package SGX::TFSDisplay;

use strict;
use warnings;

use base qw/SGX::Strategy::Base/;

require Math::BigInt;
require Math::BigFloat;
use JSON qw/decode_json/;
use SGX::Abstract::Exception ();
use SGX::Util qw/car count_bits before_dot/;
use List::Util qw[min max];
require SGX::DBHelper;

#===  FUNCTION  ================================================================
#         NAME:  get_tfs
#      PURPOSE:  Get total flagsum (TFS), which is a sum of absolute flagsum and
#                directional flagsum.
#   PARAMETERS:  ????
#      RETURNS:  ????
#  DESCRIPTION:  ????
#       THROWS:  no exceptions
#     COMMENTS:  none
#     SEE ALSO:  n/a
#===============================================================================
sub get_tfs {
    my ( $abs_fs, $dir_fs, $num ) = @_;
    return sprintf(
        "$abs_fs.%0${num}s",
        Math::BigInt->badd(
            substr( unpack( 'b32', pack( 'V', $abs_fs ) ), 0, $num ),
            substr( unpack( 'b32', pack( 'V', $dir_fs ) ), 0, $num )
        )
    );
}

#===  FUNCTION  ================================================================
#         NAME:  breakdown_tfs
#      PURPOSE:  Get an array with a breakdown of the TFS for each experiment.
#   PARAMETERS:  ????
#      RETURNS:  ????
#  DESCRIPTION:  ????
#       THROWS:  no exceptions
#     COMMENTS:  none
#     SEE ALSO:  n/a
#===============================================================================
sub breakdown_tfs {
	my ( $abs_fs, $dir_fs, $num ) = @_;
	
    my $TFS_sum= 
	sprintf "%0${num}s",
	Math::BigInt->badd(
	substr( unpack( 'b32', pack( 'V', $abs_fs) ), 0, $num),
    substr( unpack( 'b32', pack( 'V', $dir_fs ) ), 0, $num )
	);
	
	
	my @brokendown_tfs;
	#push @brokendown_tfs,$TFS_sum;
	
	my @TFS_sum_array = split(//, $TFS_sum);
	for( my $ec=0; $ec<$num;$ec++){
		#push @brokendown_tfs," ";
		#push @brokendown_tfs,$ec;
		
		my $powerof2_ec= 
		($TFS_sum_array[$ec] == 0)
		? 0
		:2**$ec;
		
		my $left_tfs_length=$ec;
		my $left_tfs = '0' x ${left_tfs_length};
		
		my $right_tfs_len=$num - $ec-1;
		my $right_tfs = '0' x ${right_tfs_len};
		#it turns out I had things backwards 
		my $my_new_tfs= sprintf "%s.%s%s%s",$powerof2_ec,$left_tfs,$TFS_sum_array[$ec],$right_tfs; 
		#push @brokendown_tfs,substr( unpack( 'b32', pack( 'V', $ec) ),0,$eid_count);
		#push @brokendown_tfs,$TFS_sum_array[$ec];
		push @brokendown_tfs,$my_new_tfs;   
		
	}
	#debugging 
	#my $joint_string=join " - ", @brokendown_tfs;
	#printf $joint_string;
	
	return @brokendown_tfs;	
}

#===  CLASS METHOD  ============================================================
#        CLASS:  TFSDisplay
#       METHOD:  init
#   PARAMETERS:  ????
#      RETURNS:  ????
#  DESCRIPTION:
#       THROWS:  no exceptions
#     COMMENTS:  none
#     SEE ALSO:  n/a
#===============================================================================
sub init {
    my $self = shift;
    $self->SUPER::init();

    $self->loadDataFromSubmission();    # sets _format attribute

    $self->set_attributes(
        _title    => $self->get_subset_name(),
        _dbHelper => SGX::DBHelper->new( delegate => $self )
    );

    # find out what the current project is set to
    $self->{_dbHelper}->getSessionOverrideCGI();

    # warning: the line below affects which hook gets called
    $self->set_action( $self->{_format} || '' );

    $self->register_actions(
        CSV  => { head => 'CSV_head',     body => 'CSV_body' },
        HTML => { head => 'default_head', body => 'default_body' }
    );

    return $self;
}

#===  CLASS METHOD  ============================================================
#        CLASS:  TFSDisplay
#       METHOD:  CSV_head
#   PARAMETERS:  ????
#      RETURNS:  ????
#  DESCRIPTION:
#       THROWS:  no exceptions
#     COMMENTS:  none
#     SEE ALSO:  n/a
#===============================================================================
sub CSV_head {
    my $self = shift;
    my ( $s, $js_src_yui, $js_src_code ) =
      @$self{qw{_UserSession _js_src_yui _js_src_code}};

    #Clear our headers so all we get back is the CSV file.
    print $self->{_cgi}->header(
        -type       => 'text/csv',
        -attachment => 'results.csv',
        -cookie     => $s->cookie_array()
    );

    $s->commit();
    $self->getPlatformData();

