#!/usr/local/bin/perl

###############################################################################
# $Id$
#
# SBEAMS is Copyright (C) 2000-2021 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 CGI::Carp qw(fatalsToBrowser croak);
use Data::Dumper;

use lib qw (../../lib/perl);
use vars qw ($q $sbeams $sbeamsMOD $PROG_NAME
             $current_contact_id $current_username $glyco_query_o);
use SBEAMS::Connection qw($q $log);
use SBEAMS::Connection::Settings;
use SBEAMS::Connection::Tables;
use SBEAMS::Connection::DataTable;

use SBEAMS::BioLink::Tables;
use SBEAMS::BioLink::MSF;

use SBEAMS::PeptideAtlas;
use SBEAMS::PeptideAtlas::Settings;
use SBEAMS::PeptideAtlas::Tables;
use SBEAMS::Connection::TabMenu;


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

$sbeams->setSBEAMS_SUBDIR($SBEAMS_SUBDIR);

{ # Main 

  # Authenticate or exit
  $current_username = $sbeams->Authenticate(allow_anonymous_access=>1) || exit;

  #### 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";

  my $tabMenu = $sbeamsMOD->getTabMenu(
    parameters_ref => \%params,
    program_name => 'viewOrthologs',
  );
  $page .= "$tabMenu";

  $sbeamsMOD->display_page_header(project_id => $project_id);
  $log->debug( "Begin page:" .time() );


  # Use default if requested
  if ( $params{use_default} ) {
    $params{group_id} = 'OG5_126932';
  }

  if ( $params{group_id} ) {
    $page .= get_ortholog_display( %params );
  } elsif ( $params{list_groups} ) {
    $page .= get_ortholog_list( %params );
  } else {
    $page .= $sbeams->makeErrorText( "Missing required parameter group_id" );
  }
  $log->debug( "Page done:" .time() );
    

  # Display page
  print $page;
  $sbeamsMOD->display_page_footer();

} # end main

sub get_ortholog_display {
  my %args = @_;

  # Content scalar to return
  my $content = '';

  # check params
  for my $arg ( qw( group_id ) ) {
    unless ( $args{$arg} ) {
      $content .= $sbeams->makeErrorText("Missing required parameter: $arg <BR>");
      return $content;
    }
  }

  # Highlight if available.
  $args{entry_accession} ||= '';

  # limit by bioseq_id?
  my $bioseq_clause = '';
  if( $args{restore} ) {
    $log->info( "Restoring" );
    $args{bioseq_id} = '';
  } elsif( $args{bioseq_id} && !$args{search_groups} ) {
    $bioseq_clause = "AND B.biosequence_id IN ( $args{bioseq_id} )";
  }

  my $all_projects = join( ",", $sbeams->getAccessibleProjects() );

  my $curr_bid = $sbeamsMOD->getCurrentAtlasBuildID( parameters_ref => \%args );
#  my $null_clause = ( $args{show_all} ) ? 'OR search_key_type IS NULL' : '';

  # SQL to fetch ortholog groups and bioseqs in them.
  my $sql =<<"  END_SQL";
  SELECT DISTINCT ortholog_group,
	                biosequence_name,
									organism_name,
									search_key_name,
									CAST( biosequence_seq AS VARCHAR(4000) ),
									biosequence_id,
									B.biosequence_set_id,
                  ORG.organism_id
  FROM biolink.dbo.ortholog O
  JOIN $TBAT_BIOSEQUENCE B ON O.entry_accession = B.biosequence_name
  JOIN $TBAT_ATLAS_BUILD AB ON AB.biosequence_set_id = B.biosequence_set_id
  JOIN $TB_ORGANISM ORG ON O.ortholog_organism_id = ORG.organism_id
  LEFT JOIN $TBAT_SEARCH_KEY SK ON SK.resource_name = B.biosequence_name
  WHERE ortholog_group = '$args{group_id}'
--  AND AB.project_id IN ( $all_projects )
    AND ( search_key_type = 'Full Name'
     OR search_key_type = 'Description'
     OR search_key_type LIKE '%Symbol'
     OR search_key_type LIKE 'Annotation ID'
     OR search_key_type IS NULL
     OR search_key_type = 'RefSeq'
     OR search_key_type = 'ORF Name'
    )
	$bioseq_clause
--  AND ORG.organism_id = 38
  ORDER BY organism_name, B.biosequence_name ASC
  END_SQL

