#!/usr/local/bin/perl

###############################################################################
# $Id: $
#
# SBEAMS is Copyright (C) 2000-2014 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.
#..o##############################################################################


###############################################################################
# Get the script set up with everything it will need
###############################################################################
use strict;
use lib qw (../../lib/perl);
use Data::Dumper;

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


###############################################################################
# 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();
$params->{build_id} ||= 393;

my $show_image = 0;


{ # Main 

    # Authenticate or exit
    my $username = $sbeams->Authenticate( allow_anonymous_access => 1) || exit;



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

    my $page = $sbeams->getGifSpacer( 700 ) . "<BR>\n";

    # Get the HTML to display the tabs
    my $tabMenu = $atlas->getTabMenu(
      parameters_ref => $params,
      program_name => 'proteinList',
    );

    $page .=<<"    END";
		$tabMenu
     <br>
    END

    # Add general section 
    $page .= get_list_selector();
    my $proteome_cover = $atlas->get_proteome_coverage( $params->{build_id} );
    $page .= $proteome_cover;

    $page .= get_list_table();

    # Print what we already have, speed up apparent page loading time.
    $atlas->display_page_header( onload => "sortables_init(); set_toggle_box( 'protein_list_table' );" );
		print $page;
		$atlas->display_page_footer();

} # end main

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 => '# Samples', value => 'The number of individual samples which comprise this build.  Each sample contains one or more LCMS/MS runs, and generally corresponds to a single scientific experiment.' } ,
                 { key => 'Distinct 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 => 'Total Observations ', value => 'The total number of spectra that yeilded identifications above the build threshold.  Observations of the same base peptide sequences multiple times or in various charge states/modifications, whould each contribute to the total' }
        );
                 
    $showtext = 'show row descriptions';
    $hidetext = 'hide row descriptions';
    $heading = 'Build Overview';
    $description= 'These values pertain to the atlas build as a whole';


  } elsif ( $name eq 'batch' ) {
    @entries = ( { key => 'ID', value => 'Database ID for this sample (search batch) ' },
                 { key => 'Sample_Name', value => 'Simple name for this sample/experiment. ' },
                 { key => '#_Spectra_Searched', value => 'The total number of spectra searched in the sample. ' },
                 { key => "#_Spectra_ID'd", value => 'The number of spectra identifed with a probability greater than the atlas threshold ' },
                 { key => '#_Distinct', value => 'The number of distinct peptide sequences, seen more than once (multiobs), in this build that are seen in this sample. ' },
                 { key => '#_Unique', value => "The number of distinct, multiobs peptides that are seen only in this sample (unique contribution).  This discriminates against smaller samples, and is less useful in atlas' with a large number of samples. " },
                 { key => '#_Progressive', value => 'Order-dependent unique multiobs peptides contributed by a given sample.  The contribution for each sample is based on the samples that have gone before it, so later samples tend to have a lower progressive contribution. ' },
                 { key => '#_Cumulative', value => 'Order-dependent cumulative number of unique multiobs peptides contributed to build by this and previous samples. ' },
                 { key => '#_Proteins', value => 'The number of canonical (highly distinguishable, non-redundant) protein sequences identified from the peptides in this sample.' },
                 { key => '#_Cum_Prots', value => 'Order-dependent cumulative number of canonical proteins contributed to build by this and previous samples.<br>Counts non-human contaminants, so final tally may be greater than Canonical Proteins count in Build Overview. ' },
#                 { key => 'Sens', value => 'The sensitivity of the Peptide Prophet model at a probablility of 0.9, the percent of true positives that would be included at that threshold was used as a cutoff. ' },
                 { key => 'FDR_(%)', value => 'The error rate of peptides above the threshold Peptide Prophet model at a probablility of 0.9, the percent of false positives that would be included at the build threshold. ' },
                 { key => 'Sample_Date', value => ''},
        );
    $heading = 'Sample Overview'; 
    $description = 'These values pertain to individual samples within the atlas';

  } elsif ( $name eq 'mayu' ) {
   @entries = ( { key => 'nr_runs', value => 'Number of MS runs contributing to this build '},
  
		{ key => 'nr_files', value => 'Always 1 '},
  
		{ key => 'mFDR', value => 'Data in current row applies to all data meting this PSM (spectrum) FDR threshold. '},
		{ key => 'target_PSM', value => 'Number of non-decoy PSMs at this mFDR (counts peptides mappable to protein reference set only)'},
  
