#!/usr/local/bin/perl

###############################################################################
# Program     : BrowseAPD
# Author      : Eric Deutsch <edeutsch@systemsbiology.org>
# $Id$
#
# Description : This program that allows users to
#               browse through data in the Annotated Peptide Database.
#
# SBEAMS is Copyright (C) 2000-2005 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.
#
###############################################################################


###############################################################################
# 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 qw($q);
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;
use CGI::Carp qw(fatalsToBrowser croak);
#$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 kay=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(
    permitted_work_groups_ref=>['Proteomics_user','Proteomics_admin',
      'Proteomics_readonly'],
    #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);


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


  #### Decide what action to take based on information so far
  if ($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 Annotated Peptide Database";
  $TABLE_NAME="APD_BrowseAPD" unless ($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);
    $n_params_found = 99;
  }


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


  #### 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 PEPTIDE SUMMARY constraint
  my $peptide_summary_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"P.peptide_summary_id",
    constraint_type=>"int_list",
    constraint_name=>"Peptide Summary List",
    constraint_value=>$parameters{peptide_summary_id} );
  return if ($peptide_summary_clause eq '-1');
  unless ($parameters{peptide_summary_id}) {
    print "<H4>You must select at least one APD summary through which ".
      "to browse!</H4>\n\n";
    return;
  }


  #### Build PROBABILITY constraint
  my $probability_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"MP.maximum_probability",
    constraint_type=>"flexible_float",
    constraint_name=>"Probability",
    constraint_value=>$parameters{probability_constraint} );
  return if ($probability_clause eq '-1');


  #### Build APD PEPTIDE ACCESSION constraint
  my $APD_accession_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"PI.peptide_identifier_str",
    constraint_type=>"plain_text",
    constraint_name=>"APD Accession",
    constraint_value=>$parameters{APD_accession_constraint} );
  return if ($APD_accession_clause eq '-1');


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

  #### If there is a constraint, also apply it to BS.biosequence_name
  my $biosequence_name_clause = "";
#  if ($reference_clause) {
#    $biosequence_name_clause = $reference_clause;
#    $biosequence_name_clause =~ s/P\.biosequence/BS\.biosequence_name/;
#  }


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


  #### Build TRANSMEMBRANE CLASS constraint
  my $transmembrane_class_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"BPS.transmembrane_class",
    constraint_type=>"text_list",
    constraint_name=>"Transmembrane Class",
    constraint_value=>$parameters{transmembrane_class_constraint} );
  return if ($transmembrane_class_clause eq '-1');


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


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


  #### Build PEPTIDE constraint
  my $peptide_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"P.peptide",
    constraint_type=>"plain_text",
    constraint_name=>"Peptide",
    constraint_value=>$parameters{peptide_constraint} );
  return if ($peptide_clause eq '-1');


  #### Build PEPTIDE STRING constraint
  my $peptide_string_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"MP.peptide_string",
    constraint_type=>"plain_text",
    constraint_name=>"Peptide String",
    constraint_value=>$parameters{peptide_string_constraint} );
  return if ($peptide_string_clause eq '-1');


  #### Build CHARGE constraint
  my $charge_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"MP.charge_state",
    constraint_type=>"int_list",
    constraint_name=>"Charge",
    constraint_value=>$parameters{charge_constraint} );
  return if ($charge_clause eq '-1');


  #### Build PRECURSOR MASS constraint
  my $precursor_mass_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"MP.precursor_mass_avg",
    constraint_type=>"flexible_float",
    constraint_name=>"Precursor_Mass Constraint",
    constraint_value=>$parameters{precursor_mass_constraint} );
  return if ($precursor_mass_clause eq '-1');


  #### Build PERCENT BUFFER B constraint
  my $percent_buffer_b_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"MP.percent_ACN_avg",
    constraint_type=>"flexible_float",
    constraint_name=>"Percent ACN Constraint",
    constraint_value=>$parameters{percent_buffer_b_constraint} );
  return if ($percent_buffer_b_clause eq '-1');


