#!/usr/local/bin/perl

###############################################################################
# $Id: $
#
# SBEAMS is Copyright (C) 2000-2007 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 qw (../../lib/perl);

use GD::Graph::bars;
use GD::Graph::xypoints;

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

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();


{ # 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;

    exit if !$params->{atlas_build_id};

    $params->{type} ||= 'bar';

    my $plot;
    if ( $params->{type} =~ /pie/i ) {
      $plot = make_pie();
    } else {
      $plot = make_bar();
    }
    print $sbeams->get_http_header( type => 'png' );
    print STDERR $sbeams->get_http_header( type => 'png' );

    print $plot;
    exit;
}

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

sub make_pie {
}

sub make_bar {
  print STDERR "err is " . $!;
  my @sample_info = $sbeams->selectSeveralColumns ( <<"  END" );
  SELECT ASB.atlas_search_batch_id, n_progressive_peptides, rownum, cumulative_n_peptides
  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 ( ABSB.atlas_search_batch_id = ASB.atlas_search_batch_id )
  WHERE ABSB.atlas_build_id = $params->{atlas_build_id}
  ORDER BY rownum, cumulative_n_peptides, ASB.atlas_search_batch_id ASC
  END
  my ( @x, @y );
  my $total = 0;
  for my $batch ( @sample_info ) {
    push @x, $batch->[0];
    $batch->[1] ||= 0;
    $total += $batch->[1];
    push @y, $total; 
  }
  my $skip = ( $#x < 20 ) ? 0 :
             ( $#x < 40 ) ? 1 :
             ( $#x < 60 ) ? 2 : 
             ( $#x < 80 ) ? 3 : 
             ( $#x < 100 ) ? 4 : 5;
             
  my $graph = GD::Graph::bars->new(800, 600);
  $graph->set(   x_label           => "Sample",
                 y_label           => 'Cumulative Distinct Peptides',
                 title             => "Progressive Sample Contribution",
                 x_tick_length     => -4,
                 axis_space        => 6,
                 x_label_position  => 0.5,
                 x_label_skip      => $skip,
                 y_min_value       => 0,
                 x_halfstep_shift  => 0,
                  );  

  print STDERR "X is $#x and Y is $#y\n";
  binmode STDOUT;
  my $png = $graph->plot( [ \@x, \@y ] )->png();
  print STDERR "plot is " . length( $png );
  return $png;
}


__DATA__

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

    # We are not forcing the user into the new build - is that correct?
    my $build_id = $params->{atlas_build_id} || $atlas->getCurrentAtlasBuildID(parameters_ref => $params);
    if ( !grep /^$build_id$/, $atlas->getAccessibleBuilds() ) {
      die( "Access to specified build is not allowed" );
    }

    my $help = get_help_section();

    
    my $page = $sbeams->getGifSpacer( 700 ) . "<BR>\n";
    $page .=<<"    END";
    <P>
    This shows some information about the currently selected build.  Peptide
    numbers are for peptides seen more than once, except as denoted by an
    asterisk (*).  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>
    $help->{build}
    END

    

    # Add general section 
#  print STDERR 'build overV ' . time() . "\n";
    $page .= get_build_overview ( $build_id );
    $page .= "<BR>$help->{batch}\n";
#  print STDERR 'sample info ' . time() . "\n";
    $page .= get_sample_info( $build_id );
#  print STDERR 'showtime ' . time() . "\n";
    # Add peptide stats section
    # Add graphic
   

    # Display page
    $atlas->display_page_header(project_id => $project_id, onload => 'sortables_init()', sortable => 1 );
    print $page;
		$atlas->display_page_footer();

} # end main

sub get_help_section {
  my $build_table = "<TABLE>\n";
  $build_table .= $atlas->encodeSectionItem( key => 'Build Name', value => 'The simple name for this build, usually contains organism, prophet cutoff, and other information. ' ) . "\n";
  $build_table .= $atlas->encodeSectionItem( key => 'Build Description', value => 'More detailed information about build. ' ) . "\n";
  $build_table .= $atlas->encodeSectionItem( 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. ' ) . "\n";
  $build_table .= $atlas->encodeSectionItem( key => 'Build Date', value => 'Date upon which build was finished. ' ) . "\n";
  $build_table .= $atlas->encodeSectionItem( 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.' ) . "\n";
  $build_table .= $atlas->encodeSectionItem( 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.  The first number shows the distinct sequences that were seen more than once, the asterisked number in parenthesis shows a count of all distinct observed peptide sequences  ' ) . "\n";
  $build_table .= $atlas->encodeSectionItem( key => 'Total Observations ', value => 'The total number of spectra that yeilded identifications above the build threshold, generally 0.9.  Observations of the same base peptide sequences multiple times or in various charge states/modifications, whould each contribute to the total' ) . "\n";
  $build_table .= "</TABLE>\n";