    $self->loadDataCSV();
    $self->displayDataCSV();
    exit;
}

#===  CLASS METHOD  ============================================================
#        CLASS:  TFSDisplay
#       METHOD:  default_head
#   PARAMETERS:  ????
#      RETURNS:  ????
#  DESCRIPTION:  Override CRUD default_head
#       THROWS:  no exceptions
#     COMMENTS:  none
#     SEE ALSO:  n/a
#===============================================================================
sub default_head {
    my $self = shift;
    my ( $s, $js_src_yui, $js_src_code ) =
      @$self{qw{_UserSession _js_src_yui _js_src_code}};

    push @{ $self->{_css_src_yui} },
      (
        'paginator/assets/skins/sam/paginator.css',
        'datatable/assets/skins/sam/datatable.css'
      );
    push @$js_src_yui,
      (
        'yahoo-dom-event/yahoo-dom-event.js', 'element/element-min.js',
        'paginator/paginator-min.js',         'datasource/datasource-min.js',
        'datatable/datatable-min.js',         'yahoo/yahoo.js'
      );

    $self->loadDataHTML();
    my $jsresults = $self->displayDataHTML();

    push @$js_src_code,
      ( { -code => $jsresults }, { -src => 'TFSDisplay.js' } );
    return 1;
}

#===  CLASS METHOD  ============================================================
#        CLASS:  TFSDisplay
#       METHOD:  get_subset_name
#   PARAMETERS:  ????
#      RETURNS:  ????
#  DESCRIPTION:
#       THROWS:  no exceptions
#     COMMENTS:  none
#     SEE ALSO:  n/a
#===============================================================================
sub get_subset_name {
    my $self = shift;
    my $fs   = $self->{_fs};
    return (
        defined($fs) ? "Subset $fs"
        : (
            $self->{_allProbes} ? 'Subset: all probes'
            : 'Subset: all significant probes'
        )
    );
}

#===  CLASS METHOD  ============================================================
#        CLASS:  TFSDisplay
#       METHOD:  default_body
#   PARAMETERS:  ????
#      RETURNS:  ????
#  DESCRIPTION:
#       THROWS:  no exceptions
#     COMMENTS:  none
#     SEE ALSO:  n/a
#===============================================================================
sub default_body {
    my $self = shift;
    my $q    = $self->{_cgi};

    return $q->h2( { -id => 'summary_caption' }, $self->get_subset_name() ),
      $q->div( { -id => 'summary_table', -class => 'table_cont' }, '' ),
      $q->h2( { -id => 'tfs_caption' }, '' ),
      $q->div( $q->a( { -id => 'tfs_astext' }, 'View as plain text' ) ),
      $q->div( { -id => 'tfs_table', -class => 'table_cont' } );
}

#===  CLASS METHOD  ============================================================
#        CLASS:  SGX::TFSDisplay
#       METHOD:  loadDataFromSubmission
#   PARAMETERS:  ????
#      RETURNS:  ????
#  DESCRIPTION:  LOAD DATA FROM FORM
#       THROWS:  no exceptions
#     COMMENTS:  none
#     SEE ALSO:  n/a
#===============================================================================
sub loadDataFromSubmission {
    my $self = shift;
    my $q    = $self->{_cgi};

    $self->{_xExpList} =
      decode_json( car( $q->param('user_selection') ) || '[]' );
    $self->{_allProbes}    = $q->param('includeAllProbes') || '';
    $self->{_searchFilter} = $q->param('searchFilter')     || '';

    $self->{_opts} = $q->param('opts') || '0';

    # The $self->{_fs} parameter is the flagsum for which we filter data
    my $fs = car $q->param('selectedFS');
    $self->{_fs} = ( defined($fs) && $fs ne '' ) ? $fs : undef;
    $self->{_expected} = decode_json( car( $q->param('selectedExp') ) || '{}' );
    $self->{_format} = car $q->param('get');

    return 1;
}

#===  CLASS METHOD  ============================================================
#        CLASS:  SGX::TFSDisplay
#       METHOD:  loadDataHTML
#   PARAMETERS:  ????
#      RETURNS:  ????
#  DESCRIPTION:  LOAD TFS DATA
#       THROWS:  no exceptions
#     COMMENTS:  This code is very old... Refactoring it would be desirable.
#     SEE ALSO:  n/a
#===============================================================================
sub loadDataHTML {
    my $self = shift;

    # index of the column that is the beginning of the "numeric" half of the
    # table (required for table sorting)
    $self->{_numStart} = 5;

    my $experiment_rows = $self->{_xExpList};
    return if !@$experiment_rows;

    # Build the SQL query that does the TFS calculation
    my $having =
      ( defined( $self->{_fs} ) ) ? "HAVING abs_fs=$self->{_fs}" : '';