  #### Build ISOELECTRIC_POINT constraint
  my $isoelectric_point_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"pI_avg",
    constraint_type=>"flexible_float",
    constraint_name=>"Isoelectric Point",
    constraint_value=>$parameters{isoelectric_point_constraint} );
  return if ($isoelectric_point_clause eq '-1');


  #### Build GENE ANNOTATION LEVEL constraint
  $parameters{gene_annotation_level_constraint} = 'leaf'
    unless ($parameters{gene_annotation_level_constraint});
  my $gene_annotation_level_clause = $sbeams->parseConstraint2SQL(
    constraint_column=>"hierarchy_level",
    constraint_type=>"plain_text",
    constraint_name=>"Gene Annotation Level Constraint",
    constraint_value=>$parameters{gene_annotation_level_constraint} );
  return if ($gene_annotation_level_clause eq '-1');


  #### 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 Additional peptide constraints
  my $second_peptide_clause = "";
  if ($parameters{peptide_options}) {
    if ($parameters{peptide_options} =~ /SELECT|TRUNCATE|DROP|DELETE|FROM|GRANT/i) {
      print "<H4>Cannot parse Peptide Options!  Check syntax.</H4>\n\n";
      return;
    } else {
      my $C = "";
      $C = "C" if ( $parameters{peptide_options} =~ /C_containing/ );
      if ( $parameters{peptide_options} =~ /DoublyTryptic/ ) {
        $second_peptide_clause = "   AND MP.peptide_string LIKE '[RK].%${C}%[RK]._'";
      } elsif ( $parameters{peptide_options} =~ /SinglyTryptic/ ) {
        $second_peptide_clause = "   AND ( MP.peptide_string LIKE '[RK].%${C}%._' OR ".
                                          "MP.peptide_string LIKE '_.%${C}%[RK]._' )";
      } else {
        $second_peptide_clause = "   AND MP.peptide_string LIKE '_.%${C}%._'";
      }
    }
  }


  #### Build ROWCOUNT constraint
  $parameters{row_limit} = 5000
    unless ($parameters{row_limit} > 0 && $parameters{row_limit}<=1000000);
  my $limit_clause = "TOP $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 $TBPR_BIOSEQUENCE_ANNOTATED_GENE AG
             ON ( BS.biosequence_id = AG.biosequence_id )
        LEFT JOIN $TBBL_GENE_ANNOTATION MFA
             ON ( AG.annotated_gene_id = MFA.annotated_gene_id
                   AND MFA.gene_annotation_type_id = 1 AND MFA.idx = 0
                   AND MFA.hierarchy_level = '$parameters{gene_annotation_level_constraint}' )
        LEFT JOIN $TBBL_GENE_ANNOTATION BPA
             ON ( AG.annotated_gene_id = BPA.annotated_gene_id
                   AND BPA.gene_annotation_type_id = 2 AND BPA.idx = 0
                   AND BPA.hierarchy_level = '$parameters{gene_annotation_level_constraint}' )
        LEFT JOIN $TBBL_GENE_ANNOTATION CCA
             ON ( AG.annotated_gene_id = CCA.annotated_gene_id
                   AND CCA.gene_annotation_type_id = 3 AND CCA.idx = 0
                   AND CCA.hierarchy_level = '$parameters{gene_annotation_level_constraint}' )
        LEFT JOIN $TBBL_GENE_ANNOTATION IPDA
             ON ( AG.annotated_gene_id = IPDA.annotated_gene_id
                   AND IPDA.gene_annotation_type_id = 4 AND IPDA.idx = 0
                   AND IPDA.hierarchy_level = '$parameters{gene_annotation_level_constraint}' )
    ~;
  }


