#!/usr/local/bin/perl -w

#!/usr/local/bin/perl

###############################################################################
# Program     : ShowProteinTransitions
#
# Description : page retrieve peptides and MS/MS fragment ions from PABST
#               and PATR tables 
###############################################################################

$|++;

## Setup objects and globals 
use strict;
use Getopt::Long;
use FindBin;

use lib "$FindBin::Bin/../../lib/perl";
use vars qw ( $q $current_contact_id $current_username
$PROG_NAME $USAGE %OPTIONS $QUIET $VERBOSE $DEBUG $DATABASE
$TABLE_NAME $PROGRAM_FILE_NAME $CATEGORY $DB_TABLE_NAME
@MENU_OPTIONS $SBEAMS_PART);

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

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

# Set up Atlas objects
my $sbeams = new SBEAMS::Connection;
my $atlas = new SBEAMS::PeptideAtlas;
$atlas->setSBEAMS($sbeams);
$sbeams->setSBEAMS_SUBDIR( 'PeptideAtlas' );
my $best_peptide = new SBEAMS::PeptideAtlas::BestPeptideSelector;
$best_peptide->setAtlas( $atlas );
$best_peptide->setSBEAMS( $sbeams );
my $pabst_build_id;

my $is_html = 0;
$SBEAMS_PART = 'PeptideAtlas';

my $preferred = getPreferredPeptides();

main();
exit(0);

# Main Program
sub main 
{
  # Authenticate and exit if a username is not returned
  $current_username = $sbeams->Authenticate( allow_anonymous_access => 0 );
  exit unless $current_username;


  $is_html = ( $sbeams->output_mode() eq 'html' ) ? 1 : 0;

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

  $parameters{uploaded_file_not_saved} = 1;

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

  # $sbeams->printCGIParams($q);

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

  # This will look for mod-specific params and do the right thing
  $atlas->processModuleParameters(parameters_ref=>\%parameters);

  $parameters{pabst_build_id} = $pabst_build_id;

  # Decide what action to take based on information so far

  $atlas->display_page_header();
#  if ( $sbeams->isProjectAccessible( project_id => 1066 ) ) {
    display_peptides( \%parameters );
#  } else {
#    print "<H3>You are not permitted to view this page with your current credentials</H3>";
#  }

  $atlas->display_page_footer();

} # end main




sub display_peptides {

  my $params = shift;
  my $paranoid = 0;
  print "In display_peptides at " . time() . "<BR>\n" if $paranoid;

##  #  peptides_only
##  if ( $parameters{peptides_only} ) {
##    splice( @headings, 5, 8 );
##  }

## my $headings = $atlas->get_column_defs( labels => \@headings, plain_hash => 1 );
##
##  my $headings_ref = ( $sbeams->output_mode() =~ /html/i ) ? 
##           $best_peptide->make_sort_headings( headings => $headings, default => 'adj_SS' ) :
##           \@headings;
##           
##  my @peptides = ( $headings_ref );
##
##  my @headings = ( 'Protein', 'Pre AA', 'Sequence', 'Fol AA', 'Adj SS', 'Source', 'q1_mz', 'q1_chg', 'q3_mz', 'q3_chg', 'Label', 'Rank', 'RI', 'SSRT', 'n_obs' );
##

  my @headers = ( 'Protein', 'Atlas Builds', 'Pre AA', 'Sequence', 'Fol AA', 'Adj SS', 'SSRT', 'Source', 'q1_mz', 'q1_chg', 'q3_mz', 'q3_chg', 'Label', 'RI', qw( QTOF QTRAP IonTrap CE_range QQQ ) );
  my $headings = $atlas->get_column_defs( labels => \@headers );

  my $help_text = $atlas->make_table_help( description => 'Q1/Q3 transition pairs for SRM experiments',
                                               entries => $headings,
                                          );

  my $fields = join( ", ", @headers );

  print "Getting protlist at " . time() . "<BR>\n" if $paranoid;
  my $protlist = getProtList( $params );
  my @protlist = sort( keys( %{$protlist} ) );

  if ( !scalar( @protlist ) ) {
    print "<H4>No proteins found for user $current_username</H4>";
    exit;
  }