  my $batch_table = "<TABLE>\n";
  $batch_table .= $atlas->encodeSectionItem( key => 'Sample Name', value => 'Simple name for this sample/experiment. ' ) . "\n";
  $batch_table .= $atlas->encodeSectionItem( key => '# Spectra', value => 'The total number of spectra searched for the sample. ' ) . "\n";
  $batch_table .= $atlas->encodeSectionItem( key => '# Distinct', value => 'The number of distinct peptide sequences, seen more than once (multiobs), in this build that are seen in this sample. ' ) . "\n";
  $batch_table .= $atlas->encodeSectionItem( key => '# Contrib', value => 'The number of distinct, multiobs peptides that are only seen in this sample (unique contribution).  This discriminates against smaller samples, and is less useful in atlas&quot; with a large number of samples. ' ) . "\n";
  $batch_table .= $atlas->encodeSectionItem( key => '# Progressive', value => 'Order-dependant 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. ' ) . "\n";
  $batch_table .= $atlas->encodeSectionItem( key => 'Model Sens', value => 'The sensitivity of the Protein 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. ' ) . "\n";
  $batch_table .= $atlas->encodeSectionItem( key => 'Model Err', value => 'The error of the Protein Prophet model at a probablility of 0.9, the percent of false positives that would be included at that threshold was used as a cutoff. ' ) . "\n";
  $batch_table .= "</TABLE>\n";

  my $css =<<"  END";
  <style type="text/css">
  .section_heading {  font-family: Helvetica, Arial, sans-serif; font-size: 10pt; font-weight: Bold; }
  .description { font-family: Helvetica, Arial, sans-serif; color:#333333; font-size: 9pt; font-style: italic;  }
  .help_key {  font-family: Helvetica, Arial, sans-serif; font-size: 9pt; font-weight: Bold; }
  .help_val {  font-family: Helvetica, Arial, sans-serif; font-size: 9pt; }
  </style>
  END

  my $build_content =<<"  END";
  <span class=section_heading>Build Overview</span> 
  <span class=description>These values pertain to the atlas build as a whole</span>
  $build_table
  END

  my $batch_content =<<"  END";
  <span class=section_heading>Sample Overview</span> 
  <span class=description>These values pertain to individual samples within the atlas</span>
  $batch_table
  END

  my $build_tg = $sbeams->make_toggle_section( content => $build_content,
                                           sticky      => 0,
                                           visible     => 0,
                                           imglink     => 0,
                                           textlink    => 1,
                                           name        => 'build_help',
                                           showtext    => 'show help',
                                           hidetext    => 'hide help',
                                          );
  my $batch_tg = $sbeams->make_toggle_section( content => $batch_content,
                                           sticky      => 0,
                                           visible     => 0,
                                           imglink     => 0,
                                           textlink    => 1,
                                           name        => 'batch_help',
                                           showtext    => 'show help',
                                           hidetext    => 'hide help',
                                          );

  my %help = ( build => $css . $build_tg, batch => $batch_tg );
  return \%help;
}

# 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
  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 $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 $multi_pep_count = $sbeams->selectrow_hashref( <<"  MPEP" );
  SELECT COUNT(*) cnt, SUM(n_observations) obs
  FROM $TBAT_PEPTIDE_INSTANCE  
  WHERE atlas_build_id = $build_id 
  AND n_observations > 1 
  MPEP
  $log->debug( $sbeams->evalSQL( <<"  END" ) );
  SELECT COUNT(*) cnt, SUM(n_observations) obs
  FROM $TBAT_PEPTIDE_INSTANCE  
  WHERE atlas_build_id = $build_id 
  AND n_observations > 1 
  END

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

  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 => 'Build Overview',
      span => 4,
      link => $link
  );

  my $spc = $sbeams->getGifSpacer(500);
  $build_info->{build_date} =~ s/^([0-9-]+).*$/$1/;
#  $smpl_count->{cnt} = sprintf( "% 10i", $smpl_count->{cnt} );
#  $smpl_count->{cnt} =~ s/ /&nbsp;/g;
#  $multi_pep_count->{cnt} = sprintf( "% 10i", $multi_pep_count->{cnt} );
#  $multi_pep_count->{cnt} =~ s/ /&nbsp;/g;
#  $multi_pep_count->{obs} = sprintf( "% 10i", $multi_pep_count->{obs} );
# $multi_pep_count->{obs} =~ s/ /&nbsp;/g;
  
