#!/usr/local/bin/perl

###############################################################################
# $Id: peptideSearch.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;


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


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

$sbeams->setSBEAMS_SUBDIR($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);
    if ( $params{unipep_build_id} ) {
      my $build_id = $sbeamsMOD->get_current_build( build_id => $params{unipep_build_id} );
      if ( $build_id != $params{unipep_build_id} ) {
        $sbeams->set_page_message( type => 'Error', msg => 'You must log in to access specified build' );
      }
    }

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

    my $page = $sbeams->getGifSpacer( 800 ) . "<BR>\n";
    if ( $params{ipi_data_id} ) {
      $page .= get_ortholog_display( \%params );
    } else {
      $page .= $sbeams->getErrorText( "Missing required parameter ipi_data_id" );
    }
      

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

} # end main

sub get_ortholog_display {
  my $params = shift;
  my $content;
  for my $arg ( qw( id_list id_type ) ) {
    unless ( $params->{$arg} ) {
      $content .= "Missing required parameter: $arg <BR>\n";
      return $content;
    }
  }
#  for my $p ( keys( %$params ) ) { $content .= "$p => " . $params->{$p} . "<BR>\n"; }
  my $id_list = $params->{id_list};
  $id_list =~ s/\s+/ /gm;
  my @ids = split( " ", $id_list );

  my $pep_o = new SBEAMS::Glycopeptide::Get_peptide_seqs(glyco_obj => $sbeamsMOD);

  my $results = $sbeamsMOD->runBulkSearch( ids => \@ids, %{$params} );
  $content .= get_submit_js();
  my $table = SBEAMS::Connection::DataTable->new( BORDER => 0 );
  $table->addRow( ['Accession', 'SwissProt', 'Symbol','Protein Name', 'Synonyms', 'Sequence', 'Prophet', 'Mass', 'dCn'  ] );
  $table->setRowAttr( ROWS => [1], BGCOLOR => '#C0D0C0' );
  my $current;
  my $prot_cnt = 1;
  my $grp_row = 2;
  my $bgcolor = '#F1F1F1';
  for my $peptide ( @$results ) {
    my ( $ipi, 
         $swiss_id,
         $ipi_data_id,
         $seq, 
         $symbol, 
         $protein_name, 
         $peptide_id,
         $prophet_score,
         $peptide_mass,
         $dcn,
         $synonyms
         ) = @$peptide;

    my $ipi_base = $ipi . $synonyms;
#    $current = $ipi_base unless $current;
#    $current = $ipi_base unless $current;

#    my $tissues = $pep_o->observed_tissues( $peptide_id ) || '';
    my $ipi_link = $ipi;
    my $motif = $sbeamsMOD->get_current_motif_type();
    if ( $params->{action} ne 'download' ) {
#      $tissues = $sbeams->truncateStringWithMouseover( string => $tissues, len => 20 );
      $protein_name= $sbeams->truncateStringWithMouseover( string => $protein_name, len => 25 );
      $ipi_link = get_search_link( name => $ipi, motif => $motif );
      $log->debug( $motif );
      $synonyms = get_kegg_link( name => $synonyms ) if $motif =~ /phospho/;
      $seq = $sbeamsMOD->decorate_phospho_sequence( $seq );
    }
    my $chk_box = "<INPUT TYPE=checkbox NAME=accession VALUE=$ipi CHECKED>$ipi_link</INPUT>";
    
    $prophet_score = sprintf( "%0.2f", $prophet_score);
    $peptide_mass = sprintf( "%0.4f", $peptide_mass);
    
    $log->debug( "ipi_base is $ipi_base, current is $current" );
    if ( !$current || $ipi_base ne $current ) {
      $table->addRow( [ $chk_box, $swiss_id, $symbol, $protein_name, $synonyms, $seq, $prophet_score, $peptide_mass, $dcn ] );
      $prot_cnt++;
      $log->debug( "In da not current loop" );
      my $current_row = $table->getRowNum();
#      $log->info( "group row is $grp_row, current row is $current_row, bgcolor is $bgcolor" );
      $table->setRowAttr( ROWS => [$grp_row..$current_row - 1], BGCOLOR => $bgcolor );
      $grp_row = $current_row;
      $bgcolor = ( $bgcolor eq '#E0E0E0' ) ? '#F1F1F1' : '#E0E0E0';
      $current = $ipi_base;
    } else {
      $table->addRow( [  '&nbsp;','&nbsp;','&nbsp;','&nbsp;', '&nbsp;',
                          $seq, $prophet_score, $peptide_mass, $dcn ] );
    }
    my $current_row = $table->getRowNum();
    $table->setRowAttr( ROWS => [$grp_row..$current_row], BGCOLOR => $bgcolor );