    #If we got a list to filter on, build the string.
    #
    # :TODO:07/07/2011 12:38:40:es: SQL injection risk: no validation done
    # one _searchFilter before being inserted into WHERE statement.
    # Fix this by using prepare/execute with placeholders.
    my $probeListQuery =
      ( defined( $self->{_searchFilter} ) && $self->{_searchFilter} ne '' )
      ? " WHERE rid IN (" . $self->{_searchFilter} . ") "
      : '';

    my @query_proj;
    my @query_join;
    my @query_body;

    my $allProbes = $self->{_allProbes};
    for ( my $i = 0 ; $i < @$experiment_rows ; $i++ ) {
        my $row = $experiment_rows->[$i];

        my $eid       = $row->{eid};
        my $fc        = $row->{fchange};
        my $pval      = $row->{pval};
        my $pValClass = $row->{pValClass};
        my $pval_sql  = "pvalue$pValClass";
        my $reverse   = $row->{reverse};

        my $abs_flag = 1 << $i;
        my $dir_flag = $reverse ? "$abs_flag,0" : "0,$abs_flag";

        my $table = "tmp_$i";    #"m${eid}_${pValClass}";
        push @query_proj,
          (
            $reverse
            ? "1/$table.ratio AS '$eid: Ratio', $table.$pval_sql AS '$eid: P-$pValClass'"
            : "$table.ratio AS '$eid: Ratio', $table.$pval_sql AS '$eid: P-$pValClass'"
          );

        if ( $self->{_opts} ne 'basic' ) {
            push @query_proj,
              (
                $reverse
                ? "-$table.foldchange AS '$eid: FC'"
                : "$table.foldchange AS '$eid: FC'"
              );
            push @query_proj,
              (
                $reverse
                ? "IFNULL($table.intensity2,0) AS '$eid: Intensity-1', IFNULL($table.intensity1,0) AS '$eid: Intensity-2'"
                : "IFNULL($table.intensity1,0) AS '$eid: Intensity-1', IFNULL($table.intensity2,0) AS '$eid: Intensity-2'"
              );
            push @query_proj, "$table.$pval_sql AS '$eid: P-$pValClass'";
        }

        push @query_join,
          "LEFT JOIN response $table ON $table.rid=d2.rid AND $table.eid=$eid";

        #This is part of the query when we are including all probes.
        push @query_body, ($allProbes)
          ? <<"END_yes_allProbes"
SELECT
    rid, 
    IF($pval_sql < $pval AND ABS(foldchange) > $fc, $abs_flag, 0) AS abs_flag,
    IF($pval_sql < $pval AND ABS(foldchange) > $fc, 
       IF(foldchange > 0, $dir_flag), 
       0
    ) AS dir_flag
FROM response
WHERE eid=$eid
END_yes_allProbes
          : <<"END_no_allProbes";
SELECT
    rid, 
    $abs_flag AS abs_flag,
    IF(foldchange > 0, $dir_flag) AS dir_flag
FROM response 
WHERE eid = $eid 
  AND $pval_sql < $pval 
  AND ABS(foldchange) > $fc
END_no_allProbes
    }

    # build record names (sample2 / sample 1, etc)
    $self->build_headerRecords();

    if ( $self->{_opts} eq 'annot' ) {
        $self->{_numStart} += 3;
        unshift @query_proj,
          (
            qq{probe.probe_sequence AS 'Probe Sequence'},
qq{GROUP_CONCAT(DISTINCT IF(gene.gname='', NULL, gene.gname) SEPARATOR '; ') AS 'Gene Description'}
          );
    }

    my $d1SubQuery   = join( ' UNION ALL ', @query_body );
    my $selectSQL    = join( ',',           @query_proj );
    my $predicateSQL = join( "\n",          @query_join );

    # pad TFS decimal portion with the correct number of zeroes
    my $query = <<"END_query";
SELECT
    abs_fs, 
    dir_fs, 
    probe.reporter AS 'Probe ID',
    GROUP_CONCAT(DISTINCT if(gene.gtype=0, gene.gsymbol, NULL) separator ' ') AS 'Accession No.',
    GROUP_CONCAT(DISTINCT if(gene.gtype=1, gene.gsymbol, NULL) separator ' ') AS 'Gene Symbol',
    $selectSQL
FROM (
    SELECT 
        rid, 
        BIT_OR(abs_flag) AS abs_fs, 
        BIT_OR(dir_flag) AS dir_fs 
    FROM ($d1SubQuery) AS d1 
    $probeListQuery
    GROUP BY rid $having
) AS d2
$predicateSQL
LEFT JOIN probe     ON d2.rid        = probe.rid
LEFT JOIN ProbeGene ON d2.rid        = ProbeGene.rid
LEFT JOIN gene      ON ProbeGene.gid = gene.gid
LEFT JOIN (select platform.pid, species.sname FROM platform LEFT JOIN species USING(sid)) AS platform_species USING(pid)
GROUP BY probe.rid
ORDER BY abs_fs DESC
END_query

    my $dbh = $self->{_dbh};
    $self->{_Records}     = $dbh->prepare($query);
    $self->{_RowCountAll} = $self->{_Records}->execute;

    return 1;
}

#===  CLASS METHOD  ============================================================
#        CLASS:  SGX::TFSDisplay
#       METHOD:  getPlatformData
#   PARAMETERS:  ????
#      RETURNS:  ????
#  DESCRIPTION:  LOAD PLATFORM DATA FOR CSV OUTPUT
#       THROWS:  no exceptions
#     COMMENTS:  none
#     SEE ALSO:  n/a
#===============================================================================
sub getPlatformData {
    my $self      = shift;
    my $dbh       = $self->{_dbh};
    my $data_rows = $self->{_xExpList};

    my @eidList = map { $_->{eid} } @$data_rows;
    my $placeholders =
      (@$data_rows)
      ? join( ',', map { '?' } @eidList )
      : 'NULL';