#  my %prot2build;
#  for my $prot ( @protlist ) {
#  use Data::Dumper;
#  die Dumper( $protlist->{$prot}->[0] );

#    die $protlist->{$prot}->[0];
#    $prot2build{$prot} ||= {};
#    $prot2build{$prot}->{$protlist->{$prot}->[0]} = $protlist->{$prot}->[1];
#  }

  my $prots = "'" . join( "','", @protlist ) . "'";

  print "protMappings at " . time() . "<BR>\n" if $paranoid;
  my $protMappings = getProtMappings();

  print "get Consensus at " . time() . "<BR>\n" if $paranoid;
	my $libs = getConsensus( protlist => \@protlist );

  print "Plate Mappings  at " . time() . "<BR>\n" if $paranoid;
	my $pep_info = getPlateMappings();

  my $peplist = getPeptideList( $params );

#  my @rows;
  my @rows = ( \@headers );

  my $min_mz = ( $params->{min_mz} ) ? $params->{min_mz} : 0;
  my $max_mz = ( $params->{max_mz} ) ? $params->{max_mz} : 5000;

#  my $table = new SBEAMS::Connection::DataTable();
#  $table ->addRow( \@headers );
#  $table->setRowAttr(  COLS => [1..scalar(@headers)], ROWS => [1], BGCOLOR => '#bbbbbb', ALIGN=>'CENTER' );
#  $table->setHeaderAttr( BOLD => 1 );

  print "Instr2code at " . time() . "<BR>\n" if $paranoid;
  my $instr2code = $best_peptide->getStaticInstrumentMap();

  my $sql = qq~
SELECT DISTINCT biosequence_accession, preceding_residue, peptide_sequence, following_residue,
synthesis_adjusted_score, ssrcalc_relative_hydrophobicity, transition_source,
precursor_ion_mass, precursor_ion_charge, fragment_ion_mass, fragment_ion_charge,
fragment_ion_label, ion_rank, relative_intensity
FROM $TBAT_BIOSEQUENCE B 
JOIN $TBAT_PABST_PEPTIDE_MAPPING PPM ON B.biosequence_id = PPM.biosequence_id
JOIN $TBAT_PABST_PEPTIDE PP ON PP.pabst_peptide_id = PPM.pabst_peptide_id
JOIN $TBAT_PABST_TRANSITION PT ON PT.pabst_peptide_id = PP.pabst_peptide_id
 WHERE B.biosequence_accession  IN ( $prots )
 AND pabst_build_id = 59
 AND precursor_ion_mass BETWEEN $min_mz AND $max_mz
 AND fragment_ion_mass BETWEEN $min_mz AND $max_mz
ORDER BY biosequence_accession DESC, synthesis_adjusted_score DESC, peptide_sequence,
ion_rank ASC, relative_intensity DESC
  ~;
  $paranoid++;
  print "<H4>Generating protein list for $current_username</H4><BR>\n" if $paranoid;
  print "SQL statement at " . time() . "<BR>\n" if $paranoid;
  my $sth = $sbeams->get_statement_handle( $sql );
  
  my %src_name;
  for my $src ( keys( %{$instr2code} ) ) {
    my $code = $instr2code->{$src};
    if ( $src =~ /PATR/ ) {
      $src_name{$code} = $src . '-validated';
    } elsif ( $src =~ /Predicted/ ) {
      $src_name{$code} = $src;
    } else { 
      $src_name{$code} = $src . '-observed';
    }
  }

# 0 biosequence_accession
# 1 preceding_aa
# 2 peptide_sequence
# 3 following_aa
# 4 synthesis_adjusted_score
# 5 ssrcalc_relative_hydrophobicity
# 6 transition_source
# 7 precursor_ion_mass
# 8 precursor_ion_charge
# 9 fragment_ion_mass
# 10 fragment_ion_charge
# 11 fragment_ion_label
# 12 ion_rank
# 13 relative_intensity

  my %protpep;  # acc plus sequence
  my %prot;  # accession
	my %survey;
  my $sp = '&nbsp;&nbsp;';
  my $num_peptides = $params->{num_peptides} || 6;

  while ( my @row = $sth->fetchrow_array() ) {

#    next if $row[6] eq 'P';

    # Prot + pep is key, 5 trans per pep, 6 peps per prot
    next if $protpep{$row[0] . $row[2]}++ > $num_peptides;
    $prot{$row[0]}++ if $protpep{$row[0] . $row[2]} == 1;
    next if $prot{$row[0]} > $num_peptides;
    
