#!/usr/local/bin/perl

###############################################################################
# $Id: Glyco_prediction.cgi 4670 2006-04-22 01:54:05Z dcampbel $
#
# 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.
###############################################################################


###############################################################################
# Get the script set up with everything it will need
###############################################################################
use strict;
use vars qw ($q $sbeams $sbeamsMOD $PROG_NAME
             $current_contact_id $current_username $glyco_query_o);
use lib qw (../../lib/perl);
use CGI::Carp qw(fatalsToBrowser croak);
use Data::Dumper;

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

use SBEAMS::Glycopeptide;
use SBEAMS::Glycopeptide::Settings;
use SBEAMS::Glycopeptide::Tables;

use SBEAMS::Glycopeptide::Get_glyco_seqs;
use SBEAMS::Glycopeptide::Glyco_query;

$sbeams = new SBEAMS::Connection;
$sbeamsMOD = new SBEAMS::Glycopeptide;
$sbeamsMOD->setSBEAMS($sbeams);


$glyco_query_o = new SBEAMS::Glycopeptide::Glyco_query;
$glyco_query_o->setSBEAMS($sbeams);


###############################################################################
# Global Variables
###############################################################################
$PROG_NAME = 'main.cgi';
$sbeams->setSBEAMS_SUBDIR($SBEAMS_SUBDIR);
my $base_url = "$CGI_BASE_DIR/$SBEAMS_SUBDIR/massSearch";


{ # Main 

    # Authenticate or exit
    exit unless ($current_username = $sbeams->Authenticate(
       permitted_work_groups_ref=>['Glycopeptide_user','Glycopeptide_admin', 'Glycopeptide_readonly'],
       # connect_read_only=>1,
        allow_anonymous_access=>1,
    ));

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

    ## get project_id to send to HTMLPrinter display
    my $project_id = $sbeams->getCurrent_project_id();

    my $page = $sbeams->getGifSpacer( 800 ) . "<BR>\n";

    #### Decide what action to take based on information so far
	  if( $params{action} eq 'search') {
      $page .= print_form( \%params );
      $page .= run_search( \%params ); 
    } else {
      $page .= print_form( \%params );
    }

    # Display page
    $sbeamsMOD->display_page_header(project_id => $project_id);
#    $sbeams->printStyleSheet();
    print "$page";
		$sbeamsMOD->display_page_footer();

} # end main

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;
}