  # :TODO:07/25/2011 02:39:05:es: Since experiments from different platforms
  # cannot be compared using Compare Experiments, this query is a little bit too
  # fat for what we need.
    my $singleItemQuery = <<"END_LoadQuery";
SELECT
    platform.pname            AS 'Platform',
    species.sname             AS 'Species',
    probes.id_count           AS 'Probe Count',
    probes.sequence_count     AS 'Sequences Loaded'
FROM platform
LEFT JOIN species USING(sid)
LEFT JOIN (
    SELECT
        pid,
        COUNT(probe.rid) AS id_count,
        COUNT(probe_sequence) AS sequence_count
    FROM probe
    WHERE probe.pid IN (SELECT DISTINCT pid FROM experiment WHERE eid IN($placeholders))
    GROUP BY pid
) AS probes USING(pid)
WHERE pid IN (SELECT DISTINCT pid FROM experiment WHERE eid IN($placeholders))
GROUP BY platform.pid
END_LoadQuery

    my $sth = $dbh->prepare($singleItemQuery);
    my $rc = $sth->execute( @eidList, @eidList );
    $self->{_FieldNames}   = $sth->{NAME};
    $self->{_DataPlatform} = $sth->fetchall_arrayref;
    $sth->finish;

    return 1;
}

#===  CLASS METHOD  ============================================================
#        CLASS:  SGX::TFSDisplay
#       METHOD:  build_headerRecords
#   PARAMETERS:  ????
#      RETURNS:  ????
#  DESCRIPTION:
#       THROWS:  no exceptions
#     COMMENTS:  none
#     SEE ALSO:  n/a
#===============================================================================
sub build_headerRecords {
    my $self = shift;
    $self->{_headerRecords} = +{
        map {
            $_->{eid} => +{
                study_desc  => $_->{study_desc},
                exp_info    => $_->{exp_info},
                exp_samples => (
                    $_->{reverse}
                    ? ( $_->{sample1} . '/' . $_->{sample2} )
                    : ( $_->{sample2} . '/' . $_->{sample1} )
                )
            };
          } @{ $self->{_xExpList} }
    };
    return 1;
}

#===  CLASS METHOD  ============================================================
#        CLASS:  SGX::TFSDisplay
#       METHOD:  loadDataCSV
#   PARAMETERS:  ????
#      RETURNS:  ????
#  DESCRIPTION:  LOAD ALL DATA FOR CSV OUTPUT
#       THROWS:  no exceptions
#     COMMENTS:  This code is very old... Refactoring it would be desirable.
#     SEE ALSO:  n/a
#===============================================================================
sub loadDataCSV {
    my $self = shift;

    my $experiment_rows = $self->{_xExpList};
    return if !@$experiment_rows;

    #This is the different parts of the experiment and titles query.
    my @query_body;
    my @query_proj;
    my @query_join;

    #If we got a list to filter on, build the string.
    my $probeListQuery =
      ( defined( $self->{_searchFilter} ) && $self->{_searchFilter} ne '' )
      ? " WHERE rid IN (" . $self->{_searchFilter} . ") "
      : '';

    for ( my $i = 0 ; $i < @$experiment_rows ; $i++ ) {
        my $row = $experiment_rows->[$i];

        my $eid       = $row->{eid};
        my $fc        = $row->{fchange};
        my $pval      = $row->{pval};
        my $reverse   = $row->{reverse};
        my $pValClass = $row->{pValClass};
        my $pval_sql  = "pvalue$pValClass";

        my $abs_flag = 1 << $i;
        my $dir_flag = $reverse ? "$abs_flag,0" : "0,$abs_flag";

        my $table = "tmp_$i";    #"m${eid}_${pValClass}";
        push @query_proj,
          (
            $reverse
            ? "1/$table.ratio AS '$eid: Ratio'"
            : "$table.ratio AS '$eid: Ratio'"
          );

        push @query_proj,
          (
            $reverse
            ? "-$table.foldchange AS '$eid: FC'"
            : "$table.foldchange AS '$eid: FC'"
          );

        push @query_proj,
          (
            $reverse
            ? "IFNULL($table.intensity2,0) AS '$eid: Intensity-1', IFNULL($table.intensity1,0) AS '$eid: Intensity-2'"
            : "IFNULL($table.intensity1,0) AS '$eid: Intensity-1', IFNULL($table.intensity2,0) AS '$eid: Intensity-2'"
          );

        push @query_proj, "$table.$pval_sql AS '$eid: P-$pValClass'";

        push @query_join,
          "LEFT JOIN response $table ON $table.rid=d2.rid AND $table.eid=$eid";

        push @query_body, ( $self->{_allProbes} )
          ? <<"END_yes_allProbesCSV"
SELECT
    rid,
    IF($pval_sql < $pval AND ABS(foldchange) > $fc, $abs_flag, 0) AS abs_flag,
    IF($pval_sql < $pval AND ABS(foldchange) > $fc, IF(foldchange > 0, $dir_flag), 0) AS dir_flag
FROM response
WHERE eid=$eid
END_yes_allProbesCSV
          : <<"END_no_allProbesCSV";
SELECT
    rid, 
    $abs_flag AS abs_flag,
    IF(foldchange > 0, $dir_flag) AS dir_flag
FROM response 
WHERE eid = $eid 
  AND $pval_sql < $pval 
  AND ABS(foldchange) > $fc
END_no_allProbesCSV
    }

