id}) {
      next if ( ! $batch->[$idx]);
      my @ids = split(",", $batch->[$idx]);
      $batch->[$idx] ='';
      foreach my $id(@ids){
        if ($id =~ /^\d+$/){
          $batch->[$idx] .= "<a href='http://www.ncbi.nlm.nih.gov/pubmed/?term=$id' target='_blank'>$id</a>,";
        }else{
          $batch->[$idx] .= "<a href='https://doi.org/$id' target='_blank'>$id</a>,";
        }
      }
      $batch->[$idx] =~ s/,$//;
    }
    my $annotation_url = '';
    for my $idx ($colnameidx{'repository_identifiers'}) {
      next if ( ! $batch->[$idx]);
      ($batch->[$idx], $annotation_url) = $atlas->get_dataset_url($batch->[$idx]);
    }
    push @annotation_urls, $annotation_url;
    $anno = 1 if ($annotation_url ne '');
    my @row_data;
    my $idx = 0;
    foreach my $col (sort {$colnameidx{$a} <=> $colnameidx{$b}} keys %colnameidx){
      if (not defined $hidden_cols{$col}){
         $row_data[$idx] = $batch->[$colnameidx{$col}];
         $idx++;
         next if ($col eq 'sample_category_id'); 
         push @column_names, $column_titles[$colnameidx{$col}] if (! $rownum);
      }
    }
    push @samples, \@row_data; 
    my @tmp2 = @row_data; 
    pop @tmp2;
    push @samples2, \@tmp2;
    $rownum++;
  }

  for my $samp ( @samples2 ) {
    for my $col_name (qw
		      (n_runs
		       n_searched_spectra
		       n_good_spectra
		       n_distinct_peptides
		       n_uniq_contributed_peptides
		       n_progressive_peptides
		       cumulative_n_peptides
		       n_canonical_proteins
		       n_unique_canonical_prots
		       n_unique_prots
		       n_added_canonical_prots
		       cumulative_n_proteins)
	){
      $samp->[$colnameidx{$col_name}] = $sbeams->commifyNumber($samp->[$colnameidx{$col_name}]);
    }

  }
  ## insert annotation column to second column
  my @column_names_copy = @column_names;
  my @align = qw(left left left center center center center center center center center center center center center center);
  my @noWrap = (3,17,19,20);
  if ($anno){
    for (my $i=0; $i<=$#samples2; $i++){
      splice @{$samples2[$i]}, 1, 0, $annotation_urls[$i];
    }
    splice @column_names, 1, 0, 'Experiment Annotation';
    splice @align, 1, 0, 'center';
  }
  my $html = $atlas->create_table (data => \@samples2,
				   column_names=> \@column_names,
				   table_name => "Experiment Contribution",
				   table_id => "exp_contribution",
           nowrap => \@noWrap, 
				   align => \@align,
				   sortable => 0,
				   download_table => 1);

  push @column_names_copy , "sample_category_id";
  return ( $html, \@samples, \@column_names_copy);
}

sub get_dataset_contrib_info {
  my $build_id = shift;

  # Get a list of accessible project_ids
  my @project_ids = $sbeams->getAccessibleProjects();
  my $project_ids = join( ",", @project_ids ) || '0';
  #### Define some variables needed to build the query
  my @column_array = (
      ["repository_identifiers","repository_identifiers","Dataset"],
      ["n_runs","n_runs", "MS Runs"],
      ["n_searched_spectra", "n_searched_spectra", "Spectra Searched"],
      ["n_good_spectra", "n_good_spectra", "Spectra ID'd"],
      ["per_id", "CASE WHEN n_searched_spectra > 0 THEN FORMAT((n_good_spectra*1.00)/(n_searched_spectra/1.00), 'P2') ELSE '' END", "%Spectra ID'd"],
      ["n_distinct_peptides", "n_distinct_peptides","Distinct Peptides"],
      ["n_uniq_contributed_peptides", "n_uniq_contributed_peptides", "Unique Peptides"],
      ["n_progressive_peptides", "n_progressive_peptides", "Added Peptides"],
      ["cumulative_n_peptides", "cumulative_n_peptides", "Cumulative Peptides"],
      ["n_canonical_proteins", "n_canonical_proteins", "Distinct Canonical Proteins"],
      ["n_uniq_contributed_proteins", "n_uniq_contributed_proteins", "Unique Canonical Proteins"],
      ["n_progressive_proteins", "n_progressive_proteins", "Added Canonical Proteins"],
      ["cumulative_n_proteins", "cumulative_n_proteins", "Cumulative Canonical Proteins"]
    );

  #### Build the columns part of the SQL statement
  my %colnameidx = ();
  my @column_titles = ();
  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 $columns_clause
  FROM $TBAT_DATASET_STATISTICS
  WHERE ATLAS_BUILD_ID = $build_id 
  ORDER BY rownum
  ~;
  my @info = $sbeams->selectSeveralColumns ( $sql );
  return '' if (! @info);

  my (@samples);
  my @annotation_urls;
  my $anno = 0;
  for my $batch ( @info ) {
    for my $idx ($colnameidx{'repository_identifiers'}) {
      next if ( ! $batch->[$idx]);
      my $annotation_url = '';
      ($batch->[$idx], $annotation_url) = $atlas->get_dataset_url($batch->[$idx]);
      if ($annotation_url ne ''){
        $anno=1;
      }
      push @annotation_urls, $annotation_url;  
    }
    push @samples, $batch;
  }


  for my $samp ( @samples ) {
    for my $col_name (qw
		      (n_runs
		       n_searched_spectra
		       n_good_spectra
		       n_distinct_peptides
		       n_uniq_contributed_peptides
		       n_progressive_peptides
		       cumulative_n_peptides
		       n_canonical_proteins
		       n_uniq_contributed_proteins
		       n_progressive_proteins
		       cumulative_n_proteins)
	){
      $samp->[$colnameidx{$col_name}] = $sbeams->commifyNumber($samp->[$colnameidx{$col_name}]);
    }