    # Calc plot range
		my $xmax = int( ($row[7] * $row[8])/100 ) * 100;
		$xmax = 3000 if $xmax > 3000;
		my $xmin = 100;

    next if $prot{$row[0] . $row[2]}++ > 5;

    my $atitle = "Look up protein in Peptide Atlas";
    my $utitle = "Look up protein in Uniprot";

    for my $idx ( 4,5 ) {
      $row[$idx] = sprintf( "%0.1f", $row[$idx] );
    }
    $row[6] = $src_name{$row[6]};
    for my $idx ( 7, 9  ) {
			if ( $row[6] =~ /QTOF/i ) {
        $row[$idx] = sprintf( "%0.3f", $row[$idx] );
			} else {
        $row[$idx] =  sprintf( "%0.1f", $row[$idx] ) . '&nbsp;' x 4;
			}
    }
    $row[12] = int( $row[13] );

		$survey{$row[6]}++;


    my $spectrum_key = $row[2] . $row[8];

    if ( $libs->{qtof}->{$spectrum_key} ) {
      my $title = "View +$row[8] spectrum for $row[2] in QTOF library";
      $row[13] = "<A HREF='ShowConsensusSpectrum?consensus_library_spectrum_id=$libs->{qtof}->{$spectrum_key};xmax=$xmax;xmin=$xmin' TARGET='_qtof_spectrum'><IMG BORDER=0 SRC='$HTML_BASE_DIR/images/spectrum.gif' TITLE='$title'></A>";
    } else {
      $row[13] = '';
    }
    if ( $libs->{qtrap}->{$spectrum_key} ) {
      my $title = "View +$row[8] spectrum for $row[2] in QTrap5500 library";
      $row[14] = "<A HREF='ShowConsensusSpectrum?consensus_library_spectrum_id=$libs->{qtrap}->{$spectrum_key};xmax=$xmax;xmin=$xmin' TARGET='_qtrap_spectrum'><IMG BORDER=0 SRC='$HTML_BASE_DIR/images/spectrum.gif' TITLE='$title'></A>";
    } else {
      $row[14] = '';
    }
    if ( $libs->{it}->{$spectrum_key} ) {
      my $title = "View +$row[8] spectrum for $row[2] in NIST IonTrap library";
      $row[15] = "<A HREF='ShowConsensusSpectrum?consensus_library_spectrum_id=$libs->{it}->{$spectrum_key};xmax=$xmax;xmin=$xmin' TARGET='_it_spectrum'><IMG BORDER=0 SRC='$HTML_BASE_DIR/images/spectrum.gif' TITLE='$title'></A>";
    } else {
      $row[15] = '';
    }

    my $title = "View predicted +$row[8] spectrum for $row[2] ";
    $row[16] = "<A HREF='ShowConsensusSpectrum?assumed_charge=$row[8];peptide=$row[2];xmax=$xmax;xmin=$xmin' TARGET='_pred_spectrum'><IMG BORDER=0 SRC='$HTML_BASE_DIR/images/spectrum.gif' TITLE='$title'></A>";

    if ( $libs->{CE}->{$spectrum_key} ) {
      my $title = "View +$row[8] spectra for $row[2] on QTOF at various CE values";
      my $param_str;
      for my $opt ( 'medium','high','low','mhigh', 'mlow', 'avg' ) {
        $libs->{$opt}->{$spectrum_key} ||= '';
        $param_str .= ";$opt=$libs->{$opt}->{$spectrum_key}";
      }

      my $alt_title = $title;
			$alt_title =~ s/spectra/normalized spectra/;
      $row[16] = "<A HREF='ShowCESpectralPlot?xmax=$xmax;xmin=$xmin$param_str' TARGET='_CE_spectrum'><IMG BORDER=0 SRC='$HTML_BASE_DIR/images/spectrum.gif' TITLE='$title'></A>";
#, <A HREF='ShowSpectrumPanelNorm?xmax=$xmax;xmin=$xmin$param_str' TARGET='_CE_spectrum'><IMG BORDER=0 SRC='$HTML_BASE_DIR/images/spectrum.gif' TITLE='$alt_title'></A>";
    } else {
      $row[16] = '';
    }
    if ( $libs->{qqq}->{$spectrum_key} ) {
      my $title = "View +$row[8] spectrum for $row[2] in QQQ library";
      $row[17] = "<A HREF='ShowConsensusSpectrum?consensus_library_spectrum_id=$libs->{qqq}->{$spectrum_key};xmax=$xmax;xmin=$xmin' TARGET='_it_spectrum'><IMG BORDER=0 SRC='$HTML_BASE_DIR/images/spectrum.gif' TITLE='$title'></A>";
    } else {
      $row[17] = '';
    }