    #This is the having part of the data query.
    my $having =
      ( defined( $self->{_fs} ) && $self->{_fs} )
      ? "HAVING abs_fs=$self->{_fs}"
      : '';

    my $d1SubQuery   = join( ' UNION ALL ', @query_body );
    my $selectSQL    = join( ',',           @query_proj );
    my $predicateSQL = join( "\n",          @query_join );

    # pad TFS decimal portion with the correct number of zeroes
    my $query = <<"END_queryCSV";
SELECT
    abs_fs, 
    dir_fs, 
    probe.reporter       AS 'Probe ID', 
    probe.probe_sequence AS 'Comment',
    probe.probe_comment  AS 'Probe Note',
    GROUP_CONCAT(DISTINCT format_locus(locus.chr, locus.zinterval) separator ' ') AS 'Mapping Location(s)',
    GROUP_CONCAT(DISTINCT IF(gene.gtype=0, gene.gsymbol, NULL) separator ' ') AS 'Accession No.',
    GROUP_CONCAT(DISTINCT IF(gene.gtype=1, gene.gsymbol, NULL) separator ' ') AS 'Gene Symbol',
    GROUP_CONCAT(DISTINCT CONCAT(gene.gname, IF(ISNULL(gene.gdesc), '', CONCAT(', ', gene.gdesc))) separator '; ') AS 'Gene Name/Desc.',
    GROUP_CONCAT(DISTINCT CONCAT(go_term.go_name, ' (GO:', go_term.go_acc, ')' ) ORDER BY go_term.go_acc SEPARATOR '; ') AS 'GO terms',
    $selectSQL
FROM (
    SELECT
       rid, 
       BIT_OR(abs_flag) AS abs_fs, 
       BIT_OR(dir_flag) AS dir_fs 
    FROM ($d1SubQuery) AS d1 
    $probeListQuery
    GROUP BY rid $having
) AS d2
$predicateSQL
LEFT JOIN probe     ON d2.rid = probe.rid
LEFT JOIN ProbeGene ON d2.rid = ProbeGene.rid
LEFT JOIN locus     ON d2.rid = locus.rid
LEFT JOIN gene      USING(gid)
LEFT JOIN GeneGO    USING(gid) 
LEFT JOIN go_term   USING(go_acc)
LEFT JOIN (select platform.pid, species.sname FROM platform LEFT JOIN species USING(sid)) AS platform_species USING(pid)
GROUP BY probe.rid
ORDER BY abs_fs DESC
END_queryCSV

    # build record names (sample2 / sample 1, etc)
    $self->build_headerRecords();

    #Run the query for the actual data records.
    my $dbh = $self->{_dbh};
    $self->{_Records}     = $dbh->prepare($query);
    $self->{_RowCountAll} = $self->{_Records}->execute;

    return 1;
}

#===  CLASS METHOD  ============================================================
#        CLASS:  SGX::TFSDisplay
#       METHOD:  displayDataCSV
#   PARAMETERS:  ????
#      RETURNS:  ????
#  DESCRIPTION:  DISPLAY PLATFORM,EXPERIMENT INFO, AND EXPERIMENT DATA TO A CSV
#  FILE
#       THROWS:  no exceptions
#     COMMENTS:  none
#     SEE ALSO:  n/a
#===============================================================================
sub displayDataCSV {
    my $self      = shift;
    my $data_rows = $self->{_xExpList};

    require SGX::CSV;
    my $print = SGX::CSV::bind_handle( \*STDOUT );

    my $sth_records = $self->{_Records};

    # get name array from statement handle
    my $record_names = $sth_records->{NAME};
    shift @$record_names;
    shift @$record_names;
    unshift @$record_names, 'TFS';
	

	# Report Header
    
	#modification by GB: we want the report header to use fewer rows, so some of the bottom rows will become columns on the top rows
	
	#since the 2 parts at the top will have varying lengths, we need to pad the shortest with empty lines, to make things match
	
	
	my @left_fields;
	
	## new right fields 
		
	my @new_right_fields;
	push @new_right_fields, ['Compare Experiments Report', scalar localtime(),(undef) x5 ];
    #$print->( [ 'Generated By',               $self->{_UserFullName} ] );
    #$print->( [ 'Working Project',            $self->{_WorkingProjectName} ] );
    #$print->();

	    # Print Platform info.
    push @new_right_fields, $self->{_FieldNames} ;
    push @new_right_fields,($_) for @{ $self->{_DataPlatform} };
	
	
	################## old right fields
	# Print Platform info.
	