  }
  ## insert annotation column to second column
  my @align = qw(left center center center center center center center center center center center center center center);
  if ($anno){
    for (my $i=0; $i<=$#samples; $i++){
      splice @{$samples[$i]}, 1, 0, $annotation_urls[$i];
    }
    splice @column_titles, 1, 0, 'Experiment Annotation';
    splice @align, 1, 0, 'center';
  }
  my $html = $atlas->create_table (data => \@samples,
                          column_names=> \@column_titles,
                          table_name => "Dataset Contribution",
                          table_id => "datasetContri_info",
													header_sticky => 1,
                          align => \@align,
                          sortable => 0,
                          download_table => 1);

  return $html;

}

sub process_params {
  my $params = {};
  $sbeams->parse_input_parameters( q => $q, parameters_ref => $params );
  $sbeams->processStandardParameters( parameters_ref => $params );
  return( $params );
}

sub get_build_path {
  my %args = @_;
  return unless $args{build_id};
  my $path = $atlas->getAtlasBuildDirectory( atlas_build_id => $args{build_id} );
  $path =~ s/DATA_FILES//;
  return $path;
}
##################################################################################
### check protein existence in a dataset. 
##################################################################################
sub get_dataset_protein_info {
  my %args = @_;
  my $atlas_build_id = $args{build_id};
  my $sql =qq~;
    SELECT SAMPLE_ID, REPOSITORY_IDENTIFIERS 
    FROM $TBAT_SAMPLE 
    WHERE REPOSITORY_IDENTIFIERS IS NOT NULL
    AND REPOSITORY_IDENTIFIERS != ''
  ~;
  my %sample_repository_ids = $sbeams->selectTwoColumnHash($sql);

  $sql = qq~
     SELECT BS.BIOSEQUENCE_NAME, PR.NAME, S.sample_id
      FROM $TBAT_BIOSEQUENCE_ID_ATLAS_BUILD_SEARCH_BATCH BIABSB
      JOIN $TBAT_BIOSEQUENCE BS ON ( BIABSB.BIOSEQUENCE_ID = BS.BIOSEQUENCE_ID )
      JOIN $TBAT_ATLAS_BUILD_SEARCH_BATCH ABSB
      ON (ABSB.ATLAS_BUILD_SEARCH_BATCH_ID = BIABSB.ATLAS_BUILD_SEARCH_BATCH_ID
         AND ABSB.atlas_build_id = $atlas_build_id )
      JOIN $TBAT_SAMPLE S ON (S.sample_id = ABSB.sample_id)
     JOIN (
       SELECT A.NAME, A.ID
       FROM (
         SELECT PRL.LEVEL_NAME AS NAME,
                PID.biosequence_id as ID
         FROM $TBAT_PROTEIN_IDENTIFICATION PID
         JOIN  $TBAT_PROTEIN_PRESENCE_LEVEL PRL
         ON (PID.PRESENCE_LEVEL_ID = PRL.PROTEIN_PRESENCE_LEVEL_ID)
         WHERE 1 = 1
               AND atlas_build_id IN ($atlas_build_id)
         UNION
         SELECT BRT.RELATIONSHIP_NAME AS NAME,
                BR.RELATED_BIOSEQUENCE_ID as ID
         FROM $TBAT_BIOSEQUENCE_RELATIONSHIP BR
         JOIN $TBAT_BIOSEQUENCE_RELATIONSHIP_TYPE BRT
         ON (BR.RELATIONSHIP_TYPE_ID = BRT.BIOSEQUENCE_RELATIONSHIP_TYPE_ID)
         WHERE 1 = 1
               AND atlas_build_id IN ($atlas_build_id)
       ) AS A ) PR  ON (PR.ID = BS.biosequence_id)
     WHERE 1 = 1
          AND ABSB.atlas_build_id IN ( $atlas_build_id )
          AND BS.BIOSEQUENCE_ID NOT IN (
            SELECT BR.RELATED_BIOSEQUENCE_ID
             FROM $TBAT_BIOSEQUENCE_RELATIONSHIP BR
             WHERE RELATIONSHIP_TYPE_ID = 2
          )

  ~;
  my @rows = $sbeams->selectSeveralColumns($sql);
  my %dataset_prot_cnt;
  my $possibly_distinguished = 0;
  foreach my $row(@rows){
    my ($bs_name,$protein_level, $sample_id ) =@$row;
    next if ($bs_name =~ /(decoy|contam)/i);
    if ($protein_level =~ /possibly_distinguished/i){
      $possibly_distinguished++;
    }
    $dataset_prot_cnt{$sample_repository_ids{$sample_id}}{$protein_level}{$bs_name} =1;
  }
  ## older builds, skip
  return '' if ($possibly_distinguished > 0);
  return '' if (scalar keys %dataset_prot_cnt == 0);
  my $sql =qq~;
    SELECT LEVEL_NAME AS NAME, PROTEIN_PRESENCE_LEVEL_ID AS ID
    FROM $TBAT_PROTEIN_PRESENCE_LEVEL
    UNION
    SELECT RELATIONSHIP_NAME AS NAME, BIOSEQUENCE_RELATIONSHIP_TYPE_ID AS ID
    FROM $TBAT_BIOSEQUENCE_RELATIONSHIP_TYPE
  ~;
  my %protein_level_ids = $sbeams->selectTwoColumnHash($sql);