		{ key => 'decoy_PSM', value => 'Number of decoy PSMs at this mFDR '},
  
		{ key => 'FP_PSM', value => 'Number of false positive PSMs predicted by Mayu for this mFDR. Usually near, but not exactly the same as, the number of decoys. '},
  
		{ key => 'TP_PSM', value => 'target_PSM - FP_PSM '},
  
		{ key => 'target_pepID', value => 'Number of non-decoy unique peptides at this mFDR (counts peptides mappable to protein reference set only) '},
  
		{ key => 'decoy_pepID', value => 'Number of decoy unique peptides at this mFDR '},
  
		{ key => 'FP_pepID', value => 'Number of false positive unique peptides predicted by Mayu for this mFDR. Usually near, but not exactly the same as, the number of decoys. '},
  
		{ key => 'FP_pepID_stdev', value => ' '},
  
		{ key => 'TP_pepID', value => 'target_pepID - FP_pepID '},
  
		{ key => 'pepFDR', value => 'Peptide FDR (unique peptides)'},
  
		{ key => 'target_protID', value => 'Number of non-decoy protein identifications at this mFDR. Applied to the covering set of proteins -- a set that is close to the smallest necessary to explain all the pepIDs. Includes all canonicals and some possibly_distinguished. '},
  
		{ key => 'decoy_protID', value => 'Number of decoy protein identifications at this mFDR. '},
  
		{ key => 'FP_protID', value => 'Number of false postiive protein identifications predicted by Mayu for this mFDR.  Usually near, but not exactly the same as, the number of decoys. '},
  
		{ key => 'FP_protID_stdev', value => ' '},
  
		{ key => 'TP_protID', value => 'target_protID - FP_protID '},
  
		{ key => 'protFDR', value => 'Protein FDR. The largest value in this column is the protein FDR for the entire build. '},
		{ key => 'lFDR1, lFDR5, lFDR10,2 lFDR5', value => 'Local protein FDR, computed over the previous step (i.e. between the previous row in the table and the current row), the previous 5 steps, the previous 10 steps, and the previous 25 steps.<br>Often there are fewer than 25 rows in the table, in which case column lFDR25 is uninformative. '},
  
		{ key => 'target_protIDs, decoy_protIDs, etc.', value => 'Same as above, except for singleton proteins (those identified by only one PSM) only. '},
		{ key => 'target_protIDns, decoy_protIDns, etc.', value => 'Same as above, except for multiply-observed proteins only. '},
  
        );
    $heading = 'Mayu'; 
    $description = 'Reiter L, Claassen M, et al., Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry, Mol Cell Proteomics. 2009 Nov;8(11):2405-17 ';
  }


  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


# General list information
sub get_list_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 $info = $sbeams->selectrow_hashref( <<"  BUILD" );
  SELECT title, description, n_proteins, original_file, protein_list_id,
         contributors, url, image_path, abstract, image_caption
  FROM $TBAT_DOMAIN_PROTEIN_LIST 
  WHERE protein_list_id = $params->{protein_list_id}
  AND record_status <> 'D'
  AND project_id IN ( $project_ids );
  BUILD


  my $table = "<TABLE WIDTH=800>\n";

  my ( $tr, $link ) = $sbeams->make_table_toggle( name    => 'build_overview',
                                                  visible => 1,
                                                  tooltip => 'Show/Hide Section',
                                                  imglink => 1,
                                                  sticky  => 1 );

  $table .= $atlas->encodeSectionHeader(
      text => ' Protein List Overview',
      span => 4,
      link => $link
  );
  for my $key ( keys( %{$info} ) ) {
    $info->{lc($key)} = $info->{$key};
  }

  my $file_url = "$CGI_BASE_DIR/PeptideAtlas/ManageTable.cgi/$info->{original_file}?TABLE_NAME=AT_Domain_Protein_list;ForceDownload=1;protein_list_id=" . $info->{protein_list_id} . ";GetFile=original_file";
  my $file_link = "<a href='$file_url'>$info->{original_file}</a>";

  my $spc = $sbeams->getGifSpacer(500);
  my $tab = $sbeams->getGifSpacer(25);

  my $img = '';
  my $caption = '';
  if ( $info->{image_path} ) {
    my @path = split( /\//, $info->{image_path});
    my $web_path = "/devDC/sbeams/images/$path[$#path]";
    $img = "$tab<img src=$web_path height=80 width=80></img>\n";
    $caption = $info->{image_caption} || '';
  }

  my $abstract = '';
  if ( $info->{abstract} ) {
    $abstract = $info->{abstract};
    $abstract =~ s/\r//;
    $abstract =~ s/\n/<br>/g;
  }


