#!/usr/local/bin/perl

###############################################################################
# Program     : BrowseProteinSummary
# Author      : Eric Deutsch <edeutsch@systemsbiology.org>
# $Id: BrowseProteinSummary,v 1.1 2003/01/17 17:24:18 edeutsch Exp $
#
# Description : This program that allows users to
#               browse through a summary of proteins from experiments.
#
# SBEAMS is Copyright (C) 2000-2002 by Eric Deutsch
# 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.
#
###############################################################################


###############################################################################
# Set up all needed modules and objects
###############################################################################
use strict;
use Getopt::Long;
use FindBin;

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

use SBEAMS::Connection;
use SBEAMS::Connection::Settings;
use SBEAMS::Connection::Tables;

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

$sbeams = new SBEAMS::Connection;
$sbeamsMOD = new SBEAMS::Proteomics;
$sbeamsMOD->setSBEAMS($sbeams);
$sbeams->setSBEAMS_SUBDIR($SBEAMS_SUBDIR);


use CGI;
$q = new CGI;


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

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

EOU

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

$VERBOSE = $OPTIONS{"verbose"} || 0;
$QUIET = $OPTIONS{"quiet"} || 0;
$DEBUG = $OPTIONS{"debug"} || 0;
if ($DEBUG) {
  print "Options settings:\n";
  print "  VERBOSE = $VERBOSE\n";
  print "  QUIET = $QUIET\n";
  print "  DEBUG = $DEBUG\n";
}


###############################################################################
# Set Global Variables and execute main()
###############################################################################
main();
exit(0);


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

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


  #### Read in the default input parameters
  my %parameters;
  my $n_params_found = $sbeams->parse_input_parameters(
    q=>$q,parameters_ref=>\%parameters);
  #$sbeams->printDebuggingInfo($q);


  #### Decide what action to take based on information so far
  if (defined($parameters{action}) && $parameters{action} eq "???") {
    # Some action
  } else {
    $sbeamsMOD->display_page_header();
    handle_request(ref_parameters=>\%parameters);
    $sbeamsMOD->display_page_footer();
  }


} # end main



###############################################################################
# Handle Request
###############################################################################
sub handle_request {
  my %args = @_;


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


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


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


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


  #### Set some specific settings for this program
  #my $CATEGORY="Browse Protein Summary";
  my $CATEGORY="This interface is experimental";
  $TABLE_NAME="PR_BrowseProteinSummary" unless ($TABLE_NAME);
  ($PROGRAM_FILE_NAME) =
    $sbeamsMOD->returnTableInfo($TABLE_NAME,"PROGRAM_FILE_NAME");
  my $base_url = "$CGI_BASE_DIR/$SBEAMS_SUBDIR/$PROGRAM_FILE_NAME";


  #### Get the columns and input types for this table/query
  my @columns = $sbeamsMOD->returnTableInfo($TABLE_NAME,"ordered_columns");
  my %input_types = 
    $sbeamsMOD->returnTableInfo($TABLE_NAME,"input_types");


  #### Read the input parameters for each column
  my $n_params_found = $sbeams->parse_input_parameters(
    q=>$q,parameters_ref=>\%parameters,
    columns_ref=>\@columns,input_types_ref=>\%input_types);


  #### If the apply action was to recall a previous resultset, do it
  my %rs_params = $sbeams->parseResultSetParams(q=>$q);
  if ($apply_action eq "VIEWRESULTSET") {
    $sbeams->readResultSet(
      resultset_file=>$rs_params{set_name},
      resultset_ref=>$resultset_ref,
      query_parameters_ref=>\%parameters,
      resultset_params_ref=>\%rs_params,
    );
    $n_params_found = 99;
  }


  #### Set some reasonable defaults if no parameters supplied
  unless ($n_params_found) {
    $parameters{input_form_format} = "minimum_detail";
    $parameters{probability_constraint} = '>0.9';
  }