    my $cmt = $protMappings->{$row[0]}->{comment} || '';

    my $atitle = "View protein $row[0] ($cmt) in the Peptide Atlas";
    my $utitle = "Look up protein $row[0] ($cmt) in Uniprot";

    my $name = $protMappings->{$row[0]}->{name} || '';
    my $sp = "<A TITLE='$utitle' TARGET='_uniprot' HREF='http://www.uniprot.org/uniprot/$row[0]'>$row[0] </A>";
    
    my $build_link = '';
    my $sep = '';
    for my $build ( keys( %{$protlist->{$row[0]}} ) ) {
      $build_link .= "$sep <A TARGET='${build}_protein' HREF='GetProtein?atlas_build_id=$build&protein_name=$row[0]&action=GO' TITLE='$atitle'>$protlist->{$row[0]}->{$build}</A>";
      $sep = ',&nbsp;';
    }

    my $stripped = $row[1];
    $stripped =~ s/\[\d+\]//g;
    if ( $pep_info->{$stripped} ) {
#      $row[14] = $pep_info->{$stripped};
    } else {
#      $row[14] = '';
    }

    next if $row[6] !~ /^Q/i;

    unshift @row, "$sp ( $name )";
    $row[1] = $build_link;


    if ( $params->{peptides} ) {
      if ( $peplist->{$row[2]} ) {
#				my $pepseq = $row[2];
#				$pepseq =~ s/\W//g;
#				$row[2] =~ s/\W//g;
#				$row[2] = "GetP <A TARGET='_peptide' HREF='GetPeptide?atlas_build_id=$build=$row[2]&action=GO' TITLE='$atitle'>$protlist->{$row[0]}->{$build}</A>";
        push @rows, [@row, $build_link];
      }
    } else {
       push @rows, \@row;
    }
#    $table->addRow( \@row );
  }
  
  my %seen_proteins;
  for my $row ( @rows ) {
    my $prot = $row->[0];
    my $pep = $row->[2];
    $seen_proteins{$prot} ||= {};
    next if scalar( keys ( %{$seen_proteins{$prot}} ) ) > 5;
    $seen_proteins{$prot}->{$pep} ||= [];
    push @{$seen_proteins{$prot}->{$pep}}, $row;
  }

  my @final_rows = ( \@headers );
  for my $prot ( sort( keys ( %seen_proteins ) ) ) {
    for my $pep ( sort( keys ( %{$seen_proteins{$prot}} ) ) ) {
      push @final_rows, @{$seen_proteins{$prot}->{$pep}};
    }
  }

  my $rt_file = {};
#  if ( $params->{read_rt} && $params->{read_rt} eq 'qtrap_5500' ) {
	if ( 1 ) {
  print "read qtrap rt file at " . time() . "<BR>\n" if $paranoid;
    $rt_file = read_qtrap5500_rt_file();
    my $cnt = scalar( keys( %{$rt_file} ) );
    print "read $cnt peptide RT values at " . time() . "<BR>\n" if $paranoid;

    # Just for grins...
#    open( RTSSR, ">/tmp/rt2ssr.tsv" );
#    for my $row ( @rows ) {
#      my $seq = $row->[2];
#      $seq =~ s/\[\d+\]//gm;
#      my $rt = $row->[5];
#      if ( $rt_file->{$seq} ) {
#        print RTSSR join( "\t", $seq, $rt, $rt_file->{$seq} ) . "\n";
#      } else {
#        print RTSSR join( "\t", $seq, $rt, 'Nada' ) . "\n";
#      }
#
#    }
#    close RTSSR;
#    print "printed RT2SSR values at " . time() . "<BR>\n" if $paranoid;