 
    # Print Experiment info header.
    push @new_right_fields,
        [
			#(undef) x 2,
            'Exp. no.',
            '|FC| >',
            'P-value used',
            'P <',
            #'Signif. in',
            'Study',
            'Exp. info',
            'Exp. samples'
        ];
	
	## test printing those 2 sections, just to see if my use of push is working. The version with the magic character worked
    my $eid_count = @{ $self->{_xExpList} };
	###### data by probe starts here
    # The line with the experiment name and eid above the data columns has 6
    # fields: TFS, Probe ID, Accession No., Gene Symbol, Probe Sequence, Gene
    # Name
    my @experimentNameHeader = (undef) x ($eid_count+9); #this is leaving 9 empty cells  = (undef) x 9; #this is leaving 9 empty cells 
	my @brokendownTFSHeader;
    # Print Experiment info.
    my $headerRecords = $self->{_headerRecords};
    my $currFS        = $self->{_fs};

    my $signExpCount = 0;
    for ( my $i = 0 ; $i < @$data_rows ; $i++ ) {
        my $row      = $data_rows->[$i];
        my $eid      = $row->{eid};
        my $eid_node = $headerRecords->{$eid};

        # Form the line that displays experiment names above data columns.
        # Offsetting by 4 fields: FC, Intensity-1, Intensity-2, P-value
        push @experimentNameHeader,
          $eid . ':' . $eid_node->{exp_samples},
          (undef) x 4;

		push @brokendownTFSHeader,$eid . ':' . "FS";
		  
        my $signCell = '';
        if ( defined $currFS ) {

            # Test for bit presence, print out 'Yes' if present, 'No' if absent
            if ( 1 << $i & $currFS ) {

                # significant experiment
                $signCell = 'Y';
                $signExpCount++;
            }
            else {

                # not significant experiment
                $signCell = 'N';
            }
        }
        my $currLine = [
            $eid,                  $row->{fchange},
            $row->{pValClass},     $row->{pval},
			#$signCell,
            $eid_node->{study_desc},
            $eid_node->{exp_info}, $eid_node->{exp_samples},
        ];
		push @new_right_fields,$currLine;
        #$print->($currLine);
    }
	push @$record_names,@brokendownTFSHeader;
    #push @right_fields,[""];
	#push @right_fields, ["end of right fields"];
	
	my @TFS_fields;
		
    # Calculate TFS along with distinct counts

    my %TFSCounts;

    my $data_array = $sth_records->fetchall_arrayref;
    $sth_records->finish;

	#$print->(); ## yes, it does

	#$print->($joint_string) ;
	
    foreach (@$data_array) {

        # for each row
		my $val1= shift @$_;
		my $val2= shift @$_;
		
        my $currentTFS = get_tfs( $val1, $val2, $eid_count );
		my @brokendown_tfs= breakdown_tfs( $val1, $val2, $eid_count );

        unshift @$_, $currentTFS;
        push @$_, @brokendown_tfs;
		
		$TFSCounts{$currentTFS} =
          ( defined $TFSCounts{$currentTFS} )
          ? 1 + $TFSCounts{$currentTFS}
          : 1;
    }

    # print comparison stats
    Math::BigFloat->accuracy(3);
    my $observed = scalar(@$data_array);
    my $expected = $self->{_expected};

	#push @TFS_fields,[(undef) x 4];	#removed empty space at the top
	#push @TFS_fields,['TFS Summary',(undef) x 3]; #removed the header "TFS Summary"
	#push @TFS_fields,[ 'TFS', 'Probe Count' #,
	#,'Log Odds Over Expected' 
	#(undef) x 2
	#];
	push @TFS_fields,
	[
		undef,
		$observed #,
		# ,
		# # log_odds
		# eval {
			# Math::BigFloat->new( log( $observed / $expected->{null} ) );
		# }
		#(undef) x 2
	];
    push @TFS_fields,
        [
            $_,
            $TFSCounts{$_}#,
			#,
			# log_odds
            # eval {
                # Math::BigFloat->new(
                    # log(
                        # $TFSCounts{$_} /
                          # $expected->{ ( before_dot($_) ) } *
                          # ( 1 << count_bits( before_dot($_) ) + 0.0 )
                    # )
                # );
            # }
			#(undef) x 2
        ]
      for sort { $TFSCounts{$b} <=> $TFSCounts{$a} }
      keys %TFSCounts;
    #$print->();

	my $length_of_left_side = scalar @TFS_fields;
	my $length_of_right_side = scalar @new_right_fields;
	
	# print $length_of_left_side;
	# print "\n";
	# print $length_of_right_side;
	# print "\n";
	
	## 13 is hardcoded, because it's the length we've chosen as the max for the spreadsheet
	my $TFS_max=min($length_of_left_side,8);
	my $row_max=max(5,$length_of_right_side,$TFS_max);
	# print $row_max;
	# if TFS is longer than 13, then split TFS into into chunks
	