  my @level_names = ('canonical','noncore-canonical','indistinguishable representative'  ,'representative'
                     ,'marginally distinguished','weak','insufficient evidence','indistinguishable','subsumed'); 

  my @headings =('Dataset',@level_names);
  my @sortable=();
  my @align=();
  for my $col ( @headings ) {
    $col =~ s/(\w+)/\u$1/g;
    push @sortable, $col,$col;
    push @align, 'center';
  }
  $align[0] = 'left';
  my $headings_ref = $atlas->make_sort_headings( headings => \@sortable);
  my @records = ();
  my @annotation_urls;
  my $anno = 0;
  foreach my $repository_id (sort {$a cmp $b} keys %dataset_prot_cnt){
    my @row =();
    my ($repository_id_w_links, $annotation_url) = $atlas->get_dataset_url($repository_id);
    push @row , $repository_id_w_links;
    push @annotation_urls, $annotation_url;
    $anno = 1 if ($annotation_url ne ''); 
    foreach my $level_name (@level_names){
      my $cnt = scalar keys %{$dataset_prot_cnt{$repository_id}{$level_name}} || 0;
      if ( $cnt){
         my $level_id = $protein_level_ids{$level_name};
         my $constraint = '';
         if($level_name =~ /^indistinguishable$/i){
            $constraint = "redundancy_constraint=1";
         }elsif ($level_name =~ /(subsumbed_by|identical)/i){
            $constraint = "redundancy_constraint=$level_id";
         }else{
           $constraint = "presence_level_constraint=$level_id&redundancy_constraint=4";
        }
         my $str  = $atlas->make_pa_tooltip( tip_text => $cnt,
           link_text => "<a href='$CGI_BASE_DIR/PeptideAtlas/GetProteins?atlas_build_id=$atlas_build_id&biosequence_name_constraint=!DECOY%&dataset_id=$repository_id&$constraint&apply_action=QUERY' target='_blank'>$cnt</a>" );
         push @row , $str;
      }else{
         push @row ,'';
      }
    }
    push @records, \@row;
  }
  ## insert annotation column to second column
  if ($anno){
    for (my $i=0; $i<=$#records; $i++){
      splice @{$records[$i]}, 1, 0, $annotation_urls[$i];
    }
    splice @headings, 1, 0, 'Experiment Annotation';
    splice @align, 1, 0, 'center';
  }

  my $html = $atlas->create_table (data => \@records,
                          column_names=> \@headings,
                          table_name => "Dataset Protein Info",
                          table_id => "dataset_protein_info",
                          align => \@align,
                          sortable => 0);

  return ($html);
}

# less informative sample contribution plot
sub get_build_plots {
  my %args = @_;
  my $build_id = $args{build_id};
  my $sample_array_ref = $args{sample_array_ref};
  my $column_name_ref = $args{column_name_ref};
  my $chart = $atlas->displayExperiment_contri_plotly(
      data_ref=>$sample_array_ref,
      column_name_ref => $column_name_ref, 
  );

  my $html = $sbeams->make_toggle_section(
      neutraltext =>"Experiment Contribution Plots",
      sticky => 1,
      barlink => 1,
      visible => 1,
      name => "prot_plots_div",
      content => "<TABLE><TR><TD COLSPAN='5'>$chart</TD></TR></TABLE>",
  );
 
  return $html;
}
##################################################################################
### peptide charge and length distribution 
##################################################################################
sub get_peptide_length_charge_distribution {
  my %args = @_;
  my $file = $args{data_path};
  my @charge_rows = ();
  my @length_rows=();
  my @tlength_rows=();
  my @distinctPlength_rows = ();
  my @trypPlength_rows = ();
  my @peptidePerProtein_rows =();
  open (IN, "$file") or return '';
  while (my $line =<IN>){
    chomp $line;
    if ($line =~ /^length\t(\d+)\t(\d+)$/){ 
      push @length_rows, [($1, $2)];
    }elsif($line =~ /^charge\t(\d+)\t(\d+)$/){
      push @charge_rows, [($1, $2)];
    }elsif($line =~ /^tlength\t(\d+)\t(\d+)$/){
      push @tlength_rows, [($1, $2)]; 
    }elsif($line =~ /^distinctPlength\t(\d+)\t(\d+)$/){
      push @distinctPlength_rows, [($1, $2)];
    }elsif($line =~ /^trypPlength\t(\d+)\t(\d+)$/){
      push @trypPlength_rows, [($1, $2)];
    }elsif($line =~ /^peptidePerProtein\t(\S+)\t(\d+)$/){
      push @peptidePerProtein_rows, [($1,$2)];
    }
  }
  my @names = ('observed distinct peptides (including semi-tryptic and miscleaved peptides)',
               'observed distinct tryptic no-missed-cleavages peptides',
               'theoretical distinct tryptic no-missed-cleavages peptides');
  my @data = ();
  push @data, [@distinctPlength_rows];
  push @data, [@trypPlength_rows];
  push @data, [@tlength_rows];
  
  my $chart1 = $atlas->plotly_barchart (data => \@data,
                                       names => \@names, 
				       divName => 'length_plot_div',
				       xtitle => 'Peptide Length',
				       ytitle=> 'Frequency'); 