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


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

  #### If a full listing of all modified peptides
  if ( $parameters{display_options} =~ /ShowModifications/ ) {

    @column_array = (
      ["peptide_identifier_str","PI.peptide_identifier_str","APD ID"],
      ["biosequence_gene_name","BS.biosequence_gene_name","Gene Name"],
      ["accessor","DBX.accessor","accessor"],
      ["biosequence_accession","BS.biosequence_accession","Accession"],
      ["reference","P.biosequence_name","Reference"],
      ["peptide","P.peptide","Peptide"],
      ["peptide_string","MP.peptide_string","Modified Peptide"],
      ["n_modified_peptides","MP.n_modified_peptides","Number of Modified Peptides"],
      ["maximum_probability","STR(MP.maximum_probability,7,3)","Highest Probability"],
      ["peptide_mass","STR(MP.calc_peptide_mass,7,2)","Calculated Peptide Mass"],
      ["precursor_mass_avg","STR(MP.precursor_mass_avg,7,2)","Precursor Mass Average"],
      ["precursor_mass_stdev","STR(MP.precursor_mass_stdev,7,2)","Precursor Mass Stdev"],
      ["percent_ACN_avg","STR(MP.percent_ACN_avg,7,2)","Percent ACN Average"],
      ["percent_ACN_stdev","STR(MP.percent_ACN_stdev,7,2)","Percent_ACN Stdev"],
      ["charge_state","MP.charge_state","Charge"],
      ["n_experiments","MP.n_experiments","# of Exps"],
      ["observed_experiment_list","MP.experiment_list","Search Batch ID List"],
      @additional_columns,
      ["biosequence_desc","BS.biosequence_desc","Reference Description"],
      ["minimum_probability","PS.minimum_probability","minimum_probability"],
    );
    $group_by_clause = "";

  #### If grouping by peptide
  } else {
    @column_array = (
      ["peptide_identifier_str","PI.peptide_identifier_str","APD ID"],
      ["biosequence_gene_name","BS.biosequence_gene_name","Gene Name"],
      ["accessor","DBX.accessor","accessor"],
      ["biosequence_accession","BS.biosequence_accession","Accession"],
      ["reference","P.biosequence_name","Reference"],
      ["peptide","P.peptide","Peptide"],
      ["n_peptides","n_peptides","Number of Peptides"],
      ["maximum_probability","STR(P.maximum_probability,7,3)","Highest Probability"],
      ["n_experiments","P.n_experiments","# of Exps"],
      ["observed_experiment_list","P.experiment_list","Search Batch ID List"],
      @additional_columns,
      ["biosequence_desc","BS.biosequence_desc","Reference Description"],
      ["searched_experiment_list","PS.experiment_list","searched_experiment_list"],
      ["minimum_probability","PS.minimum_probability","minimum_probability"],
    );
    $group_by_clause = "  GROUP BY PI.peptide_identifier_str,BS.biosequence_gene_name,DBX.accessor,BS.biosequence_accession,P.biosequence_name,P.peptide,n_peptides,STR(P.maximum_probability,7,3),P.n_experiments,P.experiment_list,BS.biosequence_desc,PS.experiment_list,PS.minimum_probability";

    foreach $element (@additional_columns) {
      $group_by_clause .= ",".$element->[1];
    }

  }


  #### 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 $columns_clause
          FROM $TBAPD_PEPTIDE P
         INNER JOIN $TBAPD_MODIFIED_PEPTIDE MP
	       ON ( P.peptide_id = MP.peptide_id )
          LEFT JOIN $TBAPD_PEPTIDE_IDENTIFIER PI
	       ON ( P.peptide_identifier_id = PI.peptide_identifier_id )
         INNER JOIN $TBAPD_PEPTIDE_SUMMARY PS
	       ON ( P.peptide_summary_id = PS.peptide_summary_id )
	  LEFT JOIN $TBPR_BIOSEQUENCE BS
	       ON ( P.biosequence_id = BS.biosequence_id )
          LEFT JOIN $TB_DBXREF DBX ON ( BS.dbxref_id = DBX.dbxref_id )
          LEFT JOIN $TBPR_BIOSEQUENCE_PROPERTY_SET BPS
               ON ( BS.biosequence_id = BPS.biosequence_id )
          $GO_join
	 WHERE 1 = 1
	$peptide_summary_clause
	$biosequence_name_clause
        $description_clause
	$gene_name_clause
	$accession_clause
	$APD_accession_clause