	## instead of printing to the file, print to a variable
	my @right_fields_TFS;
	my @right_fields_TFS_w_header;
	my $right_field_length;
	
	if($length_of_left_side > $row_max){
		my $TFS_length=scalar @TFS_fields;
		
		#cap length of TFS patterns to 100
		my $TFS_cap = min(100, $TFS_length);
		#print $TFS_cap;
		
		my $chunk_size=$row_max-1; ## number of lines that will be added

		my $TFS_iterations=POSIX::ceil(($TFS_cap / $chunk_size) );
		
		# printf "TFS iterations\n";
		# printf $TFS_iterations;
		# printf "\n";

		# printf "chunk size\n";		
		# printf $chunk_size;
		# printf "\n";
		
		my @right_TFS_header;
		
		for(my $c_TFS_iteration=0;$c_TFS_iteration<$TFS_iterations;$c_TFS_iteration++){
			push @right_TFS_header, 'TFS', 'Probe Count',(undef) x1;
		}
		
			
		for(my $c_row=0;$c_row<$chunk_size;$c_row++){
			my @new_row;
			for(my $c_TFS_iteration=0;$c_TFS_iteration<=$TFS_iterations;$c_TFS_iteration++){
				my $c_index=($c_TFS_iteration*$chunk_size)+$c_row;
				# print $c_index;
				# print "\n";
				if ($c_index<$TFS_cap){
					push @new_row, @{$TFS_fields[$c_index]},(undef) x1;
				}
			}
			push @right_fields_TFS,[@new_row];
		}
		# my $TFS_iterations=ceil(($remaining_TFS / $chunk_size) + 0.5);
		#$print->([@right_TFS_header]);
		
		push @right_fields_TFS_w_header,[@right_TFS_header];

		# printf "concatenated space and header";
		
		$right_field_length=scalar @right_fields_TFS;
		
		# printf "right field length";
		# printf $right_field_length;
		for (my $tfs_i=0;$tfs_i<$right_field_length;$tfs_i++){

			#$print->([@{$right_fields_TFS[$tfs_i]}]);
			push @right_fields_TFS_w_header,[@{$right_fields_TFS[$tfs_i]}];
		}
		# printf "added right field TFS to right_fields_TFS_w_header";

	}
	else{
		push @right_fields_TFS_w_header, ['TFS', 'Probe Count',(undef) x1];
		push @right_fields_TFS_w_header, $_ for @TFS_fields;
	}
	 # printf "after right side";

	$right_field_length=scalar @right_fields_TFS_w_header;
	# print $right_field_length;
	# print "\n";
	#if row max > length of right side pad right fields with empty spaces until row max 
	if($row_max > $length_of_right_side){
		for (1..($row_max-$length_of_right_side)) {
			push @new_right_fields,[(undef) x7] ; 
		}
	}
	if($row_max > $right_field_length){
		for (1..($row_max-$right_field_length)) {
			push @right_fields_TFS_w_header,[(undef) x3] ; 
		}
	}
	
	## add TFS to the right of the right fields 
	my @right_fields_w_TFS;
	for (my $tfs_i=0;$tfs_i<$row_max;$tfs_i++){
		########################################### HERE ########################################
				###################################################################################
						###################################################################################
		
		my $new_line;
		if($tfs_i ==1 || $tfs_i==2){
			$new_line=[@{$new_right_fields[$tfs_i]},(undef) x11,@{$right_fields_TFS_w_header[$tfs_i]}];
		
		}
		else{
			$new_line=[@{$new_right_fields[$tfs_i]},(undef) x8,@{$right_fields_TFS_w_header[$tfs_i]}];
		}
		
		#new_right_fields , 6 empty spaces , right_fields_TFS_w_header
			#$print->([@{$right_fields_TFS[$tfs_i]}]);
			#push @right_fields_w_TFS,$new_line;
			$print->($new_line);
			
					###################################################################################
							###################################################################################
	###################################################################################
	}
	
	#$print->($_) for @left_fields;
	#$print->($_) for @right_fields;
	$print->();
	#$print->($_) for @TFS_fields;
	
    # Print header line.
    $print->( \@experimentNameHeader );
	
	my $row_test=@$data_array->[0];
	# print "\n";
	# $print->($row_test);
	
	# print "length of row";
	my $row_length=scalar @{$row_test};
	
	# print scalar @{$row_test};
	# print "\n";
	# print $_."\n" for @{$row_test};
		  
	#get the TFS columns, which are the last columns, and there are as many as experiments
	# $row_length
	my $start_of_TFS=$row_length-$eid_count;
	
	# print "start of TFS columns";
	# print $start_of_TFS;
	# print "\n";
		
    # Experiment Data header.	
	my @reordred_record_names;
	
	push @reordred_record_names,@$record_names[1,0,$start_of_TFS..($start_of_TFS+$eid_count-1),2,3,4,5,7,8,6,9..(9+5*$eid_count-1)];
    
	$print->(\@reordred_record_names);