  $table .= $atlas->encodeSectionItem( key   => 'List Name', tr_info => $tr,
                            value => $info->{title} . $spc, vspan => 3 ) . "\n";
  $table .= $atlas->encodeSectionItem( key   => 'Contributors', tr_info => $tr,
                            value => $info->{contributors}, vspan => 3 ) . "\n";
  $table .= $atlas->encodeSectionItem( key   => 'Description', tr_info => $tr,
                            value => $info->{description}, vspan => 3 ) . "\n";
  $table .= $atlas->encodeSectionItem( key   => 'Number of Proteins', tr_info => $tr,
                            value => $info->{n_proteins}, vspan => 3 ) . "\n";
  $table .= $atlas->encodeSectionItem( key   => 'Original File', tr_info => $tr,
                            value => $file_link, vspan => 3 ) . "\n";

  $table .= "<tr><td>$img</td><td>$caption</td></tr>";
  $table .= "<tr><td colspan=2>$abstract</td></tr>";
  $table .= "</TABLE>\n";
  return $table;

}

# Peptide build stats
sub get_list_table {

  my $table = "<table width=600  id='protein_list_section'>\n";

  my $atlas_select = get_atlas_select();

  my @headings = ( qw( Protein Type Peptide N_map Nobs Nobs_actyl SP NP Term Both ) );
  my %defs = ( Protein => 'Protein Accession',
                  Type => 'Peptide Type C(leaved) or P(reserved)',
               Peptide => 'Peptide Sequence',
                 N_map => 'Number of core proteins to which peptide maps', 
             N_tot_map => 'Total number of proteins to which peptide maps, including isoforms ', 
             Actl_nobs => 'Number of observations of peptide in acetylated form', 
            Total_nobs => 'Total number of observations of peptide', 
                  Both => 'Does protein have evidence for both cleaved and preserved Init Met', 
                    SP => 'SwissProt annotation regarding init_met cleavage', 
                    NP => 'NextProt annotation regarding init_met cleavage', 
                  Term => 'TermiNator prediction for protein N-terminus', 
      );

  my @db_headings = ( qw( build_id acc type cleaved cleaved_map cleaved_iso_map cleaved_alt_map cleaved_acetyl_obs cleaved_total_obs not_cleaved not_cleaved_map not_cleaved_iso_map not_cleaved_alt_map not_cleaved_acetyl_obs not_cleaved_total_obs sp np term_type term_like ) );
  my $head_str = join( ',', @db_headings );

  my @sort_headings;
  for my $heading ( @headings ) {
    push @sort_headings, $heading, $defs{$heading};
  }
  my $href = $atlas->make_sort_headings( headings => \@sort_headings, default => 'Protein' );
  my @samples;
  push @samples, $href;

  my $sql = "SELECT $head_str FROM peptideatlas.dbo.initiator_methionine_evidence WHERE build_id = $params->{build_id}";
  my $sth = $sbeams->get_statement_handle( $sql );
  while ( my @row = $sth->fetchrow_array() ) {
# 0 build_id
# 1 acc
# 2 type
# 3 cleaved
# 4 cleaved_map
# 5 cleaved_iso_map
# 6 cleaved_alt_map
# 7 cleaved_acetyl_nobs
# 8 cleaved_total_nobs
# 9 not_cleaved
# 10 not_cleaved_map
# 11 not_cleaved_iso_map
# 12 not_cleaved_alt_map
# 13 not_cleaved_acetyl_nobs
# 14 not_cleaved_total_nobs
# 15 sp
# 16 np
# 17 term_type
# 18 term_like
#
# 0 Protein
# 1 Type
# 2 Peptide
# 3 N_map
# 4 Nobs
# 5 Nobs_actyl
# 6 SP
# 7 NP
# 8 Term
# 9 Both
    my $t = 'C';
    my $b = 'N';
    my $na = $sbeams->makeInactiveText( 'n/a' ); 
    $row[16] = $na if !$params->{is_human};

    if ( !$row[15] && length($row[1]) > 6 ) {
      $row[15] = $na;
    } elsif ( $row[15] =~ /Not Annotated/ ) {
      $row[15] = '';
    }