  
# 0     ortholog_group,
# 1     biosequence_name,
# 2     organism_name,
# 3     search_key_name,
# 4     CAST( biosequence_seq AS VARCHAR(4000) ),
# 5     biosequence_id
# 6     biosequence_set_id
# 7     organism_id
  $log->debug( "prepare stmt: $sql " . time() );
  my $sth = $sbeams->get_statement_handle( $sql );
  $log->debug( "prepare stmt done: " .time() );

  # array of protein/ortholog info
  my @all_proteins;

  # hash of biosequence_ids -> seq or name
  my %bioseq_id2seq;
  my %bioseq_id2name;

  # hash seq <=> accession
  my %seq2acc;
  my %acc2seq;

  # Store (degenerate) acc -> bioseq_id
  my %acc2bioseq_id;

  # Store organism for each biosequence set
  my %bss2org;
  my %organisms;

  # Counter
  my $cnt = 0;

  while ( my @row = $sth->fetchrow_array() ) {
    $organisms{$row[7]}++;
    my $seq = $row[4];
    $seq =~ s/[^a-zA-Z]//g;

    $bss2org{$row[6]} ||= $row[2];

    # Check this out later for dups...
    $seq2acc{$seq} ||= {};
    $seq2acc{$seq}->{$row[1]}++;

    $bioseq_id2seq{$row[5]} = $row[4]; 
    $bioseq_id2name{$row[5]} = $row[1]; 

    $acc2bioseq_id{$row[1]} ||= [];
    push @{$acc2bioseq_id{$row[1]}}, $row[5]; 

    # Cache first seq for each accession, and push onto display
    unless ( $acc2seq{$row[1]} ) {
      $acc2seq{$row[1]} = $seq;
      # push row info for display
      push @all_proteins, \@row;
    }

    $cnt++;
  }
  $log->debug( "Iterated $cnt rows: " .time() );

  # not quite working yet!
  my %dup_seqs;
  my $dup_char = 'A';
#	for my $seq ( keys( %seq2acc ) ) {
  for my $prot ( @all_proteins ) {
    my $seq = $prot->[4];
#		$log->debug( "SEQ is $seq" );
    next unless scalar(keys(%{$seq2acc{$seq}})) > 1;

    for my $acc ( keys ( %{$seq2acc{$seq}} ) ) {
      next if $dup_seqs{$acc};
      $dup_seqs{$acc} = $dup_char;
    }
    $dup_char++;
  }


  # Get stringified version for IN clause.
  my $bioseq_ids = join( ",", sort{ $a <=> $b } keys( %bioseq_id2name ) );

  if ( !$bioseq_ids ) {
    return "<br><br><br\n" . $sbeams->makeInfoText( "No matching sequences found for ortholog group $args{group_id}" );
  }

  my $organisms = join( ',', keys( %organisms ) );
  my $default_builds = get_default_builds( $all_projects, $organisms );

#	We will get just one build per organism for now #Punt
#	my $accessible_builds = get_accessible_builds( $all_projects, $organisms );

  # Fixed order list of builds - first use default builds, then any 
  # accessible build
  my @build_ids = sort { $default_builds->{$a} cmp $default_builds->{$b} } keys( %{$default_builds} );
#	push @build_ids, sort { $accessible_builds->{$a} cmp $accessible_builds->{$b} } keys( %{$accessible_builds} );
  my %bseen;
  my $build_str;
  for my $id ( @build_ids ) {
    next if $bseen{$id}++;
    my $sep = ( $build_str ) ? ',' : '';
    $build_str .= $sep . $id;
  }


    # hash of info keyed by build_id
  my %build_seqs;
  
  # To be passed to checkbox list routine.
  my %build_info;
  
  my %view_org2build;
  my %view_build2org;
    
  # Skip non-default builds, this var controls debug stmt
  my %skippy;
  if ( $build_str ) {
    # Define SQL to fetch info about builds in which a peptide has been observed
    my $sql =<<"    ENDSQL";
  	SELECT distinct 
  	       PI.peptide_instance_id,
  	       n_observations,
  				 PM.matched_biosequence_id,
           PI.atlas_build_id,
  				 atlas_build_name,
  				 peptide_sequence,
  				 AB.biosequence_set_id
  --				 AB.biosequence_set_id,
  --         O.organism_name
  	FROM $TBAT_PEPTIDE_MAPPING PM
    JOIN $TBAT_PEPTIDE_INSTANCE PI ON PI.peptide_instance_id = PM.peptide_instance_id
    JOIN $TBAT_PEPTIDE P ON ( PI.peptide_id = P.peptide_id )
    JOIN $TBAT_ATLAS_BUILD AB ON ( PI.atlas_build_id = AB.atlas_build_id )
  --  JOIN $TBAT_BIOSEQUENCE_SET BS ON ( AB.biosequence_set_id = BS.biosequence_set_id )
  --  JOIN $TB_ORGANISM O ON ( O.organism_id = BS.organism_id )
    WHERE PM.matched_biosequence_id IN ( $bioseq_ids )
  	AND AB.atlas_build_id IN ( $build_str )
    ORDER BY PI.atlas_build_id DESC
  --  ORDER BY organism_name ASC, PI.atlas_build_id DESC
    ENDSQL
    $log->debug( "prepare instance stmt: " . time() );
  #  $log->debug( $sql );
    my $sth = $sbeams->get_statement_handle( $sql );
  	$log->debug( "prepare instance stmt done: " .time() );
  