  
#  my $deltacnt = $multi_pep_count->{cnt} - $pep_count->{cnt};
#  my $deltaobs = $multi_pep_count->{obs} - $pep_count->{obs};
#  $table .= $atlas->encodeSectionItem( key   => 'Deltas ', tr_info => $tr,
#                                          value => "$deltacnt ( $deltaobs )" ) . "\n";


  $table .= $atlas->encodeSectionItem( key   => 'Build Name', tr_info => $tr,
                            value => $build_info->{atlas_build_name} . $spc, 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";
  $table .= $atlas->encodeSectionItem( key   => '# Samples', tr_info => $tr,
                            value => $smpl_count->{cnt}, align => 'right' ) . "\n";
  $table .= $atlas->encodeSectionItem( key   => 'Distinct Peptides', tr_info => $tr,
                                          value => "$multi_pep_count->{cnt} ( $pep_count->{cnt}* )" ) . "\n";
  $table .= $atlas->encodeSectionItem( key   => 'Total Observations', tr_info => $tr,
                                          value => "$multi_pep_count->{obs} ( $pep_count->{obs}* )" ) . "\n";
#  $table .= $atlas->encodeSectionDblItem( key   => ['Build Date', '# Samples'], tr_info => $tr,
#                            value => [$build_info->{build_date}, $smpl_count->{cnt}] ) . "\n";
#  $table .= $atlas->encodeSectionDblItem( key   => ['Total Observations', 'Distinct Peptides'], 
#                                          tr_info => $tr,
#                                          value => [$pep_count->{obs}, $pep_count->{cnt}] ) . "\n";
#  $table .= $atlas->encodeSectionDblItem( key   => ['Total Observations n_obs > 1', 'Distinct Peptides n_obs > 1'], 
#                                          tr_info => $tr,
#                                          value => [$multi_pep_count->{obs}, $multi_pep_count->{cnt}] ) . "\n";

  $table .= "</TABLE>\n";
  return $table;

}

# 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';


  my $table = "<TABLE WIDTH=600>\n";

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

#  search_batch_statistics_id
#  atlas_build_search_batch_id
#  n_observations
#  n_searched_spectra
#  n_distinct_peptides
#  n_distinct_multiobs_peptides
#  n_uniq_contributed_peptides
#  n_progressive_peptides
#  model_90_sensitivity
#  model_90_error_rate
# ASB.atlas_search_batch_id, proteomics_search_batch_id

#  my @sample_info;
#  $log->debug( $sbeams->evalSQL ( <<"  END" ) );
#  SELECT sample_tag, sample_description, SBS.n_searched_spectra, n_distinct_peptides,
#         n_uniq_contributed_peptides n_observations, n_searched_spectra,
#         n_distinct_multiobs_peptides, n_uniq_contributed_peptides,
#         n_progressive_peptides, model_90_sensitivity, model_90_error_rate
  my @sample_info = $sbeams->selectSeveralColumns ( <<"  END" );
  SELECT sample_tag, SBS.n_searched_spectra,
         n_distinct_multiobs_peptides, n_uniq_contributed_peptides,
         n_progressive_peptides, model_90_sensitivity, model_90_error_rate
  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_SAMPLE S ON s.sample_id = ABSB.sample_id
  JOIN $TBAT_ATLAS_BUILD_SAMPLE ABS ON ( s.sample_id = ABS.sample_id )
  WHERE ABS.atlas_build_id = $build_id
  AND ABSB.atlas_build_id = $build_id
  END

  # Format loop
 
  my $dag = '<sup>&dagger;</sup>';
  my @headings = ( 'Sample Name',
                   '# Spectra', 
                   '# Distinct', 
                   '# Contrib', 
                   '# Progessive',
                   'Model Sens',
                   'Model Err'
      );

  $table .= $atlas->encodeSectionHeader(
      text => 'Sample Contribution',
      link => $link
  );

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

  $table .= $atlas->encodeSectionTable( rows => [ \@headings, @sample_info ], 
                                        header => 1, 
                                        nowrap => 1, 
                                        align => [ qw(left right right right right right right right) ], 
                                        tr_info => $tr,
                                        bg_color => '#EAEAEA',
                                        sortable => 1 );
  $table .= '</TABLE>';
  return $table;