  @data = ();
  @names = ();
  push @data, [@length_rows];
  push @names , '';

  my $chart2 = $atlas->plotly_barchart (data => \@data,
                                       names => \@names,
                                       divName => 'length_vs_psm_div',
                                       xtitle => 'Peptide Length',
                                       ytitle=> 'Spectra Count');


  my $chart = qq~
    <div style="width: 60vw">
    <div id="length_plot_div"></div>
    $chart1
    <div id="length_vs_psm_div"></div>
    $chart2
    </div>
  ~;
  my $html = $sbeams->make_toggle_section(
      neutraltext =>"Peptide Length Distribution",
      sticky => 1,
      barlink => 1,
      visible => 0,
      name => "peptidelen_plots_div",
      content => "<TABLE><TR><TD COLSPAN='5'>$chart</TD></TR></TABLE>",
  );
  
  @data = ();
  @names = ();
  push @data, [@charge_rows];
  push @names , 'Charge';
  $chart = $atlas->plotly_barchart (data =>  \@data,
				    names => \@names,
				    divName => 'pepitde_charge_plot_div',
				    xtitle => 'Peptide Charge',
				    dtick => 1,
				    ytitle=> 'Spectra Count');

   $chart = qq~
    <div style="width: 50vw">
    <div id="pepitde_charge_plot_div"></div>
    $chart
    </div>
  ~;
  $html .= $sbeams->make_toggle_section(
      neutraltext =>"Peptide Charge Distribution",
      sticky => 1,
      barlink => 1,
      visible => 0,
      name => "pepcharge_plots_div",
      content => "<TABLE><TR><TD COLSPAN='5'>$chart</TD></TR></TABLE>",
  );


  if (@peptidePerProtein_rows){
    @data = ();
    @names = ();
    push @data, [@peptidePerProtein_rows];
    push @names , 'Count';
    $chart = $atlas->plotly_barchart (data =>  \@data,
				      names => \@names,
				      divName => 'pepitdePerProtein_distribution_div',
				      xtitle => 'Peptide/Protein',
				      dtick => 5,
				      ytitle=> 'Protein Count');

    $chart .= qq~
			<div style="width: 80vw">
			<div id="pepitdePerProtein_distribution_div"></div>
			$chart
			</div>
		~;
    my $html = $sbeams->make_toggle_section(
      neutraltext =>"Peptide Per Protein",
      sticky => 1,
      barlink => 1,
      visible => 0,
      name => "pp_div",
      content => "<TABLE><TR><TD COLSPAN='5'>$chart</TD></TR></TABLE>",
    );

  }

  return ($html);
}

###########################################################################
### read build_detail_tables.tsv in build directory and create tables######
###########################################################################
sub generate_html_from_file {
  my %args = @_;
  my $file = $args{file};
  my $build_id = $args{build_id};
  my $build_path = $args{build_path};

  my (@sample_array, @column_names); 

  my %table_names = (
   exp_contrib_table => 'Experiment Contribution',
   dataset_contrib_table => 'Dataset Contribution',
   dataset_protein_info => 'Dataset Protein Info',
   dataset_spec_protein_info => 'Dataset Specific Protein Identification',
   proteome_coverage => 'Proteome Coverage (exhaustive)',
   ptm_coverage => 'PTM Coverage',
 );
 my %column_align = (
   exp_contrib_table => [qw(left left left center center center center center center center center center center center center center)], 
   dataset_contrib_table => [qw(left center center center center center center center center center center center center center center)], 
   dataset_protein_info => [qw(left center center center center center center center center)], 
   dataset_spec_protein_info => [qw(left center center center center center center center center)], 
   proteome_coverage => [qw(left center center center center center)],
   ptm_coverage =>  [qw(left)],
 );
  my $sql =qq~;
    SELECT LEVEL_NAME AS NAME, PROTEIN_PRESENCE_LEVEL_ID AS ID
    FROM $TBAT_PROTEIN_PRESENCE_LEVEL
    UNION
    SELECT RELATIONSHIP_NAME AS NAME, BIOSEQUENCE_RELATIONSHIP_TYPE_ID AS ID
    FROM $TBAT_BIOSEQUENCE_RELATIONSHIP_TYPE
  ~;
  my %protein_level_ids = $sbeams->selectTwoColumnHash($sql);


  open (IN , "<$file") || return '';
  my ($html, $table, $pre_table);
  my @data =();
  my $build_info ={};
  my $anno =0;
  my $cat_plot_data; 
  my $chr_plot_data;

  $build_info->{atlas_build_id} = $build_id;

  while (my $line =<IN>){
    chomp $line;
    if ($line =~ /^build_overview/){
       my $protein_url = "$CGI_BASE_DIR/PeptideAtlas/GetProteins?atlas_build_id=$build_id".
                         '&redundancy_constraint=4&QUERY_NAME=AT_GetProteins&apply_action=QUERY'.
                         '&biosequence_name_constraint=%21CONTAM%25%3B%21DECOY%25' .
                         '&presence_level_constraint=';