  # 0   count(distinct PI.peptide_id),
  # 1   sum( n_observations ),
  # 2   PM.matched_biosequence_id,
  # 3   PI.atlas_build_id,
  # 4   atlas_build_name,
  # 5   peptide_sequence
  # 6   fizzle
  # 7   biosequence_set_id
  
  # 0 new	       PI.peptide_instance_id,
  # 1 new	       n_observations,
  # 2 new				 PM.matched_biosequence_id,
  # 3 new         PI.atlas_build_id,
  # 4 new				 atlas_build_name,
  # 5 new				 peptide_sequence,
  # 6 new				 biosequence_set_id,
  
    $cnt = 0;
    # Loop to calculate coverate, per prot n_obs for each build
    $log->debug( "Iterate, calc coverage: " .time() );
  
  
    while ( my @row = $sth->fetchrow_array() ) {
  
  		# Effectively eliminate non-default builds
  #		if ( !$default_builds->{$row[3]} ) {
  #			$log->debug( "skipping $row[3] 'cause its not default" ) if !$skippy{$row[3]}++; 
  #			next;
  #		}
  
      my $org = $bss2org{$row[6]};
      $build_info{$row[3]} ||= {};
      $build_info{$row[3]}->{name} = $row[4];
      $build_info{$row[3]}->{org} = $org;
      $build_info{$row[3]}->{is_default} = ( $row[6] ) ? 'yes' : 'no';
      $build_info{$row[3]}->{is_curr} = ( $row[3] == $curr_bid ) ? 1 : 0;
      $build_info{$row[3]}->{bss} = $row[7];
  
      # Simplistic initial view mechanism
      if ( !$view_org2build{$org} ) {
	$build_info{$row[3]}->{visible}++;
	$build_info{$row[3]}->{view}++;
	$view_org2build{$org} = $row[3];
	$view_build2org{$row[3]} = $org;
	#			$log->debug( "View build for $org is $row[3] ( $row[4] )" );
      } elsif ( $row[3] == $curr_bid ) {
	$build_info{$row[3]}->{visible}++;
	$build_info{$row[3]}->{view}++;
  
        # Gotta unset the build
	my $deprecated = $view_org2build{$org};
  #			$log->debug( "Replacing info from $build_info{$deprecated}->{name} with info from  $build_info{$row[3]}->{name}, 'cause its current!" );
  
	$build_info{$deprecated}->{visible} = 0;
	$build_info{$deprecated}->{view} = 0;
	delete $view_build2org{$deprecated};
	$view_org2build{$org} = $row[3];
	$view_build2org{$row[3]} = $org;
      }
  
      # error cases, shouldn't happen?
      next unless $row[0];
  #	  if ( $row[0] > 1 ) {
  #			$log->warn( "count peptide_id > 1" );
  #			$log->warn( join( ", ", @row ) );
  #		}
  
      $build_seqs{$row[3]} ||= {};
      $build_seqs{$row[3]}->{$row[2]} ||= {};
      $build_seqs{$row[3]}->{$row[2]}->{count}++;
      $build_seqs{$row[3]}->{$row[2]}->{n_obs} += $row[1];
  
      # Calc coverage for this build/protein combination
      $build_seqs{$row[3]}->{$row[2]}->{coverage} ||= {};
      my $posn = $sbeamsMOD->get_site_positions( pattern => $row[5],
						 seq => $bioseq_id2seq{$row[2]} );
      for my $p ( @$posn ) {
	for ( my $i = 0; $i < length($row[5]); $i++ ){
	  my $covered_posn = $p + $i;
	  $build_seqs{$row[3]}->{$row[2]}->{coverage}->{$covered_posn}++;
	}
      }
      # Going to cache with accession for ease of use!
      $build_seqs{$row[3]}->{$bioseq_id2name{$row[2]}}->{coverage} = $build_seqs{$row[3]}->{$row[2]}->{coverage};