  #### Apply any parameter adjustment logic
  #none


  #### Display the user-interaction input form
  $sbeams->display_input_form(
    TABLE_NAME=>$TABLE_NAME,CATEGORY=>$CATEGORY,apply_action=>$apply_action,
    PROGRAM_FILE_NAME=>$PROGRAM_FILE_NAME,
    parameters_ref=>\%parameters,
    input_types_ref=>\%input_types,
  );


  #### Display the form action buttons
  $sbeams->display_form_buttons(TABLE_NAME=>$TABLE_NAME);


  #### Finish the upper part of the page and go begin the full-width
  #### data portion of the page
  $sbeams->display_page_footer(close_tables=>'YES',
    separator_bar=>'YES',display_footer=>'NO');



  #########################################################################
  #### Process all the constraints

  #### Build SEARCH BATCH / EXPERIMENT constraint
  my $search_batch_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"SB.search_batch_id",
    constraint_type=>"int_list",
    constraint_name=>"Search Batch List",
    constraint_value=>$parameters{search_batch_id} );
  return if ($search_batch_clause eq '-1');
  unless (defined($parameters{search_batch_id}) &&
          $parameters{search_batch_id}) {
    print "<H4>You must select at least one experiment to browse!</H4>\n\n";
    return;
  }


  #### Build PROTEIN GROUP PROBABILITY constraint
  my $protein_group_probability_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"PG.probability",
    constraint_type=>"flexible_float",
    constraint_name=>"Probability",
    constraint_value=>$parameters{protein_group_probability_constraint} );
  return if ($protein_group_probability_clause eq '-1');


  #### Build PROBABILITY constraint
  my $protein_probability_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"PROT.probability",
    constraint_type=>"flexible_float",
    constraint_name=>"Probability",
    constraint_value=>$parameters{protein_probability_constraint} );
  return if ($protein_probability_clause eq '-1');


  #### Build REFERENCE PROTEIN constraint
  my $biosequence_name_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"BS.biosequence_name",
    constraint_type=>"plain_text",
    constraint_name=>"Reference",
    constraint_value=>$parameters{reference_constraint} );
  return if ($biosequence_name_clause eq '-1');


  #### Build GENE NAME constraint
  my $gene_name_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"BS.biosequence_gene_name",
    constraint_type=>"plain_text",
    constraint_name=>"Gene Name",
    constraint_value=>$parameters{gene_name_constraint} );
  return if ($gene_name_clause eq '-1');


  #### Build PROTEIN DESCRIPTION constraint
  my $description_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"BS.biosequence_desc",
    constraint_type=>"plain_text",
    constraint_name=>"Protein Description",
    constraint_value=>$parameters{description_constraint} );
  return if ($description_clause eq '-1');


  #### Build MOLECULAR FUNCTION constraint
  my $molecular_function_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"MFA.annotation",
    constraint_type=>"plain_text",
    constraint_name=>"Molecular Function",
    constraint_value=>$parameters{molecular_function_constraint} );
  return if ($molecular_function_clause eq '-1');


  #### Build BIOLOGICAL PROCESS constraint
  my $biological_process_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"BPA.annotation",
    constraint_type=>"plain_text",
    constraint_name=>"Biological Process",
    constraint_value=>$parameters{biological_process_constraint} );
  return if ($biological_process_clause eq '-1');


  #### Build CELLULAR COMPONENT constraint
  my $cellular_component_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"CCA.annotation",
    constraint_type=>"plain_text",
    constraint_name=>"Cellular Component",
    constraint_value=>$parameters{cellular_component_constraint} );
  return if ($cellular_component_clause eq '-1');


  #### Build INTERPRO PROTEIN DOMAIN constraint
  my $protein_domain_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"IPDA.annotation",
    constraint_type=>"plain_text",
    constraint_name=>"InterPro Protein Domain",
    constraint_value=>$parameters{protein_domain_constraint} );
  return if ($protein_domain_clause eq '-1');


  #### Build FAVORED CODON FREQUENCY constraint
  my $fav_codon_frequency_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"BS.fav_codon_frequency",
    constraint_type=>"flexible_float",
    constraint_name=>"Favored Codon Frequency",
    constraint_value=>$parameters{fav_codon_frequency_constraint} );
  return if ($fav_codon_frequency_clause eq '-1');