       while ($line =~ /^build_overview/){
	 $line =~ s/build_overview\|//;
	 if ($line =~ /(.*)Protein Presence Levels\|(.*)\t(\d+)$/){
	   my $level_id = $protein_level_ids{$2};
     if ($1 eq 'CoreProteome '){
       $build_info->{prot_count}->{$1}{$2} = "<a href='$protein_url$level_id&proteome=CoreProteome' target='_blank'>$3</a>";
     }elsif($1 eq 'Noncore-Proteome '){
	     $build_info->{prot_count}->{$1}{$2} = "<a href='$protein_url$level_id&proteome=NonCoreProteome' target='_blank'>$3</a>";
     }else{
       $build_info->{prot_count}->{$1}{$2} = "<a href='$protein_url$level_id' target='_blank'>$3</a>";
     }
	 }elsif ($line =~ /PhosphoProteome Summary\|(.*)\t(\d+)$/){
	   $build_info->{phospho_info}->{$1} = $2;
	 }else{
           if ($line =~ /pep_count_obs\t(\d+)/){
	     $build_info->{pep_count}{obs} = $1;
           }elsif($line =~ /pep_count_cnt\t(\d+)/){
	     $build_info->{pep_count}{cnt} = $1;
           }else{
	     $line =~ /^(.*)\t(.*)/;
	     $build_info->{$1} = $2;
           }
	 }
         $line =<IN>;
       }
       $html =  build_overview_html (build_info => $build_info);
       print $html;
       $html ='';
    }
    if($line =~ /what_is_new/){
      @data =();
      while ($line =~ /^what_is_new/ && $line !~/sample_ids/){
	chomp $line;
	$line =~ s/what_is_new\|//;
	my @values = split (/\t/, $line, -1);
	push @data , \@values;
	$line =<IN>;
      }
      $html = '<table>';
      $html .= $atlas->encodeSectionHeader(
	LMTABS => 1,
	no_toggle => 1,
	text => "What&#39s New"); 
      $html .= $atlas->encodeSectionTable( rows => \@data,
					   header => 1,
					   table_id => 'what_is_new',
					   align => [ qw(left right right right ) ],
					   bg_color => '#f3f1e4', #EAEAEA',
					   has_key => 1,
					   sortable => 1 );
      $html .= '</table>';
      print $html;
      chomp $line;
      if ($line =~ /what_is_new\|sample_ids\t(.*)/){
        $line = $1;
        $html = $atlas->getProteinSampleDisplay( sample_ids => [($line)], 
						 no_header => 1,
						 rows_to_show => 5,
						 max_rows => 500);
        $html =$sbeams->make_toggle_section( neutraltext => 'New Experiments',
					     sticky => 1,
					     name => 'getnew_samplelist_div',
					     barlink => 1,
					     visible => 1,
					     content => "<table>$html</table>" );

	print $html;
	$html ='';
      }
      @data =();
      next;
    }

    $line =~ /([^\|]+)\|(.*)/; 
    $table = $1;
    $line = $2 if ($line !~ /^ptm_coverage/);
    if ($table ne $pre_table && ($pre_table ne '' && ! 
				 ($table =~ /ptm_coverage/ && $pre_table =~ /ptm_coverage/))){ 
      if ($pre_table eq 'chr_plot'){
	@$chr_plot_data = @data;
      }else{
	my $headings = shift @data if ($pre_table !~ /ptm_coverage/);
	my $download_table = 0;
	my @noWrap = (1);

	@noWrap = (3,17,19,20) if ($pre_table eq 'exp_contrib_table');
	my $table_width = 800;
	if ($pre_table eq 'proteome_coverage'){
	  ## remove last column
	  $table_width = 400;
	  my $missing_prot_url = "$CGI_BASE_DIR/PeptideAtlas/GetCoreProteomeMapping?action=QUERY".
	      "apply_action=QUERY";
	  #'&action=QUERY&proteome_component=';
	  if (scalar @$headings >= 6){
	    ## has description column
	    $table_width = 1000 if (scalar @$headings == 7);

	    $headings->[0] =~s/^\|//;
	    foreach my $row (@data){
	      my @elms = split(/\|/, $row->[0]);
	      $row->[0] = $elms[1]; 
	      my $mapping_id = $elms[0];
	      my $uniprot_name_contraint = '';
	      if ($row->[0] =~ /Core/i){
		$uniprot_name_contraint = '&uniprot_name_constraint=%5BA-Z%5D%25';
	      }
	      ## add link to col5
	      if ($mapping_id =~ /^\d+$/){						
		$row->[5] = "<a href='$missing_prot_url$2&mapping_id=$mapping_id&atlas_build_id=$build_id".
		    "&peptideatlas_category_constraint=15&redundancy_constraint=on&".
		    "$uniprot_name_contraint' ".
		    "target='_blank' title='get missing proteins'>$row->[5]</a>" if ($row->[5] > 0);
	      }
	      $row->[4] .= '%';
	    }
	  }
	}
	add_url (table_id => $pre_table,
		 data_ref=>\@data,
		 column_name_ref => $headings,
		 build_id => $build_id,
		 align => $column_align{$pre_table},
	    ) if ($pre_table !~ /ptm_coverage/);
	
	if ($pre_table eq 'exp_contrib_table'){
	  if ($headings->[1] eq 'Experiment Annotation'){
	    $anno=1;
	  }
	  @sample_array =  map { [@$_] } @data;
	  @column_names = @$headings;
	  ## remove category id column 
	  my $n = $#column_names;
	  if ($column_names[$n] eq 'sample_category_id'){
	    foreach my $row (@data){ 
	      splice @$row, $n;
	    }
	    splice @$headings, $n;
	  }
	  $download_table =1;
	}