    if ( $row[2] eq 'Both' ) {
      $b = 'Y';
      push @samples, [ $row[1], $t, @row[3,4,8,7,15,16,17], $b];
      $t = 'P';
      push @samples, [ $row[1], $t, @row[9,10,14,13,15,16,17], $b];
    } elsif ( $row[2] eq 'Cleaved' ) {
      push @samples, [ $row[1], $t, @row[3,4,8,7,15,16,17], $b];
    } else {
      $t = 'P';
      push @samples, [ $row[1], $t, @row[9,10,14,13,15,16,17], $b];
    }
  }

  my $table = SBEAMS::Connection::DataTable->new( class => 'scrolltable', 
                                                     id => 'protein_list_table',
                                          '__use_thead' => 1 );

  $table->setRowAttr( ROWS => [1], BGCOLOR => '#0000A0', CLASS => 'sortheader' );
  my $rnum = 2;
  for my $row ( @samples ) {
    if ( $rnum > 2 ) {
      if ( length( $row->[2] ) > 30 ) {
        $row->[2] = substr( $row->[2], 0, 30 ); 
      }
      $row->[2] = "<a target=var_evidence href=GetVariantEvidence?atlas_build_id=$params->{build_id}&protein_name=$row->[0]&variant_type=init_met&apply_action=&action=GO>$row->[2]</a>";
      $row->[0] = "<a target=get_protein href=GetProtein?protein_name=$row->[0]&action=QUERY&atlas_build_id=$params->{build_id}>$row->[0]</a>";
      if ( length( $row->[7] ) > 30 ) {
        $row->[7] = substr( $row->[7], 0, 30 ); 
      }
    }
    $table->addRow( $row );
    $table->setRowAttr( ROWS => [$rnum], BGCOLOR => '#EAEAEA' );
    $rnum++;
  }
  my $nrows = $table->getRowNum();
  $table->setColAttr(  COLS => [2,6,10], ROWS => [1..$nrows], ALIGN => 'CENTER' );
  $table->setColAttr(  COLS => [4,5], ROWS => [1..$nrows], ALIGN => 'CENTER' );

my $style = qq~




  <style>
   
   table.scrolltable tbody { height:500px; overflow-y:scroll; display:block; }
   table.scrolltable thead { display:block; overflow-y: scroll; }

    .border_div { border: 1px solid }
    .border_scroll_div { border: 1px solid; height:300px; overflow-y:scroll; display:block; }
		.highlighted { background: lightskyblue; }
    .protein_list_button { -moz-box-shadow:inset 0px 1px 14px -1px #bbdaf7; -webkit-box-shadow:inset 0px 1px 14px -1px #bbdaf7; box-shadow:inset 0px 1px 14px -1px #bbdaf7; background:-webkit-gradient( linear, left top, left bottom, color-stop(0.05, #79bbff), color-stop(1, #378de5) ); background:-moz-linear-gradient( center top, #79bbff 5%, #378de5 100% ); filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#79bbff', endColorstr='#378de5'); background-color:#79bbff; -moz-border-radius:6px; -webkit-border-radius:6px; border-radius:6px; border:1px solid #84bbf3; display:inline-block; color:#ffffff; font-family:Monospace; font-size:12px; font-weight:bold; padding:4px 22px; text-decoration:none; text-shadow:1px 1px 5px #528ecc; }
    .protein_list_button:hover { background:-webkit-gradient( linear, left top, left bottom, color-stop(0.05, #378de5), color-stop(1, #79bbff) ); background:-moz-linear-gradient( center top, #378de5 5%, #79bbff 100% ); filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#378de5', endColorstr='#79bbff'); background-color:#378de5; }
    .protein_list_button:active { position:relative; top:1px; }
    /* This imageless css button was generated by CSSButtonGenerator.com */
	</style>

  ~;

  my $js = qq~
    <script type="text/javascript">
  function submit_form( table ) {
   var form = document.getElementById('build_list');
   form.submit();
   return true;
  }

  function set_toggle_box( table ) {

    toggle_table = document.getElementById( table );
    this.colwidth = new Array();

	  for (var r = 0; r < toggle_table.rows.length; r++) {
      var row = toggle_table.rows[r].cells;

      for (var c = 0; c < row.length; c++) {
        if ( !this.colwidth[c] ) {
          this.colwidth[c] = row[c].offsetWidth;
        } else if ( row[c].offsetWidth > this.colwidth[c] ) {
          this.colwidth[c] = row[c].offsetWidth;
        }
      }
    }
    set_col_widths(table);