  }
  my $current_row = $table->getRowNum();
  $table->setColAttr( COLS => [ 1 ], ROWS => [1..$current_row], NOWRAP => 1 );


  return "<FONT COLOR=BLUE SIZE=+1>Query returned no results</FONT>" unless @$results;

  if ( $params->{action} eq 'download' ) {
    $content = $table->asTSV();
    $log->debug( "Content is " . length($content) . " characters long" );
  } else {
    my $prot = ( $prot_cnt > 1 ) ? 'proteins' : 'protein';
    my $num = ( @ids > 1 ) ? 'numbers' : 'number';
    my $pep = ( $table->getRowNum() > 2 ) ? 'peptides' : 'peptide';
    $content .= "<FONT COLOR=GREEN>Search with " . scalar( @ids ) . " accession $num yeilded ";
    $content .= $table->getRowNum() - 1 . " $pep from $prot_cnt $prot </FONT><BR>\n"; 
    $content .= get_download_form($params);
    $content .=<<"    END";
    <FORM NAME=cytoscape METHOD=POST ACTION=getCytoscapeWebstart>
    <INPUT TYPE=HIDDEN NAME=apply_action VALUE=gene_list>
    END
    $content .= $table->asHTML();
    $content .= "<FORM>";
  }
  return $sbeamsMOD->get_phospho_css() . "\n" . $content;
}

sub get_submit_js {
  return( <<"  END" );
    <SCRIPT LANGUAGE="javascript">
  function submit_cytoscape() {
    document.cytoscape.submit();
  }
  </SCRIPT>
     <STYLE TYPE="text/css" media="screen">
    div.visible {
    display: inline;
    white-space: nowrap;         
    }
    div.visilink {
    color: blue;
    display: inline;
    white-space: nowrap;         
    }
    div.hidden {
    display: none;
    }
    span { 
     border: solid;
     border-width: 1px;
    }
  </STYLE> 
  END
}


__DATA__

sub get_download_form {
  my $params = shift;
  my $url = $q->url( -full => 1 );
  my $form = "<FORM NAME=download_form METHOD=POST>";
  for my $p ( keys( %$params ) ) { 
    my $value = $params->{$p};
    $value = 'download' if $p eq 'action';

    $form .= "<INPUT TYPE=HIDDEN NAME='$p' VALUE='$value'></INPUT>";
#    $log->debug( "$p -> $params->{$p}");
  }
  $form .= "</FORM>";
  my $url = "<A OnClick='document.download_form.submit();'><FONT COLOR=BLUE>Download table</FONT></A>";
  my $cytolink = '<A ONCLICK="submit_cytoscape();"><DIV CLASS="visilink" TITLE="Open cytoscape with selected proteins"> Cytoscape </DIV></A>';
  return $form . "\n" . $url . "&nbsp;|&nbsp;" . $cytolink;
#  return "<A HREF=$url>Download table</A>";
}

sub run_search {
  my $params = shift;
  my $content;
  for my $arg ( qw( id_list id_type ) ) {
    unless ( $params->{$arg} ) {
      $content .= "Missing required parameter: $arg <BR>\n";
      return $content;
    }
  }
#  for my $p ( keys( %$params ) ) { $content .= "$p => " . $params->{$p} . "<BR>\n"; }
  my $id_list = $params->{id_list};
  $id_list =~ s/\s+/ /gm;
  my @ids = split( " ", $id_list );

  my $pep_o = new SBEAMS::Glycopeptide::Get_peptide_seqs(glyco_obj => $sbeamsMOD);