	my %ptm_plot_data =();
	my %ptm_table_headings = ();
	my %ptm_table_data = ();
	if ($pre_table =~ /ptm_coverage/){
	  my $counter = 0;
	  my %colnames = ();
	  my %col2residue = ();
	  my $residue = '';
	  my ($proteome, $ptm_type,);
	  foreach my $row (@data){
	    my $ptm_summary_url = "$CGI_BASE_DIR/PeptideAtlas/GetPTMSummary?atlas_build_id=$build_id".
	      "&display_options=proteinView&action=QUERY".
	      "&redundancy_constraint=on&proteome_component=";
	    if ($row->[0] =~ /Database/){
	      $row->[0] =~ /.*ptm_coverage_([^\|]+)\|(.*)/;
	      $ptm_type = $1;
	      $row->[0] =~ s/.*\|//;
	      push @{$ptm_table_headings{$ptm_type}}, $row;
	      for (my $i=1; $i < @$row; $i++){
					if ($row->[$i] =~ /^total_(\w)_.*$/){
						$residue = $1;
					}
					my $colname = $row->[$i];
					$colname =~ s/_\w_sites/_sites/;
					$colnames{$ptm_type}{$i} = $colname;
					$col2residue{$ptm_type}{$i} = $residue;
	      } 
	      next;
	    }
	    push @{$ptm_table_data{$ptm_type}}, $row;

	    $row->[0] =~ /^ptm_coverage_([^\|]+)\|([^\|]+).*/;
	    $proteome = $2;
	    $ptm_type = $1;
	    ## add link to col1
	    if ($row->[0]=~ /^ptm_coverage_[^\|]+\|([^\|]+)\|(.*)$/){
        $ptm_summary_url = "$ptm_summary_url$2";
	      $row->[0] = "<a href='$ptm_summary_url\&ptm_type=$ptm_type' target='_blank' title='get ptm protein list'>$1</a>";
	    }else{
	      $row->[0] = $proteome;
	    }
	    if ($proteome =~ /(core|^Araport11$|^NeXtProt$)/i && ! $ptm_plot_data{$ptm_type}{data} ){
        my %probability_constraint =  ('nP.80-.95' => 1,
                                       'nP.95-.99' => 2,
                                       'nP.99-1' => 3,
                                       'no-choice' => 4);
	      foreach my $i(1..scalar @$row -1){ 
					my $val =  $row->[$i];
					$val =~ s/\s.*//;
					$val =~ s/,//g;
          my $url = '<a href="' . $ptm_summary_url . 
                    "&ptm_type=$ptm_type&probability_constraint=$probability_constraint{$colnames{$ptm_type}{$i}}\">";
          $url =~ s/proteinView/proteinResidueView/;
					if ($colnames{$ptm_type}{$i} =~ /nP(\.\d+)\-([\.\d]+)/){
						my $xlabel = '';
						if ($2 != 1){
							$xlabel = $url . "0$1<=nP<0$2</a>";
						}else{
							$xlabel = $url . "nP>=0$1</a>";
						}
						push @{$ptm_plot_data{$ptm_type}{data}{$col2residue{$ptm_type}{$i}}},["$xlabel",$val];
					}elsif($colnames{$ptm_type}{$i} =~ /no-choice/){
						push @{$ptm_plot_data{$ptm_type}{data}{$col2residue{$ptm_type}{$i}}},["$url$colnames{$ptm_type}{$i}</a>",$val];
					}
	      }
	      $ptm_plot_data{label} = $proteome;
	    }
	    my $n = scalar @$row;
	    if ($counter == 0){
	      for my $i (1..$n-1){
					push @{$column_align{$pre_table}}, 'center';
	      }
	    } 
	    $counter++;
	  }
	}
	$download_table = 1 if ($pre_table eq 'dataset_contrib_table');
	my $plot_html = '';
	my $tname = '';
	my $ptm_chart = '';
	if ($pre_table =~ /ptm_coverage/ && %ptm_plot_data){
	  my $counter = 0;
	  $plot_html = qq~<div class="tab">
										<style>
										/* Style the tab */
										.tab {
													overflow: hidden;
										}
										/* Style the buttons inside the tab */
										.tab button {
										padding: 14px 16px;
										border: none;
										outline: none;
										font-size: 14px;
										font-weight:bold;
													float:left;
													color:#555555;
													text-decoration:none;
													background:#f3f1e4;
										border-right:1.25px solid #AAAAAA;
										}

										/* Change background color of buttons on hover */
										.tab button:hover {
													background-color:#bb0000;
										color:#ffffff;
										}

										/* Create an active/current tablink class */
										.tab button.active {
													 background:#ffffff;
											color:#333333;
										}

										/* Style the tab content */
										.tabcontent {
													border-top: none;
										}
										</style>
            ~;

           foreach my $ptm_type (sort {$a cmp $b} keys %ptm_plot_data){
             next if ($ptm_type eq 'label');
             $plot_html .="<button type='button' class='ptmtablinks' onclick='openPTM(event,\"ptm_cov_div$counter\")'>$ptm_type</button>\n";
             $counter++;
           } 
           $plot_html .= "</div>\n";

						$counter = -1;
						foreach my $ptm_type (sort {$a cmp $b} keys %ptm_plot_data){
							next if ($ptm_type eq 'label');
							$counter++;
							my @residues = sort {$a cmp $b} keys %{$ptm_plot_data{$ptm_type}{data}};
							my @plot_data = ();
							foreach my $residue (@residues){
								push @plot_data, $ptm_plot_data{$ptm_type}{data}{$residue};
							}
										