      $build_seqs{$row[3]}->{$bioseq_id2name{$row[2]}}->{bioseq} = $row[2];
      $cnt++;
    }
    $log->debug( "Iterated $cnt rows: " .time() );
  }
  
  
  # Table headings
  my @headings = ( 'Accession', 'Organism' );

  # Index of build col in display row, 2 already added above
  my $b_cnt = 2;
  my %build_posn;
	
  $log->debug( "Iterate, prepare display: " .time() );
  # Seen builds skipped, allows us to use composite of default and accessible.
  my %seen;
  for my $build_id ( @build_ids ) {
    next if $seen{$build_id}++;

    $build_posn{$b_cnt++} = $build_id;
    my $dag = '';
    my $display_name = $build_info{$build_id}->{name};
#		$display_name =~ s/Yeast|Mouse|Human|Drosophila//;
    $display_name =~ s/Peptide//;
    $display_name =~ s/Atlas//;
    $display_name =~ s/P\s*>*0.\d//;
    $display_name =~ s/^_//;
    $display_name =~ s/_$//;
    $build_info{$build_id}->{display_name} = $display_name;

    if ( $view_build2org{$build_id} ) {
      $dag = '<SUP><BOLD>&#8224;</BOLD></SUP>';
    }
    push @headings, "<span title='$build_info{$build_id}->{name} ($build_id)'>$display_name $dag</span>";
  }
  push @headings, 'Protein Name/Description';
  $log->debug( "Prepare display complete: " .time() );

  # Set up display table
  my $table = SBEAMS::Connection::DataTable->new( BORDER => 0, HEADER => 1 );
  $table->addRow( \@headings );
  $table->setRowAttr( ROWS => [1], BGCOLOR => '#002664' );
  $table->setHeaderAttr( WHITE_TEXT => 1, BOLD => 1 );

  my $current;
  my %subject;
  my $bgcolor = '#f3f1e4';

  my $cnt = 0;
  my $fasta = '';
  my %bss2color;
  my %bgcolor = ( 'consensus' => '#FFFFFF' );
  my %acc_color = ( 'consensus' => '#FFFFFF' );
  $log->debug( "Iterate, build table: " .time() );
  for my $row ( @all_proteins ) {

    #Legacy...
    my @row = @{$row};
    my $seq = $row[4];

    # make fasta file in memory
    $fasta .= ">$row[1]\n";
    $fasta .= "$seq\n";

    my $acc_link = "<A HREF='Search?search_key=$row[1];action=GO;build_type_name=$row[2];all_fields=on'>$row[1]</A>";
    $row[3] = $sbeams->truncateStringWithMouseover( string => $row[3], len => 50 );

    if ( $dup_seqs{$row[1]} ) {
      $acc_link .= "<SUP><BOLD>$dup_seqs{$row[1]}</BOLD></SUP>";
    }

#    $build_seqs{$row[3]}->{$row[2]}->{n_obs} += $row[1];
#    $build_seqs{$row[3]}->{$row[2]}->{count} += $row[0];

    $current ||= $row[2];  
    if ( $current ne $row[2] ) {  # New organism
      $bgcolor = ( $bgcolor eq '#d3d1c4' ) ? '#f3f1e4' : '#d3d1c4';
      $current = $row[2];
    }
    $bgcolor{$row[1]} = $bgcolor;
    $acc_color{$row[1]} = '#FFFFFF';

    my @table_row = ( $acc_link, $row[2] );
#	  my $b_cnt = 2;
    for my $build_id ( @build_ids ) {
      $build_info{$build_id}->{bgcolor} = $bgcolor;
#			$log->debug( "build $build_id is getting color $bgcolor!" );
#			my $build_info = '*';
      my $build_info = '&nbsp;';
      my $name = $build_info{$build_id}->{name};

      for my $synon_bioseq_id ( @{$acc2bioseq_id{$row[1]}} ) {
	if ( $build_seqs{$build_id}->{$synon_bioseq_id} ) {
          my $cnt = $build_seqs{$build_id}->{$synon_bioseq_id}->{count};
          my $obs = $build_seqs{$build_id}->{$synon_bioseq_id}->{n_obs};
	  my $link = "<A HREF='GetProtein?atlas_build_id=$build_id;protein_name=$bioseq_id2name{$synon_bioseq_id};action=QUERY' TARGET='_GetProtein'>";
	  $build_info = "<span title='$cnt distinct peptides and $obs total observations for $row[1] in $name'> $link $obs ($cnt)</A> </span>";
	}
      }
      push @table_row, $build_info;
    }
    push @table_row, $row[3];