  my $results = $sbeamsMOD->runBulkSearch( ids => \@ids, %{$params} );
  $content .= get_submit_js();
  my $table = SBEAMS::Connection::DataTable->new( BORDER => 0 );
  $table->addRow( ['Accession', 'SwissProt', 'Symbol','Protein Name', 'Synonyms', 'Sequence', 'Prophet', 'Mass', 'dCn'  ] );
  $table->setRowAttr( ROWS => [1], BGCOLOR => '#C0D0C0' );
  my $current;
  my $prot_cnt = 1;
  my $grp_row = 2;
  my $bgcolor = '#F1F1F1';
  for my $peptide ( @$results ) {
    my ( $ipi, 
         $swiss_id,
         $ipi_data_id,
         $seq, 
         $symbol, 
         $protein_name, 
         $peptide_id,
         $prophet_score,
         $peptide_mass,
         $dcn,
         $synonyms
         ) = @$peptide;

    my $ipi_base = $ipi . $synonyms;
#    $current = $ipi_base unless $current;
#    $current = $ipi_base unless $current;

#    my $tissues = $pep_o->observed_tissues( $peptide_id ) || '';
    my $ipi_link = $ipi;
    my $motif = $sbeamsMOD->get_current_motif_type();
    if ( $params->{action} ne 'download' ) {
#      $tissues = $sbeams->truncateStringWithMouseover( string => $tissues, len => 20 );
      $protein_name= $sbeams->truncateStringWithMouseover( string => $protein_name, len => 25 );
      $ipi_link = get_search_link( name => $ipi, motif => $motif );
      $log->debug( $motif );
      $synonyms = get_kegg_link( name => $synonyms ) if $motif =~ /phospho/;
      $seq = $sbeamsMOD->decorate_phospho_sequence( $seq );
    }
    my $chk_box = "<INPUT TYPE=checkbox NAME=accession VALUE=$ipi CHECKED>$ipi_link</INPUT>";
    
    $prophet_score = sprintf( "%0.2f", $prophet_score);
    $peptide_mass = sprintf( "%0.4f", $peptide_mass);
    
    $log->debug( "ipi_base is $ipi_base, current is $current" );
    if ( !$current || $ipi_base ne $current ) {
      $table->addRow( [ $chk_box, $swiss_id, $symbol, $protein_name, $synonyms, $seq, $prophet_score, $peptide_mass, $dcn ] );
      $prot_cnt++;
      $log->debug( "In da not current loop" );
      my $current_row = $table->getRowNum();
#      $log->info( "group row is $grp_row, current row is $current_row, bgcolor is $bgcolor" );
      $table->setRowAttr( ROWS => [$grp_row..$current_row - 1], BGCOLOR => $bgcolor );
      $grp_row = $current_row;
      $bgcolor = ( $bgcolor eq '#E0E0E0' ) ? '#F1F1F1' : '#E0E0E0';
      $current = $ipi_base;
    } else {
      $table->addRow( [  '&nbsp;','&nbsp;','&nbsp;','&nbsp;', '&nbsp;',
                          $seq, $prophet_score, $peptide_mass, $dcn ] );
    }
    my $current_row = $table->getRowNum();
    $table->setRowAttr( ROWS => [$grp_row..$current_row], BGCOLOR => $bgcolor );

  }
  my $current_row = $table->getRowNum();
  $table->setColAttr( COLS => [ 1 ], ROWS => [1..$current_row], NOWRAP => 1 );


  return "<FONT COLOR=BLUE SIZE=+1>Query returned no results</FONT>" unless @$results;

  if ( $params->{action} eq 'download' ) {
    $content = $table->asTSV();
    $log->debug( "Content is " . length($content) . " characters long" );
  } else {
    my $prot = ( $prot_cnt > 1 ) ? 'proteins' : 'protein';
    my $num = ( @ids > 1 ) ? 'numbers' : 'number';
    my $pep = ( $table->getRowNum() > 2 ) ? 'peptides' : 'peptide';
    $content .= "<FONT COLOR=GREEN>Search with " . scalar( @ids ) . " accession $num yeilded ";
    $content .= $table->getRowNum() - 1 . " $pep from $prot_cnt $prot </FONT><BR>\n"; 
    $content .= get_download_form($params);
    $content .=<<"    END";
    <FORM NAME=cytoscape METHOD=POST ACTION=getCytoscapeWebstart>
    <INPUT TYPE=HIDDEN NAME=apply_action VALUE=gene_list>
    END
    $content .= $table->asHTML();
    $content .= "<FORM>";
  }
  return $sbeamsMOD->get_phospho_css() . "\n" . $content;
}