    // replace with count in loop above
    return false;
  }

  function set_fctl(event, table) {
    if ( event.keyCode == 13 ) {
      event.preventDefault;
    }
    var show_select = document.getElementById( 'show_select' );
    show_select.selectedIndex = 4;
    show_select[4].text = 'Filtered';
    set_col_widths( table);
    return false;
  }

  function show_proteins( table ) {
    document.getElementById( 'filterbox' ).value = '';
    var toggle_table = document.getElementById( table );
    dehighlight( toggle_table );

    var show_select = document.getElementById( 'show_select' );
    var selected = show_select.selectedIndex;
    var selected_txt = show_select[selected].value;

    var hidden = 0;
    var visible = 0;
	  for (var r = 1; r < toggle_table.rows.length; r++) {
      if ( selected_txt == 'All' ) {
        toggle_table.rows[r].style.display = '';
        visible += 1;
      } else if ( selected_txt == 'Cleaved' ) {
        if ( toggle_table.rows[r].cells[1].innerHTML == 'C' ) {
          toggle_table.rows[r].style.display = '';
          visible += 1;
        } else {
          toggle_table.rows[r].style.display = 'none';
          hidden += 1;
        }
      } else if ( selected_txt == 'Preserved' ) {
        if ( toggle_table.rows[r].cells[1].innerHTML == 'C' ) {
          toggle_table.rows[r].style.display = 'none';
          hidden += 1;
        } else {
          toggle_table.rows[r].style.display = '';
          visible += 1;
        }
      } else if ( selected_txt == 'Both' ) {
        if ( toggle_table.rows[r].cells[9].innerHTML == 'Y' ) {
          toggle_table.rows[r].style.display = '';
          visible += 1;
        } else {
          toggle_table.rows[r].style.display = 'none';
          hidden += 1;
        }
      } 
    }
    var total = visible + hidden;
    document.getElementById( 'chk_status' ).innerHTML = visible + ' of ' + total + ' evidentiary peptides are currently shown';
    set_col_widths(table);
    return false;
  }

    function set_col_widths ( table ) {
    var toggle_table = document.getElementById( table );

    var head = toggle_table.rows[0].cells;
    for ( var c = 0; c < head.length; c++ ) {
      head[c].width = window.colwidth[c];
    }

    var chk_row = 1;
	  for (var r = 1; r < toggle_table.rows.length; r++) {
      if ( toggle_table.rows[r].style.display == 'none' ) {
        continue;
      }
      chk_row = r;
      break;
    }

    var first = toggle_table.rows[chk_row].cells;
    for ( var c = 0; c < first.length; c++ ) {
      first[c].width = window.colwidth[c];
    }

    if (navigator.appName == 'Microsoft Internet Explorer') {
       var border_div = document.getElementById( 'border_div' );
       border_div.className = 'border_scroll_div';

  	  for (var r = 0; r < toggle_table.rows.length; r++) {
       toggle_table.rows[r].height = 10;
      }
    }
    cnt_visible( table );
    return false;
  }

  function cnt_visible ( table ) {
    var visible = 0;
    var hidden  = 0;
	  for (var r = 1; r < toggle_table.rows.length; r++) {
      if ( toggle_table.rows[r].style.display == 'none' ) {
        hidden += 1;
      } else {
        visible += 1;
      }
    }
    var total = visible + hidden;
    document.getElementById( 'chk_status' ).innerHTML = visible + ' of ' + total + ' evidentiary peptides are currently shown';
  }





  </script>
  <script type="text/javascript" src="$HTML_BASE_DIR/usr/javascript/filterTable/filterTable.js"></script>
  ~;
  my $spc = '&nbsp;&nbsp;';
  my $fbox = "<span title='Text entered into the box will filter the protein list (all fields)'>Filter List: $spc</span>";
  my $submit = "<span title='This will submit the selected proteins to query the SRM or Peptide Atlas'>$atlas_select $spc</span>";
  my $show = "<span title='Controls which subset of the protein list is visible'>Show: $spc</span>";

  my $form = "$style";
  $form .= "$js";

  my $type_select = qq~
  <select id=show_select onchange="show_proteins('protein_list_table');return false;">
    <option selected>All</option>
    <option>Cleaved</option>
    <option>Preserved</option>
    <option>Both</option>
    <option></option>
  </select>
  ~;