    $table->addRow( \@table_row );


    $table->setRowAttr( ROWS => [$table->getRowNum()],
			BGCOLOR => $bgcolor,
	);

    if ( $row[1] eq $args{entry_accession} ) {
      $subject{name} = $args{entry_accession};
      $table->setColAttr( ROWS => [$table->getRowNum()], COLS => [1], BGCOLOR => '#FFFACD' );
      $acc_color{$row[1]} = '#FFFACD';
    } 

    $cnt++;
  }
  $log->debug( "Build table done: " .time() );
  $table->setRowAttr( ROWS => [1], ALIGN => 'CENTER' );
  $table->setColAttr( ROWS => [1..$table->getRowNum()], COLS => [1..$table->getColNum()], NOWRAP => 1 );

  $table->setColAttr( ROWS => [1..$table->getRowNum()], COLS => [3..$table->getColNum()-1], ALIGN => 'CENTER' );
#	FIXME
#		$build_posn{$b_cnt++} = $build_id;
#			$view_org2build{$org} = $row[3];
#			$view_build2org{$row[3]} = $org;
	$log->debug( "Iterate hide cols: " .time() );
	for my $posn ( sort { $a <=> $b } keys %build_posn ) {
	  if ( $view_build2org{$build_posn{$posn}} ) {
	    $table->setColAttr( ROWS => [1..$table->getRowNum()], COLS => [$posn +  1],
				CLASS => 'tbl_visible',
				ID => $build_posn{$posn},
				NAME => $build_posn{$posn},
		);
	  } else {
	    $table->setColAttr( ROWS => [1..$table->getRowNum()], COLS => [$posn + 1],
				CLASS => 'tbl_hidden',
				ID => $build_posn{$posn},
				NAME => $build_posn{$posn},
		);
	  }

	}
  $log->debug( "Hide cols complete: " .time() );

  # finished 

  my $MSF = SBEAMS::BioLink::MSF->new();

  $log->debug( "Run alignment: " .time() );
  my $clustal_display;
  my $alignment_overview = qq~
	This display shows the protein sequences in the $args{group_id} group aligned using the Clustal algorithm, described below (click the Show Description link if necessary).  Each sequence is highlighted to show which peptide(s) have been observed for that sequence in one of the builds for the corresponding organism.  The builds used to highlight the sequences for a given organism are shown in the table above with a dagger symbol (<SUP><BOLD>&#8224;</BOLD></SUP>) in the heading, and are diplayed in the table by default.
	~;
  my $duplicate_text = '';
  if ( scalar( keys( %dup_seqs ) ) ) {
    $duplicate_text = "  Any sequence-identical proteins are denoted by a superscript letter.";
  }
		
  if ( $cnt > 1000 ) {
    $alignment_overview = '';
    $clustal_display = $sbeams->makeErrorText( "Too many sequences to run alignment, skipping" );
  } else {
    my $clustal = $MSF->runClustalW( sequences => $fasta );
    if ( ref $clustal ne 'ARRAY' ) {
      $clustal_display = $sbeams->makeErrorText( "Error running Clustal: $clustal" );
    } else {
      $clustal_display = get_clustal_display( alignments => $clustal,
					      bgcolor => \%bgcolor,
					      acc_color => \%acc_color,
					      highlight_builds => \%view_build2org,
					      build_seqs => \%build_seqs, 
					      acc2bioseq => \%acc2bioseq_id
	  );
    }
  }
  $log->debug( "ViewOrtho, fasta is " . length( $fasta ) . ", result is " . length( $clustal_display ) );

  my $alignment_text = get_alignment_text();
  $log->debug( "Run alignment Done: " .time() );
  $log->debug( "Color build seqs: " .time() );
  my $add_builds = get_add_builds_section( build_info => \%build_info );
  $log->debug( "Color build seqs done: " .time() );
  $log->debug( "Display " .time() );
  my $spc = '&nbsp;' x 50;

  my $search_help = qq~
	   <DIV class=info_box ID=help>
    To search OrthoMCL groups by name, enter group name in text box.  Use 'show_all' checkbox to show information for all 
    group members, regardless of whether they are present in a Peptide Atlas build.
     </DIV>
  ~;
  my @toggle = $sbeams->make_toggle_section( textlink => 1,
                                              imglink => 1,
                                             hidetext => "Hide Help",
                                             showtext => "Show Help",
                                              visible => 0,
                                              sticky  => 1,
                                                name  => 'search_orthologs_help',
					     content => $search_help
      );

