#!/usr/local/bin/perl

###############################################################################
# Program     : ViewPeptideExpression
# $Id: GetProtein 7773 2015-02-03 00:06:08Z zsun $
#
# Description : Prints summary of ...
#
#
# SBEAMS is Copyright (C) 2000-2015 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 Data::Dumper;
$|++;

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 $log);
use SBEAMS::Connection::Settings;
use SBEAMS::Connection::Tables;
use SBEAMS::Connection::TabMenu;
$sbeams = new SBEAMS::Connection;
my $htmlmode;

use SBEAMS::BioLink;
my $biolink = SBEAMS::BioLink->new();
$biolink->setSBEAMS($sbeams);

use SBEAMS::BioLink;
my $biolink = new SBEAMS::BioLink;

use SBEAMS::PeptideAtlas;
use SBEAMS::PeptideAtlas::Settings;
use SBEAMS::PeptideAtlas::Tables;
use SBEAMS::PeptideAtlas::ProtInfo;
use SBEAMS::PeptideAtlas::GetOrigeneCov;

$sbeamsMOD = new SBEAMS::PeptideAtlas;
$sbeamsMOD->setSBEAMS($sbeams);
$sbeams->setSBEAMS_SUBDIR($SBEAMS_SUBDIR);
my $origenecov = new SBEAMS::PeptideAtlas::GetOrigeneCov;

use SBEAMS::PeptideAtlas::KeySearch;
my $keySearch = new SBEAMS::PeptideAtlas::KeySearch;
$keySearch->setSBEAMS($sbeams);

use SBEAMS::PeptideAtlas::BestPeptideSelector;
my $bestPeptideSelector = new SBEAMS::PeptideAtlas::BestPeptideSelector;
$bestPeptideSelector->setSBEAMS($sbeams);
$bestPeptideSelector->setAtlas($sbeamsMOD);

# Global sequence coverage array, will be populated post-graphic
my @coverage;  
my $max_intensity = 1;
my %coverage=();
my @methods =  qw(ITCID FTCID ITETD FTETD HCD);

# Swiss Prot annotations
my @sp_rows;
my $sp_rationale;

my $current_page = { organism => '', atlas_build_id => '' };
my $parameters;


use constant MIN_OBS_LENGTH => 6;
use constant MAX_OBS_LENGTH => 40;

###############################################################################
# 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(
      permitted_work_groups_ref=>['PeptideAtlas_user','PeptideAtlas_admin',
      'PeptideAtlas_readonly', 'PeptideAtlas_exec'],
      #connect_read_only=>1,
      allow_anonymous_access=>1,
  ));


  #### Read in the default input parameters
  my %parameters;
  $parameters = \%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);

  # Cache current output mode
  $htmlmode = ( $sbeams->output_mode() eq 'html' ) ? 1 : 0;

  #### Decide what action to take based on information so far
  if ($parameters{action} eq "???") {
      # Some action

  } else {
      my $project_id = $sbeamsMOD->getProjectID(
          atlas_build_id => $parameters{atlas_build_id}
          );
      # TMF
      $sbeamsMOD->display_page_header(project_id => $project_id, init_tooltip => 1);
      handle_request(ref_parameters=>\%parameters);
      $sbeamsMOD->display_page_footer();
  }


} # end main




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

  my $spacer = $sbeams->getGifSpacer( 900 );

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

  my %parameters = %{$ref_parameters};


  # put a spacer so that showing hidden content doesn't mangle the layout
  print "<BR>$spacer\n" if $htmlmode;

  #### Get the HTML to display the tabs
  my $tabMenu = $sbeamsMOD->getTabMenu(
    parameters_ref => \%parameters,
    program_name => $PROG_NAME,
  );
  print $tabMenu->asHTML() if ($sbeams->output_mode() eq 'html');

  my $contact_id = $sbeams->getCurrent_contact_id();

  my $samples = getSamples();
  my $sample_list = getSampleList( sample_list => $samples );

  my $htmlmode = 1;

  #############################################################
  ## Display the samples list ##

    # Widget to allow show/hide of sample map section
    my ( $tr, $link ) = $sbeams->make_table_toggle( name => 'getprotein_samplemap',
                                                  visible => 1,
                                                tooltip => 'Show/Hide Section',
                                                 imglink => 1,
                                                  sticky => 1 );

    print "<br><br><b>";
    print " Protein Accession: $parameters->{acc}<br>";
    print " SNP position:  $parameters->{pos}<br>";
    print " SNP description:  $parameters->{desc}<br><br>";
    print " SNP supporting peptides </b><br>";
    print "<ul>\n";
    my %speps;
    for my $pep ( split( /_/, $parameters->{spep} ) ) {
      $speps{$pep}++;
      print "<li> $pep \n";
    }
    print "</ul>\n";
    print "<b> Original sequence supporting peptides </b><br>";
    print "<ul>\n";
    my %opeps;
    for my $pep ( split( /_/, $parameters->{opep} ) ) {
      $opeps{$pep}++;
      print "<li> $pep \n";
    }
    print "</ul>\n";
    my @speps;
    my @opeps;

    my $pep_seq = "'" . join( "','", keys( %speps ), keys( %opeps ) ) . "'";

    my $sql = qq~
   	SELECT DISTINCT peptide_instance_id, peptide_sequence, n_observations
	  FROM  $TBAT_PEPTIDE P 
	  JOIN $TBAT_PEPTIDE_INSTANCE PI
    ON P.peptide_id = PI.peptide_id
    WHERE peptide_sequence IN ( $pep_seq )
    AND atlas_build_id = $parameters->{atlas_build_id}
    ORDER BY n_observations DESC, peptide_sequence ASC
    ~;

    my $sth = $sbeams->get_statement_handle($sql);
    while ( my @db_row = $sth->fetchrow_array() ) {
      if ( $speps{$db_row[1]} ) {
        push @speps, $db_row[0];
      } elsif  ( $opeps{$db_row[1]} ) {
        push @opeps, $db_row[0];
      } else {
        die "Stray peptide $db_row[1]";
      }
    }
    
    my $sampleMap = $sbeamsMOD->getSampleMapDisplayMod( 
      snp_support => \@speps,
      snp_original => \@opeps,
      atlas_build_id => $parameters->{atlas_build_id},
      link => $link,
      tr_info => $tr,
      header_text => "Shows per-experiment expression observed peptides"
	);
    print "<A NAME='samplemap'></A><TABLE width='600'>$sampleMap</TABLE>" if $htmlmode;

#  die $contact_id;
}

sub getSamples {
  my %args = @_;
  my $SUB_NAME = 'getSamples';

  my $sql = qq~
    SELECT sample_id,sample_title
      FROM $TBAT_SAMPLE
     WHERE record_status != 'D'
     ORDER BY sample_id
  ~;

  my @samples = $sbeams->selectSeveralColumns($sql);

  return \@samples;

} # end getSamples


sub getSampleList {
  my %args = @_;

  #### Decode the argument list
  return [] unless $args{sample_list};

#  each row has an accession, sample_string pair.

  my %observed_samples;
  foreach my $row (@{$args{sample_list}}) {
    my $observed_sample_list = $row->[1];
    my @all = split(/[,;]/,$observed_sample_list);
    foreach my $element ( @all ) {
      $observed_samples{$element}++;
    }
  }
  my @keys = keys( %observed_samples );
  return \@keys;
}