}


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

sub get_build_name {
  my $build_id = shift;
  return unless $build_id;
  my ( $build_name ) = $sbeams->selectrow_array( <<"  END" );
  SELECT atlas_build_name
  FROM $TBAT_ATLAS_BUILD
  WHERE atlas_build_id = $build_id
  END
  return $build_name;
}

__DATA__

sub run_search {
  my $params = shift;
  my $content;
  for my $arg ( qw( mass_list mass_window) ) {
    unless ( $params->{$arg} ) {
      $content .= "Missing required parameter: $arg <BR>\n";
      return $content;
    }
  }
#  for my $p ( keys( %$params ) ) { $content .= "$p => " . $params->{$p} . "<BR>\n"; }
  my $mass_list = $params->{mass_list};
  $mass_list =~ s/\s+/ /gm;
  my @masses = split( " ", $mass_list );
  my $peptides = $sbeamsMOD->runMassSearch( masses => \@masses, %{$params} );
  my $peptide_table = SBEAMS::Connection::DataTable->new( BORDER => 0 );
  my $type = ( $params->{search} eq 'iden' ) ? 'Identified' : 'Predicted';
  $peptide_table->addRow( ['Search Mass', 'IPI', "$type sequence", 'Peptide Mass',
                           'Mass Delta', '# ox Met', 'Protein Name' ] );
  $peptide_table->setRowAttr( ROWS => [1], BGCOLOR => '#C0D0C0' );
  my $current_group;
  my $grp_row = 2;
  my $bgcolor = '#FFFFFF';
  for my $peptide ( @$peptides ) {
    my ( $grp, 
         $smass, 
         $ipi, 
         $seq, 
         $dbmass, 
         $prot, 
         $delta, 
         $ox_met ) = @$peptide;

    $current_group = $grp unless $current_group;

    $dbmass = sprintf( "%0.3f", $dbmass );
    if ( $dbmass =~ /0.000/ ) { $dbmass = 'na'; }
    $delta =  sprintf( "%0.3f", $delta );
    if ( $delta =~ /0.000/ ) { $delta = 'na'; }

    $prot = $sbeams->truncateStringWithMouseover( string => $prot, len => 50 );
    $ipi = "<A HREF='Glyco_prediction.cgi?search_type=IPI Accession Number;action=Show_hits_form;search_term=$ipi' TARGET=prot_details>$ipi</A>";
    $peptide_table->addRow( [ $smass, $ipi, $seq, $dbmass, $delta, $ox_met, $prot] );
    unless ( $grp == $current_group ) {
      my $current_row = $peptide_table->getRowNum();
#      $log->info( "group row is $grp_row, current row is $current_row, bgcolor is $bgcolor" );
      $peptide_table->setRowAttr( ROWS => [$grp_row..$current_row - 1], BGCOLOR => $bgcolor );
      $grp_row = $current_row;
      $bgcolor = ( $bgcolor eq '#E0E0E0' ) ? '#FFFFFF' : '#E0E0E0';
      $current_group = $grp;
    }
    my $current_row = $peptide_table->getRowNum();
    $peptide_table->setRowAttr( ROWS => [$grp_row..$current_row], BGCOLOR => $bgcolor );

  }
  $content .= $peptide_table->asHTML();
  return $content;
}

sub print_form {
  my $params = shift;
	
	my $content = <<"  END";
  <TABLE>
   <TR CLASS='rev_gray_head'>
    <TD class=rev_gray_head>Run Mass Search</TD>
   </TR>
   <TR>
    <TD>
    Enter desired constraints to run a mass-based search versus the identified or theoretical peptides in the database.  Note that your prophet cutoff will impact the number of results returned
    </TD>
   </TR>
  </TABLE>
  END

  # Table to hold form elements
  my $f_table = SBEAMS::Connection::DataTable->new( BORDER => 1 );

  # Hashes to hold form labels/fields
  my $input_labels = get_input_labels($params);
  my $input_fields = get_input_fields($params);

  # Loop through and add items to the form table
  for my $key ( qw(mass_list mass_window ox_met alk_cys mass_type search charge ) ) {
    $f_table->addRow(["<B>$input_labels->{$key}</B>", $input_fields->{$key}]); 
  }

  my @buttons = $sbeams->getFormButtons( types => [qw(submit reset)] );
  $f_table->addRow( [join(" ", @buttons)] );