#  my $search_groups = get_group_search_section( %args, help => "($toggle[1])" );
#  $toggle[0]
#  $search_groups

# Removed text
#   You can add information about additional builds by clicking the 'Add builds' link below and selecting the desired build(s).  Builds used to highlight the multiple sequence alignment below are shown with a dagger symbol (<SUP><BOLD>&#8224;</BOLD></SUP>).  $duplicate_text
  if ( $table->getRowNum() == 1 ) {
    return $sbeams->makeInfoText( "Unable to find an OrthoMCL group for this protein" );
  }
	$subject{name} ||= 'n/a';
  my $group_link = qq~ <a href="http://orthomcl.org/orthomcl/showRecord.do?name=GroupRecordClasses.GroupRecordClass&group_name=$args{group_id}" target="_OMCL" title="View group $args{group_id} at the OrthoMCL DB website">OG5_126932</a></H4> ~;
#	$add_builds
  return( <<"  END" );
  <script>document.title = 'PeptideAtlas: View Ortholog Group $args{group_id}';</script>
  <div style="margin-left:15px;">
  <h4>Cross-species comparison of OrthoMCL ortholog group $args{group_id} </h4>
  <P class="lg_body_text">
  The table below shows information about homologous(ortholog/paralog) proteins in the $group_link ortholog group.  The groups were computed by <A HREF='http://www.orthomcl.org/' target="_OMCL" title="Visit OrthoMCL DB Site">OrthoMCL version 5</A>, and are based on BLAST homology.  The numbers shown in the columns under each build are the total number of observations of peptides that can be mapped to a given protein, and the total number of distinct peptides seen: total observations ( number distinct peptides ).
  </P>
  </div>
  $table 
	<BR>
	<BR>
  <div style="margin-left:15px;">
  <H4>Homologous Sequence Alignment</H4>
  <P>
  $alignment_overview	
  </P>
  </div>
  $clustal_display
  <BR>
  <INPUT TYPE=HIDDEN NAME=group_id VALUE=$args{group_id}>
  <INPUT TYPE=HIDDEN NAME=entry_accession VALUE=$args{entry_accession}>
 	<INPUT TYPE=SUBMIT VALUE='Align selected sequences'>
 	<INPUT TYPE=SUBMIT VALUE='Restore Original' NAME=restore>
  
	</form>
  </P>
  <form>
    See alignment for a specific OrthoMCL 5 ortholog group: <input type=text name=group_id value="$args{group_id}"></input> <input type=submit VALUE='View Group'> 
  </form>
  <br>
  $alignment_text
	<BR>
  END
}

sub get_default_builds {
  my $accessible_projects = shift;
  my $organism_str = shift;
	my $sql = qq~
	SELECT DAB.atlas_build_id, organism_name
	FROM $TBAT_DEFAULT_ATLAS_BUILD DAB 
  JOIN $TBAT_ATLAS_BUILD AB ON AB.atlas_build_id = DAB.atlas_build_id 
  JOIN $TB_ORGANISM O ON O.organism_id = DAB.organism_id
	WHERE AB.record_status = 'N'
  AND AB.project_id IN ( $accessible_projects )
  AND DAB.organism_id IN ( $organism_str )
  ORDER BY organism_specialized_build ASC, O.organism_id ASC
	~;

  my $sth = $sbeams->get_statement_handle( $sql );
  my %mapping;
  my %organism;
  while ( my @row = $sth->fetchrow_array() ) {
    next if $organism{$row[1]}++; # Just one per organism
    $mapping{$row[0]} = $row[1];
  }
#  die Dumper %mapping;
  return \%mapping;
}

sub get_accessible_builds {
  my $accessible_projects = shift;
  my $organism_str = shift;
  my $sql = qq~
	SELECT AB.atlas_build_id, DAB.organism_id
	FROM $TBAT_DEFAULT_ATLAS_BUILD DAB 
  JOIN $TBAT_ATLAS_BUILD AB ON AB.atlas_build_id = DAB.atlas_build_id 
	WHERE DAB.record_status = 'N'
  AND DAB.organism_id IN ( $organism_str ) 
  AND AB.project_id IN ( $accessible_projects )
  ORDER BY DAB.organism_id ASC, AB.atlas_build_id DESC
	~;