							$ptm_chart .= $atlas ->plotly_barchart (data => [@plot_data],
												names => [@residues],
												divName => "ptm_cov_plot$counter",
												ytitle => 'Count',
												dtick => 1,
												title => "$ptm_type for $ptm_plot_data{label}",
												barlabel => 1
												#xtickangle => 'tickangle:25',
												#yticktype => "type:'log',range:[0,$max],dtick:1",
												#layoutmargin => 'b:50',
						);         
							unshift @{$ptm_table_data{$ptm_type}}, @{$ptm_table_headings{$ptm_type}};
							my $ptm_table = $atlas->encodeSectionTable (
								header => 1,
								unified_widgets => 1,
								set_download => 1,
								align  => [()],
								bkg_interval => 3,
								file_prefix => 'ptm_',
								rows => $ptm_table_data{$ptm_type});
							my $ptm_plot_desc = qq~
												 <p class="help_val"  style="width: 55vw; padding-left:10px;">
													The combined results from datasets searched with $ptm_type in this build yield the
													following numbers of ptm sites at several levels of
													confidence (nP == number of sites with PTMProphet probability range).
													The bar chart depicts the results for the core proteome only.
													The table provides metrics for all subsets of protein entries in the combined mapping proteome.
												</p>
											~;

							if ($counter == 0){
								$plot_html .= "\n<div id='ptm_cov_div$counter' style='display:block' class='tabcontent'>\n";
							}else{
								$plot_html .= "\n<div id='ptm_cov_div$counter' style='display:none' class='tabcontent'>\n";
							}
							$plot_html .= "$ptm_plot_desc<div style='width: 40vw' id='ptm_cov_plot$counter'></div>\n";
							$plot_html .= "<TABLE width='$table_width'>$ptm_table</TABLE>\n</div>\n";
						}
						$plot_html .= qq~
								 <!-- Latest compiled and minified plotly.js JavaScript -->
								 <script type="text/javascript" src="https://cdn.plot.ly/plotly-latest.min.js"></script>
								 <script type="text/javascript" charset="utf-8">
									function openPTM(evt, Name) {
													var i, tabcontent, ptmtablinks;
													tabcontent = document.getElementsByClassName("tabcontent");
													for (i = 0; i < tabcontent.length; i++) {
																	tabcontent[i].style.display = "none";
													}
													ptmtablinks = document.getElementsByClassName("ptmtablinks");
													for (i = 0; i < ptmtablinks.length; i++) {
																	ptmtablinks[i].className = ptmtablinks[i].className.replace(" active", "");
													}
													document.getElementById(Name).style.display = "block";
													evt.currentTarget.className += " active";
									}
								 </script>
           ~;
	}
	if ($pre_table =~ /ptm_coverage/){
    my $ptm_table_help = $atlas->get_table_help(column_titles_ref=>[qw(nP.95-.99 nP.99-1 no-choice)]);
	  $html = $sbeams->make_toggle_section(
	    neutraltext =>"PTM Coverage",
	    sticky => 1,
	    barlink => 1,
	    visible => 1,
	    name => "ptm_div",
	    content => "$ptm_table_help<TABLE><TR><TD COLSPAN='5'>$plot_html\n$ptm_chart</TD></TR></TABLE>",
	      );
	}else{
	  $html = $atlas->create_table (data => \@data,
					column_names=> $headings,
					table_name => $table_names{$pre_table},
					table_id => $pre_table,
					nowrap => \@noWrap,
					width => $table_width, 
					align => $column_align{$pre_table}, 
					sortable => 0,
					plot_html => $plot_html,
					download_table=> $download_table,
	      );
	}
	print "$html";
      }
      $html ='';
      @data = (); 
      my @values = split (/\t/, $line, -1);
      push @data , \@values;
    }else{
      my @values = split (/\t/, $line, -1);
      push @data,\@values;
    }
    $pre_table=$table;
  }

  my $mayu_data_path = "$build_path/analysis/Mayu_out.csv";
  if ( -e $mayu_data_path ) {
    my $page = get_mayu_info( $mayu_data_path );
    print $page;
  }

  if ($table eq 'cat_plot'){
    $cat_plot_data=\@data;
  }

  $html = get_build_plots ( build_id => $build_id,
			    sample_array_ref => \@sample_array,
			    column_name_ref => \@column_names);
  print $html;

  my $charge_length_data_path = "$build_path/analysis/peptide_length-charge_dist.tsv";
  if (-e $charge_length_data_path){
    $html = get_peptide_length_charge_distribution(data_path=>$charge_length_data_path);
    print $html;
  }
  if ($chr_plot_data){
    $html =  $atlas->display_chromosome_coverage_plotly(
      data_ref=> $chr_plot_data,
	);
    print "$html";
  }

  if ($cat_plot_data){
    $html = $atlas->display_peptide_sample_category_plotly(
            build_id=>$build_id,
            sample_array_ref=> \@sample_array,
            column_name_ref => \@column_names,
            data_ref=> $cat_plot_data,
              );
    print $html;
  }

  my $col=2; 
  $col = 3 if ($anno);
  print $atlas->tableHeatMap(table_id => 'dataset_spec_protein_info', column=>$col, total => $build_info->{prot_count}{canonical});
  print $atlas->tableHeatMap(table_id => 'dataset_protein_info',column=>$col, total=> $build_info->{prot_count}{canonical}); 
}
###########################################################
## add url to some columns of the tables
## dataset, Experiment_Tag, Pubmed, and Protein columns
###########################################################
sub add_url {
  my %args = @_;
  my $data_ref = $args{data_ref};
  my $build_id = $args{build_id};
  my $column_name_ref = $args{column_name_ref};
  my $align_ref = $args{align};
  my $table_id = $args{table_id};
  my %cols=();
  my @annotation_urls =();
  my $anno =0;
  my $exp_id_idx = '';
  my $n = scalar @$column_name_ref;