sub get_submit_js {
  return( <<"  END" );
    <SCRIPT LANGUAGE="javascript">
  function submit_cytoscape() {
    document.cytoscape.submit();
  }
  </SCRIPT>
     <STYLE TYPE="text/css" media="screen">
    div.visible {
    display: inline;
    white-space: nowrap;         
    }
    div.visilink {
    color: blue;
    display: inline;
    white-space: nowrap;         
    }
    div.hidden {
    display: none;
    }
    span { 
     border: solid;
     border-width: 1px;
    }
  </STYLE> 

  END
}

sub print_form {
  my $params = shift;
	
	my $content = <<"  END";
  <TABLE>
   <TR CLASS='rev_gray_head'>
    <TD><H1>Search protein list</H1></TD>
   </TR>
   <TR>
    <TD>
    Enter a list of proteins to be searched.  
    </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( id_list id_type ) ) {
    $f_table->addRow(["<B>$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 => [3], COLSPAN => 2 );
#  $f_table->setColAttr( COLS => [1], ROWS => [1..6], ALIGN => 'RIGHT' );
  $f_table->setColAttr( COLS => [1], ROWS => [3], ALIGN => 'CENTER' );
  $f_table->setColAttr( COLS => [2], ROWS => [1..3], ALIGN => 'LEFT' );

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

sub get_input_labels {
  my $params = shift;
  my %in = ( id_list => 'Protein List:',
             id_type   => 'Identifier type:',
             );
  
  return \%in;
}

sub get_input_fields {
  my $params = shift;

  my $id_list = $params->{id_list} || '';
  $id_list = "<TEXTAREA ROWS=4 COLS=30 NAME=id_list>$id_list</TEXTAREA>";


  my %id_chk = ( ipi => '', swp => '', sym => '' ); 

  if ( $params->{id_type} ) {
    for my $id_type ( qw( swp sym ipi ) ) {
      $id_chk{$id_type} = 'checked' if $params->{id_type} eq $id_type;
    }
  } else {
    $id_chk{ipi} = 'checked';
  }

  my $id_type_radio =<<"  END";
  Accession <INPUT TYPE=radio NAME=id_type VALUE=ipi $id_chk{ipi}> 
  Swiss Prot <INPUT TYPE=radio NAME=id_type VALUE=swp $id_chk{swp} > 
  Gene Symbol <INPUT TYPE=radio NAME=id_type VALUE=sym $id_chk{sym} > 
  END

  my %in = ( 
    id_list   => $id_list,
    id_type   => $id_type_radio,
    );
  return \%in;
}

sub get_search_link {
  my %args = @_;
  for my $arg ( qw( name motif ) ) {
    return "" unless $args{$arg};
  }
  if ( $args{motif} =~ /phospho/ ) {
    return "<A HREF=peptideSearch.cgi?search_type=accession&search_term=$args{name}&.submit=Submit+Query&action=Show_hits_form>$args{name}</A>";
  } elsif ( $args{motif} =~ /glyco/ ) {
    return "<A HREF='peptideSearch.cgi?search_type=IPI Accession Number;action=Show_hits_form;search_term=$args{name}' TARGET=prot_details>$args{name}</A>";
  }

}


sub get_kegg_link {
  my %args = @_;
  for my $arg ( qw( name ) ) {
    return "" unless $args{$arg};
  }
  my $kegg_name = $args{name};
  $kegg_name =~ s/(CG\d+)(-P.)*/$1/;
  my $img = "$HTML_BASE_DIR/images/kegg_sm.gif";
  return "$args{name}&nbsp;<A HREF=showPathways?ga=Dmel_$kegg_name><IMG BORDER=0 TITLE='View KEGG pathways for this gene' SRC=$img></A>";
}