  #### Build NUMBER OF TRANSMEMBRANE REGIONS constraint
  my $n_transmembrane_regions_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"BS.n_transmembrane_regions",
    constraint_type=>"flexible_int",
    constraint_name=>"Number of Transmembrane regions",
    constraint_value=>$parameters{n_transmembrane_regions_constraint} );
  return if ($n_transmembrane_regions_clause eq '-1');


  #### Build PROTEIN LENGTH constraint
  my $protein_length_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"DATALENGTH(BS.biosequence_seq)",
    constraint_type=>"flexible_int",
    constraint_name=>"Protein Length",
    constraint_value=>$parameters{protein_length_constraint} );
  return if ($protein_length_clause eq '-1');


  #### Build ACCESSION constraint
  my $accession_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"BS.biosequence_accession",
    constraint_type=>"plain_text",
    constraint_name=>"Accession",
    constraint_value=>$parameters{accession_constraint} );
  return if ($accession_clause eq '-1');


  #### Build ANNOTATION_STATUS and ANNOTATION_LABELS constraint
  my $annotation_status_clause = "";
  my $annotation_label_clause = "";

  if ($parameters{annotation_label_id}) {
    if ($parameters{annotation_status_id} eq 'Annot') {
      $annotation_label_clause = "   AND SHA.annotation_label_id IN ( $parameters{annotation_label_id} )";
    } elsif ($parameters{annotation_status_id} eq 'UNAnnot') {
      $annotation_status_clause = "   AND SHA.annotation_label_id IS NULL";
      $annotation_label_clause = "";
      print "WARNING: Annotation status and Annotation label constraints conflict!<BR>\n";
    } else {
      $annotation_label_clause = "   AND ( SHA.annotation_label_id IN ( $parameters{annotation_label_id} ) ".
        "OR SHA.annotation_label_id IS NULL )";
    }


  } else {
    if ($parameters{annotation_status_id} eq 'Annot') {
      $annotation_status_clause = "   AND SHA.annotation_label_id IS NOT NULL";
    } elsif ($parameters{annotation_status_id} eq 'UNAnnot') {
      $annotation_status_clause = "   AND SHA.annotation_label_id IS NULL";
    } else {
      #### Nothing
    }

  }


  #### Build NUMBER OF ANNOTATIONS constraint
  my $n_annotations_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"row_count",
    constraint_type=>"flexible_int",
    constraint_name=>"Number of Matches",
    constraint_value=>$parameters{n_annotations_constraint} );
  return if ($n_annotations_clause eq '-1');


  #### Build QUANTITATION constraint
  my $quantitation_clause = "";
  if ($parameters{quantitation_constraint}) {
    if ($parameters{quantitation_constraint} =~ /^[\d\.]+$/) {
      $quantitation_clause = "   AND d0_intensity/ISNULL(NULLIF(d8_intensity,0),0.01) = $parameters{quantitation_constraint}";
    } elsif ($parameters{quantitation_constraint} =~ /^between\s+[\d\.]+\s+and\s+[\d\.]+$/i) {
      $quantitation_clause = "   AND d0_intensity/ISNULL(NULLIF(d8_intensity,0),0.01) $parameters{quantitation_constraint}";
    } elsif ($parameters{quantitation_constraint} =~ /^[><=][=]*\s*[\d\.]+$/) {
      $quantitation_clause = "   AND d0_intensity/ISNULL(NULLIF(d8_intensity,0),0.01) $parameters{quantitation_constraint}";
    } else {
      print "<H4>Cannot parse Quantitation Constraint!  Check syntax.</H4>\n\n";
      return;
    }
  }


  #### Build SORT ORDER
  my $order_by_clause = "";
  if ($parameters{sort_order}) {
    if ($parameters{sort_order} =~ /SELECT|TRUNCATE|DROP|DELETE|FROM|GRANT/i) {
      print "<H4>Cannot parse Sort Order!  Check syntax.</H4>\n\n";
      return;
    } else {
      $order_by_clause = " ORDER BY $parameters{sort_order}";
    }
  }