#    my $dna = $rt_file->{DNGAIEFTFDLEK};
#    die "Cnt is $cnt and DNA is $dna!\n";
  }

  my %col_idx = ( 'Protein' => 0,
                   'Pre AA' => 2,
                 'Sequence' => 3,
                   'Fol AA' => 4,
                   'Adj SS' => 5,
                     'SSRT' => 6,
                   'Source' => 7,
                    'q1_mz' => 8,
                   'q1_chg' => 9,
                    'q3_mz' => 10,
                   'q3_chg' => 11,
                    'Label' => 12,
                       'RI' => 13 );

  print "make target list at " . time() . "<BR>\n" if $paranoid;
  my $qtrap_file = $atlas->make_qtrap5500_target_list( data => \@rows, remove_mods => 1, rt_file => $rt_file, col_idx => \%col_idx );
  print "more stuff at " . time() . "<BR>\n" if $paranoid;
  my @name = split "/", $qtrap_file;
  my $filename = $name[$#name];

  my $base = $q->url( -base => 1 );
  my $qtrap_url = "<A HREF='$base/$HTML_BASE_DIR/tmp/$filename'>QTrap</A>";

  my $qtrap_download = "<A HREF='$base/$CGI_BASE_DIR/downloadFile.cgi?name=QTrap5500.csv;tmp_file=$filename;format=csv'>QTrap5500</A>";

	for my $k ( sort (keys( %survey ) ) ) {
#		print "$k\t$survey{$k}<BR>\n";
	}

#          <TR ><TD NOWRAP bgcolor="cccccc" >QTOF</TD><TD NOWRAP >Not Defined</TD></TR>
#        <TR ><TD NOWRAP bgcolor="cccccc" >QTRAP</TD><TD NOWRAP >Not Defined</TD></TR>
#        <TR ><TD NOWRAP bgcolor="cccccc" >IonTrap</TD><TD NOWRAP >Not Defined</TD></TR>
#        <TR ><TD NOWRAP bgcolor="cccccc" >Predicted</TD><TD NOWRAP >Not Defined</TD></TR>


  my $align =  [qw(center center center center right right left right right right right left right center center center center )];

  my ( $html, $rs_name ) = $atlas->encodeSectionTable( header => 1, 
                                                        width => '800',
                                                       align  => $align,
                                                         rows => \@rows,
                                                 rows_to_show => 200,
                                                     max_rows => 5000,
                                                    help_text => $help_text,
                                                  chg_bkg_idx => 3, 
                                                 set_download => 'Download transitions', 
                                               download_links => [ $qtrap_download ], 
                                                  file_prefix => 'SRM_Atlas_', 
                                                     bg_color => '#EAEAEA',
                                                     sortable => 1,
                                                     table_id => 'srm',
                                                  close_table => 1,
                                                     );
  


#  $table->setColAttr(  COLS => [3..9,11], ROWS => [2..$table->getRowNum()], ALIGN=>'right' );
#	      $tab->setColAttr( ROWS => [2..$tot], COLS => [$i + 1], ALIGN => $args{align}->[$i] );

#  $table->alternateColors( PERIOD => 30, FIRSTROW => 2 );
#  print "$table\n";
  print "Final stuff at " . time() . "<BR>\n" if $paranoid;
  print "$html\n";

}

sub read_qtrap5500_rt_file {
	my $file = "/regis/sbeams4/nobackup/edeutsch/HumanMRMAtlas/QTrap5500/Runs_By_Order/speclib/2011-01-30/speclist_summary.tsv";
  open( RT, $file ) || die "can't open $file";
  my %rt;
  while ( my $line = <RT> ) {
    next if $line =~ /Sequence/;
    my @line = split( /\t/, $line );
    my $seq = $line[0];
    my @reps = split( /\//, $line[1] );
    my $reps = $reps[0];
    my $rt = $line[5];
#Sequence	NReps	OrigMaxInten	PrecInten	TotalIonCurr	RTAvg
#AAADFATHGK	4/5	1.7e+07	0	3.9e+08	611.4	
#AAADFATHGK	2/2	2.1e+07	0	8.2e+08	585.3	
#AAALGGPEDEPGAAEAHFLPR	1/3	7e+03	0	5.4e+05	2012.0	
    $rt{$seq} ||= {};
    $rt{$seq}->{reps} += $reps;
    $rt{$seq}->{rtime} += $rt * $reps;
  }
  my %rt_final;
  for my $seq ( keys %rt ) {
    $rt_final{$seq} = sprintf( "%0.1f", $rt{$seq}->{rtime}/$rt{$seq}->{reps} );
  }
  return \%rt_final;
}


sub getPreferredPeptides {
  my @peps = ( 

'YALSQDVCTYR',
'TVEIPGCPLHVAPYFSYPVALSCK',
'CRPINATLAVEK',
'APPPSLPSPSR',
'LPGCPR',
'DISEMFLQIYK',
'QGGFLGLSNIK',
'DTYHPMSEYPTYHTHGR',
'NYGQLDIFPAR',
'FRPGSVVVQLTLAFR',
'YVPPSSTDR',
'SSVPSSTEK' );