  my $max_builds = 3;
  my $sth = $sbeams->get_statement_handle( $sql );
  my %mapping;
  my %organism;
  while ( my @row = $sth->fetchrow_array() ) {
    next if $organism{$row[1]}++ >= $max_builds; # Just $max_builds per organism
    $mapping{$row[0]} = $row[1];
  }
  return \%mapping;
}


sub get_alignment_text {
  my $content =<<"  END";
  <div class="clear_info_box" style='background: #f1f1f1;' id="help"><pre>
  Alignment was created by the <A HREF='http://www.clustal.org' TARGET='_clustal'>ClustalW</A> program, which is maintained at the Conway Institute UCD Dublin.  
  The alignment considers physical properties of the amino acids in the protein sequence, and the 
  program was invoked using the following command-line:

   clustalw -tree -align -outorder=input -infile=clustal_file

  The consensus 'sequence' uses symbols to represent the level of conservation of amino acids at any given 
  position.  The text below, adapted from the clustal documentation, describes the various symbols used.

    CONSENSUS SYMBOLS:

       An alignment will display by default the following symbols denoting the degree of conservation observed in each column:

      "*" means that the residues or nucleotides in that column are identical in all sequences in the alignment.

      ":" means that conserved substitutions have been observed

      "." means that semi-conserved substitutions are observed. 

      " " means that substitutions are not conservative. 
      </pre></div>
  END
  my @toggle = $sbeams->make_toggle_section( textlink => 1,
                                              imglink => 1,
                                             hidetext => "Hide Description",
                                             showtext => "Show ClustalW Description",
                                              visible => 1,
                                              sticky  => 1,
                                                name  => 'viewOrthologs_description',
					     content => $content
  );
  return " $toggle[1] <BR> $toggle[0]";

}

sub get_group_search_section {
  my %args = @_;
  return '' unless $args{group_id};
  my $checked = ( $args{show_all} ) ? 'checked' : '';
  my $help = $args{help} || '';
  my $group_html = qq~
  <FORM NAME=group_search METHOD=POST>
    <TABLE NOBR><TR>
    <TD>Group Name:</TD><TD><INPUT TYPE=text NAME=group_id VALUE=$args{group_id}></INPUT></TD>
    <TD>Show All:</TD><TD><INPUT TYPE=checkbox NAME=show_all $checked></INPUT></TD>
 	  <TD><INPUT TYPE=SUBMIT VALUE='View Ortholog Group' NAME=search_groups></TD>
 	  <TD>$help</TD>
    </TR></TABLE NOBR>
  ~;
  return $group_html;
}

sub get_add_builds_section {
  my %args = @_;
	my $checklist = $sbeamsMOD->get_atlas_checklist( %args, js_call => 'toggle_view' );
	my $js = qq~
  <SCRIPT LANGUAGE=javascript>
	function toggle_view (div_id) {
		var curr_col = document.getElementsByName(div_id);

    for (var i=0; i < curr_col.length; i++) {
      var current_appearance = curr_col[i].className;

      var new_appearance = 'tbl_hidden';
      if ( current_appearance == 'tbl_hidden' ) {
        new_appearance = 'tbl_visible';
      }

      // If hidden set visible, and vice versa
      if ( current_appearance == 'tbl_hidden' ) {
        curr_col[i].className = 'tbl_visible';
      } else {
        curr_col[i].className = 'tbl_hidden';
      }
		}
	}
	</SCRIPT>
	~;

  my $content =<<"  END";
	  $js
 	  <P>
	   <DIV class=clear_info_box ID=addbuilds>
		   <PRE>
			 &nbsp;&nbsp;$checklist
		   </PRE>
     </DIV>
    </P>
  END
  my @toggle = $sbeams->make_toggle_section( textlink => 1,
	                                         imglink => 1,
                                             hidetext => "Hide Builds",
                                             showtext => "Add Builds",
                                              visible => 0,
                                              sticky  => 1,
                                                name  => 'viewOrthologs_addbuilds',
				                                      content => $content
																					);
  return "$toggle[1] <BR> $toggle[0]";

}




sub get_clustal_display {

# Passed named args
# alignments => $clustal,            # ref to array of arrayrefs of acc, seq
# bgcolor => \%bgcolor,              # ref to hash of acc => bgcolor for seq
# acc_color => \%acc_color,          # ref to hash of acc => bgcolor for acc
# highlight_builds => $highlight     # ref to hash of build_ids to color with 
# build_seqs => \%build_seqs         # ref to hash of per build seq attrs 
# acc2bioseq => \%build_seqs         # ref to hash of per build seq attrs 