  #### Build ROWCOUNT constraint
  $parameters{row_limit} = 5000
    unless ($parameters{row_limit} > 0 && $parameters{row_limit}<=1000000);
  my $limit_clause = $sbeams->buildLimitClause(
   row_limit=>$parameters{row_limit});


  #### Define some variables needed to build the query
  my $group_by_clause = "";
  my $final_group_by_clause = "";
  my @column_array;
  my $peptide_column = "";
  my $count_column = "";


  #### If the user opted to see the GO columns, add them in
  my @additional_columns = ();
  if ( $parameters{display_options} =~ /ShowGOColumns/ ||
       $molecular_function_clause.$biological_process_clause.
       $cellular_component_clause.$protein_domain_clause ) {
    @additional_columns = (
      ["molecular_function","MFA.annotation","Molecular Function"],
      ["molecular_function_GO","MFA.external_accession","molecular_function_GO"],
      ["biological_process","BPA.annotation","Biological Process"],
      ["biological_process_GO","BPA.external_accession","biological_process_GO"],
      ["cellular_component","CCA.annotation","Cellular Component"],
      ["cellular_component_GO","CCA.external_accession","cellular_component_GO"],
      ["interpro_protein_domain","IPDA.annotation","InterPro Protein Domain"],
      ["interpro_protein_domain_GO","IPDA.external_accession","interpro_protein_domain_GO"],
    );
  }

  #### If the user opted to see GO columns or provided some GO constraints,
  #### then join in the GO tables
  my $GO_join = "";
  if ( $parameters{display_options} =~ /ShowGOColumns/ ||
       $molecular_function_clause.$biological_process_clause.
       $cellular_component_clause.$protein_domain_clause ) {
    $GO_join = qq~
        LEFT JOIN flybase.dbo.annotated_gene AG
             ON ( BS.biosequence_accession = AG.gene_accession )
        LEFT JOIN flybase.dbo.gene_annotation MFA
             ON ( AG.annotated_gene_id = MFA.annotated_gene_id
                   AND MFA.gene_annotation_type_id = 1 AND MFA.idx = 0 )
        LEFT JOIN flybase.dbo.gene_annotation BPA
             ON ( AG.annotated_gene_id = BPA.annotated_gene_id
                   AND BPA.gene_annotation_type_id = 2 AND BPA.idx = 0 )
        LEFT JOIN flybase.dbo.gene_annotation CCA
             ON ( AG.annotated_gene_id = CCA.annotated_gene_id
                   AND CCA.gene_annotation_type_id = 3 AND CCA.idx = 0 )
        LEFT JOIN flybase.dbo.gene_annotation IPDA
             ON ( AG.annotated_gene_id = IPDA.annotated_gene_id
                   AND IPDA.gene_annotation_type_id = 4 AND IPDA.idx = 0 )
    ~;
  }


  #### Add in some extra columns if the user wants to see them
  if ( $parameters{display_options} =~ /ShowExtraProteinProps/ ) {
    @additional_columns = (
      ["fav_codon_frequency","STR(BS.fav_codon_frequency,10,3)","Favored Codon Frequency"],
      ["n_transmembrane_regions","BS.n_transmembrane_regions","Number of Transmembrane Regions"],
      ["protein_length","DATALENGTH(BS.biosequence_seq)","Protein Length"],
      @additional_columns,
    );
  }