my @all = (
'CNTDYSDCIHEAIK',
'YALSQDVCTYR',
'ECAYCLTINTTICAGYCMTR',
'TVEIPGCPLHVAPYFSYPVALSCK',
'TNYCTKPQK',
'CRPINATLAVEK',
'EGCPVCITVNTTICAGYCPTMTR',
'VLQGVLPALPQVVCNYR',
'APPPSLPSPSR',
'GVNPVVSYAVALSCQCALCR',
'FQDSSSSK',
'LPGCPR',
'DISEMFLQIYK',
'ATTTPASK',
'EGTINVHDVETQFNQYK',
'QGGFLGLSNIK',
'DTYHPMSEYPTYHTHGR',
'NYGQLDIFPAR',
'FRPGSVVVQLTLAFR',
'YVPPSSTDR',
'SSVPSSTEK' );
  my %peps;
  for my $pep ( @peps ) {
    $pep =~ s/C/C\[160\]/g;
    $peps{$pep}++;
  }
  return \%peps;
}

sub getConsensus {

	my %args = @_;
#	if ( $args{protlist} ) {
#		print join( ",", @{$args{protlist}} ) . "<BR>\n";;
#	}

  my %libs = ( it => {}, qtof => {}, qtrap => {}, CE => {},
          low => {}, mlow => {}, medium => {}, mhigh => {}, high=> {} );


  my $it_sql = qq~
  SELECT modified_sequence, consensus_library_spectrum_id, charge
  FROM $TBAT_CONSENSUS_LIBRARY_SPECTRUM 
  WHERE consensus_library_id = 16
  ~;
  my $sth = $sbeams->get_statement_handle( $it_sql );
  while ( my @row = $sth->fetchrow_array() ) {
    $libs{it}->{$row[0]. $row[2]} = $row[1];
  }

  my $qtof_sql = qq~
  SELECT modified_sequence, consensus_library_spectrum_id, charge
  FROM $TBAT_CONSENSUS_LIBRARY_SPECTRUM 
  WHERE consensus_library_id = 279
  ~;
  my $sth = $sbeams->get_statement_handle( $qtof_sql );
  while ( my @row = $sth->fetchrow_array() ) {
    $libs{qtof}->{$row[0]. $row[2]} = $row[1];
  }

  my $qtrap_sql = qq~
  SELECT modified_sequence, consensus_library_spectrum_id, charge
  FROM $TBAT_CONSENSUS_LIBRARY_SPECTRUM 
  WHERE consensus_library_id = 282
  ~;
  my $sth = $sbeams->get_statement_handle( $qtrap_sql );
  while ( my @row = $sth->fetchrow_array() ) {
    $libs{qtrap}->{$row[0]. $row[2]} = $row[1];
  }

  my $qqq_sql = qq~
  SELECT modified_sequence, consensus_library_spectrum_id, charge
  FROM $TBAT_CONSENSUS_LIBRARY_SPECTRUM 
  WHERE consensus_library_id = 293
  ~;
  my $sth = $sbeams->get_statement_handle( $qqq_sql );
  while ( my @row = $sth->fetchrow_array() ) {
    $libs{qqq}->{$row[0]. $row[2]} = $row[1];
  }


#  my %libmap = ( 21 => 'medium', 22 => 'high', 23 => 'low', 24 => 'mhigh', 25 => 'mlow', 26 => 'avg' );
#  my %libmap = ( 29 => 'medium', 30 => 'high', 31 => 'low', 32 => 'mhigh', 33 => 'mlow', 27 => 'avg' );
  my %libmap = ( 277 => 'low',
                 278 => 'mlow', 
                 279 => 'medium',
                 280 => 'mhigh', 
                 281 => 'high' );
	my $libs = join( ',', keys( %libmap ));
  my $ce_sql = qq~
  SELECT modified_sequence, consensus_library_spectrum_id, charge, consensus_library_id
  FROM $TBAT_CONSENSUS_LIBRARY_SPECTRUM 
  WHERE consensus_library_id IN ( $libs ); 
  ~;
  my $sth = $sbeams->get_statement_handle( $ce_sql );
  while ( my @row = $sth->fetchrow_array() ) {
    $libs{$libmap{$row[3]}}->{$row[0]. $row[2]} = $row[1];
    $libs{CE}->{$row[0]. $row[2]}++;
  }

  return \%libs;