# $build_seqs{$row[3]}->{$row[2]}->{coverage}->{$covered_posn}++;
	my %args = @_;

	my $display = qq~
	<DIV STYLE="width:calc(100% - 20px); overflow-x: scroll; scrollbar-arrow-color: blue; scrollbar- face-color: #e7e7e7; scrollbar-3dlight-color: #a0a0a0; scrollbar-darkshadow-color: #888888">
	<TABLE BORDER=0 CELLPADDNG=3>
  <form>
	~;
	for my $seq ( @{$args{alignments}} ) {
#		$log->debug( "After passing we have $seq->[0] and $seq->[1]!" );
		my $sequence = $seq->[1];
		if ( $seq->[0] eq 'consensus'  ) {
#			$log->debug( "Consensus!@!!!!!" );
		  $sequence =~ s/ /&nbsp;/g 
		} else {
#			$log->debug( "$seq->[0] isn't consensus, commence to highlighting $sequence" );
			$sequence = highlight_sites( seq => $sequence, 
                                   acc => $seq->[0], 
			                             %args
																 );
		}
		my $checkbox = '';
    unless ( $seq->[0] eq 'consensus' ) {
			my $acc_str = join( ',', sort { $a <=> $b } ( @{$args{acc2bioseq}->{$seq->[0]}} ) );
      $checkbox = "<INPUT ID=bioseq_id TYPE=checkbox CHECKED NAME=bioseq_id VALUE='$acc_str'></INPUT>";
    }
#    $build_seqs{$row[3]}->{$bioseq_id2name{$row[2]}}->{bioseq} = $row[2];


		$display .= "<TR><TD>$checkbox</TD><TD BGCOLOR=$args{acc_color}->{$seq->[0]} ALIGN=right class=sequence_font>$seq->[0]:</TD><TD NOWRAP=1 class=sequence_font BGCOLOR=$args{bgcolor}->{$seq->[0]}>$sequence</TD></TR>\n";
	}
	my $toggle_checkbox = $sbeams->get_checkbox_toggle( controller_name => 'alignment_chk',
	                                                      checkbox_name => 'bioseq_id' );

  my $toggle_text = $sbeams->makeInfoText( 'Toggle all checkboxes' );
	$display .= "<TR><TD>$toggle_checkbox</TD><TD ALIGN=left>$toggle_text </TD><TD></TD></TR>\n";
	$display .= "</TABLE>\n</DIV>\n";
	return $display;
}

sub highlight_sites {



# highlight_builds => $highlight     # ref to hash of build_ids to color with 
# build_seqs => \%build_seqs         # ref to hash of per build seq attrs 
# seq => $sequence                   # sequence to be processed, a la --A--AB-
# acc => $accession                  # accession of seq to be processed

  my %args = @_;

  my $coverage;
	for my $build ( keys( %{$args{highlight_builds}} ) ) {
		if ( $args{build_seqs}->{$build} && $args{build_seqs}->{$build}->{$args{acc}} ) {
			$coverage =  $args{build_seqs}->{$build}->{$args{acc}}->{coverage};
			last;
		}
	}
	return $args{seq} unless $coverage;

  my @aa = split( '', $args{seq} );
  my $return_seq = '';
  my $cnt = 0;
	my $in_coverage = 0;
	my $span_closed = 1;
  for my $aa ( @aa ) {
    if ( $aa eq '-' ) {
			if ( $in_coverage && !$span_closed ) {
				$return_seq .= "</span>$aa";
				$span_closed++;
			} else {
				$return_seq .= $aa;
			}
		} else { # it is an amino acid
			if ( $coverage->{$cnt} ) {
				if ( $in_coverage ) { # already in
					if ( $span_closed ) {  # Must have been jumping a --- gap
					  $span_closed = 0;
				    $return_seq .= "<span class=obs_seq_font>$aa";
					} else {
				    $return_seq .= $aa;
					}
				} else {
					$in_coverage++;
					$span_closed = 0;
				  $return_seq .= "<span class=obs_seq_font>$aa";
				}
			} else { # posn not covered!
				if ( $in_coverage ) { # were in, close now
				  $return_seq .= "</span>$aa";
					$in_coverage = 0;
					$span_closed++;
				} else {
				  $return_seq .= $aa;
				}
			}
		  $cnt++;
		}
	}
	if ( $in_coverage && !$span_closed ) {
		$return_seq .= '</span>';
	}
	return $return_seq;
}

__DATA__