  $f_table->setColAttr( COLS => [1], ROWS => [8], COLSPAN => 2 );
#  $f_table->setColAttr( COLS => [1], ROWS => [1..6], ALIGN => 'RIGHT' );
  $f_table->setColAttr( COLS => [1], ROWS => [8], ALIGN => 'CENTER' );
  $f_table->setColAttr( COLS => [2], ROWS => [1..7], ALIGN => 'LEFT' );

  $content .=<<"  END";
  <FORM NAME=mass_search_form> 
  $f_table 
  <INPUT TYPE=hidden NAME=action VALUE=search></INPUT>
  </FORM>
  END
  return $content;
}

sub get_input_labels {
  my $params = shift;

  my %in = ( mass_list   => 'Mass(es) to search, 1 per line:',
             mass_window => 'Mass search range:',
             ox_met      => 'Oxidized Methionine (+ 15.9949):',
             alk_cys     => 'Alkylated Cys (+ 57.0215):',
             mass_type   => 'Type of mass values:',
             search      => 'Search subject:',
             charge      => 'Peptide charge state:',
             );
  
  return \%in;
}

sub get_input_fields {
  my $params = shift;

  my $mass_list = $params->{mass_list} || '';
  $mass_list = "<TEXTAREA ROWS=4 COLS=12 NAME=mass_list>$mass_list</TEXTAREA>";

  my $mass_window = $params->{mass_window} || '';
  $mass_window = "<INPUT TYPE=text NAME=mass_window SIZE=10 VALUE=$mass_window></INPUT>";

  my $mw_amu = ( $params->{mw_units} && $params->{mw_units} eq 'amu' ) ? 'CHECKED' : '';
  my $mw_ppm = 'CHECKED' unless $mw_amu;
  my $mw_radio =<<"  END";
  PPM <INPUT TYPE=radio NAME=mw_units VALUE=ppm $mw_ppm> 
  AMU <INPUT TYPE=radio NAME=mw_units VALUE=amu $mw_amu> 
  END

  my $ch_neu = ( $params->{charge} && $params->{charge} eq 'neu' ) ? 'CHECKED' : '';
  my $ch_one = 'CHECKED' unless $ch_neu;
  my $ch_radio =<<"  END";
  Neutral <INPUT TYPE=radio NAME=charge VALUE=neu $ch_neu> 
  H+ <INPUT TYPE=radio NAME=charge VALUE=one $ch_one> 
  END

  my $none = ( !$params->{ox_met} || $params->{ox_met} eq 'none' ) ? 'CHECKED' : '';
  my $one = ( $params->{ox_met} eq 'one' ) ? 'CHECKED' : '';
  my $two = ( $none || $one ) ? '' : 'CHECKED';
  my $ox_met_radio =<<"  END";
  None <INPUT TYPE=radio NAME=ox_met VALUE=0 $none> 
  One <INPUT TYPE=radio NAME=ox_met VALUE=1 $one> 
  Two <INPUT TYPE=radio NAME=ox_met VALUE=2 $two> 
  END

  my $yes = ( !$params->{alk_cys} || $params->{alk_cys} eq 'yes' ) ? 'CHECKED' : '';
  my $no = ( !$yes ) ? 'CHECKED' : '';
  my $alk_cys_radio =<<"  END";
  Yes <INPUT TYPE=radio NAME=alk_cys VALUE=yes $yes> 
  No <INPUT TYPE=radio NAME=alk_cys VALUE=no $no> 
  END

  my $mono = ( !$params->{mass_type} || $params->{mass_type} eq 'mono' ) ? 'CHECKED' : '';
  my $avg = ( !$mono ) ? 'CHECKED' : '';
  my $mass_type_radio =<<"  END";
  Monoisotopic <INPUT TYPE=radio NAME=mass_type VALUE=mono $yes> 
  END
#Avg <INPUT TYPE=radio NAME=mass_type VALUE=avg $no> 

  my $iden = ( !$params->{search} || $params->{search} eq 'iden' ) ? 'CHECKED' : '';
  my $pred = ( !$iden ) ? 'CHECKED' : '';
  my $search_radio =<<"  END";
  Identifed <INPUT TYPE=radio NAME=search VALUE=iden $iden> 
  Predicted <INPUT TYPE=radio NAME=search VALUE=pred $pred> 
  END

  my %in = ( 
    mass_list   => $mass_list,
    mass_window => $mass_window . " " . $mw_radio,
    ox_met      => $ox_met_radio,
    alk_cys     => $alk_cys_radio,
    mass_type   => $mass_type_radio,
    search      => $search_radio,
    charge      => $ch_radio
    );
  return \%in;
}