  #### Define the desired columns in the query
  #### [friendly name used in url_cols,SQL,displayed column title]

  #### If grouping by reference
  if ( $parameters{display_options} =~ /GroupReference/ ) {
    @column_array = (
      ["biosequence_gene_name","BS.biosequence_gene_name","Gene Name"],
      ["accessor","DBX.accessor","accessor"],
      ["accessor_suffix","DBX.accessor_suffix","accessor_suffix"],
      ["biosequence_accession","BS.biosequence_accession","Accession"],
      ["reference","BS.biosequence_name","Reference"],
      ["count","tABS.row_count","Count"],
      ["average_quant","tABS.average_quant","Quant Avg"],
      ["stdev_quant","tABS.stdev_quant","Quant StDev"],
      ["n_quant","tABS.n_quant","Quant N"],
      @additional_columns,
      ["biosequence_desc","BS.biosequence_desc","Reference Description"],
    );
    $group_by_clause = " GROUP BY SH.reference";
    $count_column = "COUNT(*) AS 'row_count',STR(AVG(NULLIF(d0_intensity,0.0)/NULLIF(d8_intensity,0.0)/ISNULL(NULLIF(PE.quant_normalization,0.0),1.0)),10,2) AS 'average_quant',STR(STDEV(NULLIF(d0_intensity,0.0)/NULLIF(d8_intensity,0.0)/ISNULL(NULLIF(PE.quant_normalization,0.0),1.0)),10,2) AS 'stdev_quant',SUM(CASE WHEN (NULLIF(d0_intensity,0.0) IS NULL OR NULLIF(d8_intensity,0.0) IS NULL) THEN 0 ELSE 1 END) AS 'n_quant'";

  #### If no grouping
  } else {
    @column_array = (
      ["experiment_tag","experiment_tag","Exp"],
      ["search_batch_subdir","search_batch_subdir","DB"],
      ["group_number","PG.group_number","Group #"],
      ["pseudo_name","PG.pseudo_name","Group Name"],
      ["group_probability","STR(PG.probability,7,3)","Group Prob"],
      ["biosequence_name","BS.biosequence_name","Protein Name"],
      ["accessor","DBX.accessor","accessor"],
      ["accessor_suffix","DBX.accessor_suffix","accessor_suffix"],
      ["biosequence_accession","BS.biosequence_accession","Accession"],
      ["protein_probability","STR(PROT.probability,7,3)","Protein Prob"],
      @additional_columns,
      ["biosequence_desc","BS.biosequence_desc","Reference Description"],
    );
    $peptide_column = "";
    $count_column = "";
  }


  #### Limit the width of the Reference column if user selected
  if ( $parameters{display_options} =~ /MaxRefWidth/ ) {
    $max_widths{'Reference'} = 20;
  }
  #### Set flag to display SQL statement if user selected
  if ( $parameters{display_options} =~ /ShowSQL/ ) {
    $show_sql = 1;
  }


  #### Build the columns part of the SQL statement
  my %colnameidx = ();
  $colnameidx{peptide} = 99;
  $colnameidx{peptide_string} = 99;
  my @column_titles = ();
  my $columns_clause = $sbeams->build_SQL_columns_list(
    column_array_ref=>\@column_array,
    colnameidx_ref=>\%colnameidx,
    column_titles_ref=>\@column_titles
  );


  #### Define the SQL statement
  $sql = qq~
	SELECT $limit_clause->{top_clause} $columns_clause
	  FROM $TBPR_PROTEIN PROT
          JOIN $TBPR_PROTEIN_GROUP PG
               ON ( PROT.protein_group_id = PG.protein_group_id )
	  JOIN $TBPR_BIOSEQUENCE BS
               ON ( PROT.biosequence_id = BS.biosequence_id )
	  JOIN $TBPR_SEARCH_BATCH SB
	       ON ( BS.biosequence_set_id = SB.biosequence_set_id )
	  JOIN $TBPR_PROTEOMICS_EXPERIMENT PE
               ON ( SB.experiment_id = PE.experiment_id )
          LEFT JOIN $TB_DBXREF DBX ON ( BS.dbxref_id = DBX.dbxref_id )
          $GO_join
	 WHERE 1 = 1
	$search_batch_clause
	$biosequence_name_clause
        $description_clause
	$gene_name_clause
	$accession_clause
        $molecular_function_clause
        $biological_process_clause
        $cellular_component_clause
	$protein_domain_clause
        $n_transmembrane_regions_clause
        $fav_codon_frequency_clause
        $protein_length_clause
	$protein_group_probability_clause
	$protein_probability_clause
	$quantitation_clause
	$annotation_label_clause
	$annotation_status_clause
	$group_by_clause
	$order_by_clause
	$limit_clause->{trailing_limit_clause}