  my $sql =qq~;
    SELECT LEVEL_NAME AS NAME, PROTEIN_PRESENCE_LEVEL_ID AS ID
    FROM $TBAT_PROTEIN_PRESENCE_LEVEL
    UNION
    SELECT RELATIONSHIP_NAME AS NAME, BIOSEQUENCE_RELATIONSHIP_TYPE_ID AS ID
    FROM $TBAT_BIOSEQUENCE_RELATIONSHIP_TYPE
  ~;
  my %protein_level_ids = $sbeams->selectTwoColumnHash($sql);

  for (my $idx=0; $idx < $n; $idx++){ 
    if ($column_name_ref->[$idx] =~ /(Dataset|Experiment Tag|Pubmed|^Canonical$|noncore|Indistinguish|Representative|Marginally|Weak|Insufficient|Subsumed|Unique All Proteins|Unique Canonical Proteins)/i){
			$cols{$idx} = $column_name_ref->[$idx];
    }
    if ($column_name_ref->[$idx] =~ /Experiment ID/){
      $exp_id_idx = $idx;
    }
  }
  foreach my $row (@$data_ref){
    my $n = scalar @$row;
    my $repository_id = '';
    for (my $i=0;$i<$n;$i++){
      if ($cols{$i}){
        if ($cols{$i} =~ /Dataset/){
          my $annotation_url='';
          $repository_id = $row->[$i];
          ($row->[$i], $annotation_url) = $atlas->get_dataset_url ($row->[$i]);         
	  $anno = 1 if ($annotation_url ne '');
	  push @annotation_urls, $annotation_url;
        }elsif($cols{$i} =~ /Experiment Tag/){
	  if ($exp_id_idx){
	    $row->[$i] = '<a href="https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ManageTable.cgi?TABLE_NAME=AT_SAMPLE&sample_id=' .
		$row->[$exp_id_idx] . '">'. $row->[$i] ."</a>";
	  }
        }elsif($cols{$i} =~ /Pubmed/){
          my @ids = split(",", $row->[$i]);
          $row->[$i] = '';
	  foreach my $id(@ids){
	    if ($id =~ /^\d+$/){
	      $row->[$i] .= "<a href='http://www.ncbi.nlm.nih.gov/pubmed/?term=$id' target='_blank'>$id</a>,";
	    }else{
	      $row->[$i] .= "<a href='https://doi.org/$id' target='_blank'>$id</a>,";
	    }
	  }
          $row->[$i] =~ s/,$//;
        }elsif ($cols{$i} =~ /(^Canonical$|noncore|Indistinguish|Representative|Marginally|Weak|Insufficient|Subsumed)/i){
          my $level_id = $protein_level_ids{lc($cols{$i})};
          my $level_name = $cols{$i};
	  my $constraint = '';
	  if($level_name =~ /^indistinguishable$/i){
	    $constraint = "redundancy_constraint=1";
	  }elsif ($level_name =~ /(subsumbed_by|identical)/i){
	    $constraint = "redundancy_constraint=$level_id";
	  }else{
	    $constraint = "presence_level_constraint=$level_id&redundancy_constraint=4";
	  }
          if ($repository_id){
            if ($table_id eq 'dataset_protein_info'){ 
	      $row->[$i] = "<a href='$CGI_BASE_DIR/PeptideAtlas/GetProteins?atlas_build_id=$build_id&dataset_id=$repository_id&$constraint&apply_action=QUERY' target='_blank'>$row->[$i]</a>";
            }elsif($table_id eq 'dataset_spec_protein_info'){
              $row->[$i] = "<a href='$CGI_BASE_DIR/PeptideAtlas/GetProteins?atlas_build_id=$build_id&dataset_specific_id=$repository_id&biosequence_name_constraint=!DECOY%&$constraint&apply_action=QUERY' target='_blank'>$row->[$i]</a>";
            }
          }
        }elsif($cols{$i} eq 'Unique All Proteins' and $table_id eq 'exp_contrib_table'){
	  $row->[$i] = "<a href='$CGI_BASE_DIR/PeptideAtlas/GetProteins?atlas_build_id=$build_id&".
	      "sample_specific_id=$row->[$exp_id_idx]&apply_action=QUERY' target='_blank'>$row->[$i]</a>";
        }elsif($cols{$i} eq 'Unique Canonical Proteins' && $table_id eq 'exp_contrib_table'){
	  $row->[$i] = "<a href='$CGI_BASE_DIR/PeptideAtlas/GetProteins?atlas_build_id=$build_id&".
	      'presence_level_constraint=1&redundancy_constraint=4&' .
	      "sample_specific_id=$row->[$exp_id_idx]&apply_action=QUERY' target='_blank'>$row->[$i]</a>";

        }
      }##cols[$i]
    }##for
  }## data_ref   
  ## add dataset annotation column
  if ($anno){
    my $n_rows = scalar @$data_ref;
    for (my $i=0; $i< $n_rows; $i++){
      splice @{$data_ref->[$i]}, 1, 0, $annotation_urls[$i];
    }
    splice @$column_name_ref, 1, 0, 'Experiment Annotation';
    splice @$align_ref, 1, 0, 'center';
  }
}