}

sub getProtList {
  my $params = shift;
  my %proteins;
  my $contact_id = $sbeams->getCurrent_contact_id();
  my $sql = qq~ 
    SELECT DISTINCT protein_name, atlas_build_id, build_name 
    FROM $TBAT_PROTEIN_LIST PL
    JOIN $TBAT_PROTEIN_LIST_PROTEIN PLP
      ON PL.protein_list_id = PLP.protein_list_id
    JOIN $TBAT_PROTEIN_LIST_BUILD PLB
      ON PL.protein_list_id = PLB.protein_list_id
    WHERE PL.contributor_contact_id = $contact_id
  ~;

  my $sth = $sbeams->get_statement_handle( $sql );
  while ( my @line = $sth->fetchrow_array() ) {
    $proteins{$line[0]} ||= {};
    $proteins{$line[0]}->{$line[1]} = $line[2];
  }
  return \%proteins;
}

sub getPeptideList {
  my $params = shift;
  return undef unless $params->{peptides};
  my %peps;
  if ( $params->{peptides} ) {
    my @peptides = split( /\,/, $params->{peptides} );
    print "Found " . scalar( @peptides ) . " peptides <BR>\n";
    for my $pep ( @peptides ) { $peps{$pep}++ }  
  } else {
    use Data::Dumper;
    die Dumper $params;
    while ( my $line = <DATA> ) {
      chomp $line;
      next if $line =~ /^\s*$/;
      $line =~ s/\s//g;
      $line =~ s/C/C[160]/g;
      $peps{$line}++;
    }
  }
  return \%peps;
}


sub getProtMappings {
  my %prots;
  open SPFIL, "sprot_acc.txt" || die "No sprot file!";
  while ( my $line = <SPFIL> ) {
    chomp $line;
    $line =~ s/\s+/ /g;
    my @line = split( " ", $line );
    $line[0] =~ s/>//g;
    $prots{$line[0]} ||= { name => $line[1], comment => '' };
    my $sep = '';
    for ( my $i = 2; $i <= $#line; $i++ ) {
      last if $line[$i] =~ /OS=/;
      $prots{$line[0]}->{comment} = $prots{$line[0]}->{comment} . $sep . $line[$i];
      $sep = ' ';
    }
  }
  return \%prots;
}



sub getPlateMappings {

  my $driver = 'DBI:mysql:mrmatlas_lims:mslims';
  my $user = 'mrm_ro';
  my $pass = 'Tsr3#@gfA356!&5';
  my %error = ( PrintError => 1, RaiseError => 1);
  my $dbh = DBI->connect($driver,$user,$pass,\%error);
  my $sql = qq~
  SELECT sequence, plate_barcode_id, row, col, peptides.status, orders.name
  FROM plates JOIN orders ON plates.order_id = orders.id
  JOIN plate_peptides ON plate_peptides.plate_id = plates.id
  JOIN peptides  ON peptides.id = plate_peptides.peptide_id
  WHERE plate_type = 'MASTER'
  ORDER BY orders.id ASC, isb_index ASC
  ~;
  my $sth = $dbh->prepare( $sql );
  $sth->execute();

  my %pep;
  while ( my @row = $sth->fetchrow_array() ) {
    if ( $pep{$row[0]} ) {
      next if $row[5] =~ /^ZH/i;
    }
    $pep{$row[0]} = "$row[5] $row[1]_$row[2]$row[3]";
  }
  return \%pep;

}

__DATA__
P09544
P56703
P56704
P56705
O00755
P56706
Sequence	NReps	OrigMaxInten	PrecInten	TotalIonCurr	RTAvg
AAADFATHGK	4/5	1.7e+07	0	3.9e+08	611.4	
AAADFATHGK	2/2	2.1e+07	0	8.2e+08	585.3	
AAALGGPEDEPGAAEAHFLPR	1/3	7e+03	0	5.4e+05	2012.0	
AAALVDEGLDPEEHTADGEPSAK	4/7	9.4e+04	0	1.2e+07	1608.1	
AAAPTGLQPPGC[160]K	12/12	1.7e+08	0	4.5e+09	1057.7	
AAAPTGLQPPGC[160]K	2/3	8.9e+06	0	1.6e+08	1013.1	
AADEESLEGEGAGGADAAEESSGTK	2/11	1.6e+06	0	1.5e+08	1031.5