  ~;


  #### Ad-Hoc, and sort of dangerous way of reversing the sense of the
  #### quantitation ratio
  if ( $parameters{quantitation_values} eq "d0d8" ) {
    #### This is the default
  #### Swap the numerator and denominator
  } elsif ( $parameters{quantitation_values} eq "d8d0" ) {
    $sql =~ s/d0\_/dQQQ_/g;
    $sql =~ s/d8\_/d0_/g;
    $sql =~ s/dQQQ\_/d8_/g;
  }


  #### Certain types of actions should be passed to links
  my $pass_action = "QUERY";
  $pass_action = $apply_action if ($apply_action =~ /QUERY/i); 


  #### Pass nearly all of the constraints down to a child query
  my @parameters_to_pass;
  my $parameters_list = '';
  while ( ($key,$value) = each %input_types ) {
    if ($key ne 'sort_order' && $key ne 'display_options' &&
        $key ne 'reference_constraint') {
      if ($parameters{$key}) {
        push(@parameters_to_pass,"$key=$parameters{$key}");
      }
    }
  }
  if (@parameters_to_pass) {
    $parameters_list = join('&',@parameters_to_pass);
  }


  #### Define the hypertext links for columns that need them
  %url_cols = ('Accession' => "\%$colnameidx{accessor}V\%$colnameidx{biosequence_accession}V\%$colnameidx{accessor_suffix}V",
    	       'Accession_ATAG' => 'TARGET="Win1" ONMOUSEOVER="window.status=\'Show more information about this protein in source database\'; return true"',

               'Reference' => "$CGI_BASE_DIR/Proteomics/GetSearchHits?QUERY_NAME=PR_GetSearchHits&search_batch_id=$parameters{search_batch_id}&reference_constraint=\%$colnameidx{reference}V&display_options=BSDesc,MaxRefWidth&apply_action=$pass_action",
    	       'Reference_ATAG' => 'TARGET="Win2" ONMOUSEOVER="window.status=\'Show all occurrences of this protein in these experiments\'; return true"',

    	       'Peptide' => "$CGI_BASE_DIR/Proteomics/GetSearchHits?QUERY_NAME=PR_GetSearchHits&search_batch_id=$parameters{search_batch_id}&peptide_constraint=\%$colnameidx{peptide}V&display_options=BSDesc,MaxRefWidth&apply_action=$pass_action",
    	       'Peptide_ATAG' => 'TARGET="Win2" ONMOUSEOVER="window.status=\'Show all occurrences of this peptide in these experiments\'; return true"',

	       'Peptide String' => "$CGI_BASE_DIR/Proteomics/GetSearchHits?QUERY_NAME=PR_GetSearchHits&search_batch_id=$parameters{search_batch_id}&peptide_string_constraint=\%$colnameidx{peptide_string}V&display_options=BSDesc,MaxRefWidth&apply_action=$pass_action",
	       'Peptide String_ATAG' => 'TARGET="Win2" ONMOUSEOVER="window.status=\'Show all occurrences of this exact peptide instance in these experiments\'; return true"',

	       'Count' => "$CGI_BASE_DIR/Proteomics/GetSearchHits?QUERY_NAME=PR_GetSearchHits&search_batch_id=$parameters{search_batch_id}&reference_constraint=\%$colnameidx{reference}V&peptide_constraint=\%$colnameidx{peptide}V&peptide_string_constraint=\%$colnameidx{peptide_string}V&${parameters_list}&display_options=BSDesc,MaxRefWidth&apply_action=$pass_action",
	       'Count_ATAG' => 'TARGET="Win2" ONMOUSEOVER="window.status=\'Show just this many that match all above criteria\'; return true"',