  $form .= qq~
  <BR>
  <BR>
  <BR>
  <form name=build_list id=build_list>
  <table>
   <tr>
    <td align=right>Select an Atlas build to investigate:</td><td> $atlas_select </td>
   </tr>
  </table>
  </form>
  <BR>
  <BR>
  <table border=0>
   <tr>
    <td class=bold_text align=left$fbox<input type="text" size=32 id="filterbox" onkeyup="filterTable(this, protein_list_table);set_fctl(event, 'protein_list_table');return false"></input>
    </td> <td>&nbsp;</td>
    <td class=bold_text align=right>$show $type_select</td>
   </tr>
   <tr>
    <td colspan=3><div class=border_div id=border_div> $table </div></td>
   </tr>
   <tr>
    <td align=right class=bold_text>&nbsp;</td> 
    <td align=right class=bold_text>&nbsp;</td> 
    <td align=right><div class=description id=chk_status></div></td>
   </tr>
  </table>
  </form>



  ~;
  return ( "$form" );

}

sub get_atlas_select {

  my $sql = qq~
  SELECT DISTINCT atlas_build_id, atlas_build_name 
  FROM $TBAT_ATLAS_BUILD A 
  JOIN peptideatlas.dbo.initiator_methionine_evidence I
    ON I.build_id = A.atlas_build_id
  ORDER BY atlas_build_name ASC
  ~;

  my $select = "<select name=build_id onchange=submit_form()>\n";
  my $sth = $sbeams->get_statement_handle( $sql );

  while ( my @row = $sth->fetchrow_array() ) {
    my $build_name = $row[1];
    my $selected = '';
    if ( $params->{build_id} == $row[0] ) {
      $selected = 'selected';
      $params->{is_human} = ( $build_name =~ /human/i ) ? 1 : 0;
    }
    $select .= "<option $selected value=$row[0]>$build_name</option>\n";
  }
  $select .= "</select>\n";
  return $select;

}


sub get_btxt {
  my @tags = @_;
  my $max = 0;
  for my $tag ( @tags ) {
    $max = length( $tag ) if length( $tag ) > $max;
  }
  my %btxt;
  for my $tag ( @tags ) {
    my $len = length( $tag );
    my $delta = $max - $len;
    my $pad = 0;
    if ( $delta ) {
      $pad = int($delta/2 + 0.5);
    }
    my $prepad = '&nbsp;' x $pad; 
    my $postpad = '&nbsp;' x ($max - $len - $pad); 
    $btxt{$tag} = $prepad . $tag . $postpad;
  }
  return \%btxt; 

}
sub get_list_selector {

#  <div id=gradient style="background-image: -linear-gradient(to left,#FF5A00,#FFAE00})"> Foofoo </div>

  my $sql =<<"  END";
  SELECT title, first_name, last_name, protein_list_id
  FROM $TBAT_DOMAIN_PROTEIN_LIST DPL
  JOIN $TB_CONTACT C ON DPL.owner_contact_id = C.contact_id
  ORDER BY title
  END

  my $sth = $sbeams->get_statement_handle( $sql );
  my $help = qq~
   <div style="font-family:Helvetica, Arial, sans-serif;font-size:200%;font-weight:bold" id=heading> Initiator Methionine Evidence </div>
   <br>
   <div id=help style="width:800px"> 
   This tool list proteins with evidence for/against init_met cleavage in PeptideAtlas.

  </div>
  <br>
  <br>
  ~;


  return $help;
}

sub process_params {
  my $params = {};
  $sbeams->parse_input_parameters( q => $q, parameters_ref => $params );
  $sbeams->processStandardParameters( parameters_ref => $params );
  $params->{protein_list_id} ||= 1;
  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;
}

sub get_draw_chart_function {
	my $sample_arrayref = shift || return '';

	my @samples;
	for my $s ( @{$sample_arrayref} ) {
		push @samples, [ $s->[1], $s->[4], $s->[7] ];
	}
	my $GV = SBEAMS::Connection::GoogleVisualization->new();
  my ( $chart ) = $GV->setDrawBarChart(  samples => \@samples,
                                    	data_types => [ 'string', 'number', 'number' ],
                                      	headings => [ 'Sample', 'Distinct peptides (n_obs > 1)', 'Cumulative peptides (n_obs > 1)' ],
                                      show_table => 0,
                                 truncate_labels => 24
 	);
	my $header = $GV->getHeaderInfo();
  return ( $chart, $header );
}

__DATA__