	$probability_clause
	$charge_clause
	$reference_clause
	$peptide_clause
	$peptide_string_clause
	$second_peptide_clause
	$precursor_mass_clause
        $percent_buffer_b_clause
	$isoelectric_point_clause

        $molecular_function_clause
        $biological_process_clause
        $cellular_component_clause
	$protein_domain_clause
        $transmembrane_class_clause
        $n_transmembrane_regions_clause
        $fav_codon_frequency_clause
	$group_by_clause
	$order_by_clause

  ~;


  #### 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' && $key ne 'peptide_string_constraint' &&
        $key ne 'charge_constraint' && $key ne 'APD_accession_constraint' && $key ne 'xx_constraint'
      ) {
      if ($parameters{$key}) {
        #### HACK! FIXME
        my $tmp = $parameters{$key};
        $tmp =~ s/\+/%2b/g;
        push(@parameters_to_pass,"$key=$tmp");
      }
    }
  }
  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",
    	       'Accession_ATAG' => 'TARGET="Win1" ONMOUSEOVER="window.status=\'Show more information about this protein in source database\'; return true"',

               'Reference' => "$CGI_BASE_DIR/Proteomics/BrowseAPD?QUERY_NAME=APD_BrowseAPD&peptide_summary_id=$parameters{peptide_summary_id}&reference_constraint=\%$colnameidx{reference}V&display_options=$parameters{display_options}&input_form_format=minimum_detail&apply_action=$pass_action",
    	       'Reference_ATAG' => 'TARGET="Win2" ONMOUSEOVER="window.status=\'Show all APD peptides for this protein\'; return true"',

    	       'Peptide' => "$CGI_BASE_DIR/Proteomics/BrowseAPD?QUERY_NAME=APD_BrowseAPD&peptide_summary_id=$parameters{peptide_summary_id}&peptide_constraint=\%$colnameidx{peptide}V&display_options=ShowModifications&input_form_format=minimum_detail&apply_action=$pass_action",
    	       'Peptide_ATAG' => 'TARGET="Win2" ONMOUSEOVER="window.status=\'Show all occurrences of this peptide in these experiments\'; return true"',

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

	       'Number of Peptides' => "$CGI_BASE_DIR/Proteomics/GetSearchHits?QUERY_NAME=PR_GetSearchHits&search_batch_id=\%$colnameidx{observed_experiment_list}V&peptide_constraint=\%$colnameidx{peptide}V&${parameters_list}&probability_constraint=>\%$colnameidx{minimum_probability}V&display_options=BSDesc,MaxRefWidth&apply_action=$pass_action",
	       'Number of Peptides_ATAG' => 'TARGET="Win2" ONMOUSEOVER="window.status=\'Show just this many that match all above criteria\'; return true"',

	       'Number of Modified Peptides' => "$CGI_BASE_DIR/Proteomics/GetSearchHits?QUERY_NAME=PR_GetSearchHits&search_batch_id=\%$colnameidx{observed_experiment_list}V&peptide_string_constraint=\%$colnameidx{peptide_string}V&charge_constraint=\%$colnameidx{charge_state}V&${parameters_list}&probability_constraint=>\%$colnameidx{minimum_probability}V&display_options=BSDesc,MaxRefWidth&apply_action=$pass_action",
	       'Number of Modified Peptides_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,
                  'molecular_function_GO' => 1,
                  'biological_process_GO' => 1,
                  'cellular_component_GO' => 1,
                  'interpro_protein_domain_GO' => 1,
                  'minimum_probability' => 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);
    }

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


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