               'Molecular Function' => "http://www.ebi.ac.uk/ego/QuickGO?mode=display&entry=\%$colnameidx{molecular_function_GO}V",
               'Molecular Function_ATAG' => 'TARGET="WinExt"',
               'Molecular Function_OPTIONS' => {semicolon_separated_list=>1},
               'Biological Process' => "http://www.ebi.ac.uk/ego/QuickGO?mode=display&entry=\%$colnameidx{biological_process_GO}V",
               'Biological Process_ATAG' => 'TARGET="WinExt"',
               'Biological Process_OPTIONS' => {semicolon_separated_list=>1},
               'Cellular Component' => "http://www.ebi.ac.uk/ego/QuickGO?mode=display&entry=\%$colnameidx{cellular_component_GO}V",
               'Cellular Component_ATAG' => 'TARGET="WinExt"',
               'Cellular Component_OPTIONS' => {semicolon_separated_list=>1},
               'InterPro Protein Domain' => "http://www.ebi.ac.uk/interpro/IEntry?ac=\%$colnameidx{interpro_protein_domain_GO}V",
               'InterPro Protein Domain_ATAG' => 'TARGET="WinExt"',
               'InterPro Protein Domain_OPTIONS' => {semicolon_separated_list=>1},
  );


               ##'Reference_ATAG' => "TARGET=\"Win1\" ONMOUSEOVER=\"window.status='%V'; return true\"",

  #### Define columns that should be hidden in the output table
  %hidden_cols = ('accessor' => 1,
                  'accessor_suffix' => 1,
                  'molecular_function_GO' => 1,
                  'biological_process_GO' => 1,
                  'cellular_component_GO' => 1,
                  'interpro_protein_domain_GO' => 1,
  );


  #########################################################################
  #### If QUERY or VIEWRESULTSET was selected, display the data
  if ($apply_action =~ /QUERY/i || $apply_action eq "VIEWRESULTSET") {

    #### If the action contained QUERY, then fetch the results from
    #### the database
    if ($apply_action =~ /QUERY/i) {

      #### Show the SQL that will be or was executed
      $sbeams->display_sql(sql=>$sql) if ($show_sql);

      #### Fetch the results from the database server
      $sbeams->fetchResultSet(
        sql_query=>$sql,
        resultset_ref=>$resultset_ref,
      );

      #### Store the resultset and parameters to disk resultset cache
      $rs_params{set_name} = "SETME";
      $sbeams->writeResultSet(
        resultset_file_ref=>\$rs_params{set_name},
        resultset_ref=>$resultset_ref,
        query_parameters_ref=>\%parameters,
        resultset_params_ref=>\%rs_params,
        query_name=>"$SBEAMS_SUBDIR/$PROGRAM_FILE_NAME",
      );
    }

    #### Display the resultset
    $sbeams->displayResultSet(
      resultset_ref=>$resultset_ref,
      query_parameters_ref=>\%parameters,
      rs_params_ref=>\%rs_params,
      url_cols_ref=>\%url_cols,
      hidden_cols_ref=>\%hidden_cols,
      max_widths=>\%max_widths,
      column_titles_ref=>\@column_titles,
      base_url=>$base_url,
    );


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


    #### Display a plot of data from the resultset
    $sbeams->displayResultSetPlot(
      rs_params_ref=>\%rs_params,
      resultset_ref=>$resultset_ref,
      query_parameters_ref=>\%parameters,
      column_titles_ref=>\@column_titles,
      base_url=>$base_url,
    );


  #### If QUERY was not selected, then tell the user to enter some parameters
  } else {
    if ($sbeams->invocation_mode() eq 'http') {
      print "<H4>Select parameters above and press QUERY</H4>\n";
    } else {
      print "You need to supply some parameters to contrain the query\n";
    }
  }


} # end handle_request



###############################################################################
# evalSQL
#
# Callback for translating Perl variables into their values,
# especially the global table variables to table names
###############################################################################
sub evalSQL {
  my $sql = shift;

  return eval "\"$sql\"";

} # end evalSQL