    # Print Experiment data sorting by TFS in descending order, then by gene
    # name in ascending order.
	
	my @sorted_data_array;
	
	push @sorted_data_array,$_
		for sort { $b->[0] cmp $a->[0] || ( $a->[3] || '' ) cmp( $b->[3] || '' ) }
		@$data_array;
	
    # $print->($_)
      # for sort { $b->[0] cmp $a->[0] || ( $a->[3] || '' ) cmp( $b->[3] || '' ) }
      # @$data_array;

     # print "\n";
	# $print->(@$data_array->[0]);
	  
    # print "\n";
	# print  @sorted_data_array->[0];
	  
	# print scalar @sorted_data_array;
	# print "\n";
	
	# print scalar @sorted_data_array->[0];
	# print "\n";
	
	my @reordered_columns; 
	push @reordered_columns, [@{$_}[1,0,$start_of_TFS..($start_of_TFS+$eid_count-1),2,3,4,5,7,8,6,9..(9+5*$eid_count-1)]] for @sorted_data_array;
	   
	$print->($_) for @reordered_columns;
		
    return 1;
	
}

#===  CLASS METHOD  ============================================================
#        CLASS:  SGX::TFSDisplay
#       METHOD:  displayDataHTML
#   PARAMETERS:  ????
#      RETURNS:  ????
#  DESCRIPTION:  Display TFS info
#       THROWS:  no exceptions
#     COMMENTS:  none
#     SEE ALSO:  n/a
#===============================================================================
sub displayDataHTML {
    my $self = shift;
    my $q    = $self->{_cgi};

    # Fields with indexes less num_start are formatted as strings, fields with
    # indexes equal to or greater than num_start are formatted as numbers.
    my @table_header;
    my @table_parser;
    my @table_format;

    my $sth_records = $self->{_Records};
    my $record_names = $sth_records->{NAME} || [];

    for ( my $j = 2 ; $j < $self->{_numStart} ; $j++ ) {
        push @table_header, $record_names->[$j];
        push @table_parser, 'string';
        push @table_format, 'formatText';
    }
    for ( my $j = $self->{_numStart} ; $j < @$record_names ; $j++ ) {
        push @table_header, $record_names->[$j];
        push @table_parser, 'number';
        push @table_format, 'formatNumber';
    }

    # wrapping block below in curly brackets because of "Insecure dependency
    # when running with -T" (taint mode) Perl message
    my %format_template;
    {
        my $findProbesHTML = $q->a(
            {
                -title  => 'Find all %1$ss related to %1$s {0}',
                -target => '_blank',
                -href   => $self->url( -absolute => 1 )
                  . '?a=findProbes&b=Search&scope=%1$s&q={0}',
            },
            '{0}'
        );
        $format_template{probe} = sprintf( $findProbesHTML, 'Probe IDs' );
        $format_template{accnum} =
          sprintf( $findProbesHTML, 'Genes/Accession Nos.' );
        $format_template{gene} =
          sprintf( $findProbesHTML, 'Genes/Accession Nos.' );
    };

    $table_format[0] = 'formatProbe';
    $table_format[1] = 'formatAccNum';
    $table_format[2] = 'formatGene';

    if ( $self->{_opts} eq 'annot' ) {
        $table_format[3] = 'formatProbeSequence';
        $format_template{probeseq} = $q->a(
            {
                -title  => 'UCSC BLAT on DNA',
                -target => '_blank',
                -class  => 'external',
                -href =>
'http://genome.ucsc.edu/cgi-bin/hgBlat?org={1}&type=DNA&userSeq={0}'
            },
            '{0}'
        );
    }

    #---------------------------------------------------------------------------
    #  print table body
    #---------------------------------------------------------------------------
    my $data_array = eval {
        my $cache = $sth_records->fetchall_arrayref;
        $sth_records->finish;
        $cache;
    } || [];

    my $eid_count = @{ $self->{_xExpList} };
    unshift( @$_, get_tfs( shift @$_, shift @$_, $eid_count ) )
      for @$data_array;

    my $js = $self->{_js_emitter};
    return '' . $js->let(
        [
            _xExpList => $self->{_xExpList},
            _expected => $self->{_expected},
            _fs       => $self->{_fs},
            tfs       => {
                caption => sprintf( 'This subset includes %d probes',
                    ( $self->{_RowCountAll} || 0 ) ),
                headers => [ 'TFS',        @table_header ],
                parsers => [ 'string',     @table_parser ],
                formats => [ 'formatText', @table_format ],
                frm_tpl => \%format_template,
                records => [
                    sort {
                        $b->[0] cmp $a->[0]
                          || ( $a->[3] || '' ) cmp( $b->[3] || '' )
                      } @$data_array
                ]
            }
        ],
        declare => 1
    );
}

1;

__END__


=head1 NAME

SGX::TFSDisplay

=head1 SYNOPSIS

=head1 DESCRIPTION

=head1 AUTHORS
Eugene Scherba
Michael McDuffie

=head1 SEE ALSO


=head1 COPYRIGHT


=head1 LICENSE

Artistic License 2.0
http://www.opensource.org/licenses/artistic-license-2.0.php

=cut