#!/usr/bin/perl
package sdevGeneInfoUserPage;
#######################################################################
##### Author :	Shuai Weng
##### Date   :  Feb. 2001
##### Description : This package contains all necessary methods for 
#####               displaying GENE INFO to user. 
##### 
# $Author: emj466 $
# $Date: 2006/10/25 18:29:12 $
# $Header: /projects/dicty/build/source_files/db/lib/site_name/user/sdevGeneInfoUserPage.pm,v 1.1 2006/10/25 18:29:12 emj466 Exp $
# $Log: sdevGeneInfoUserPage.pm,v $
# Revision 1.1  2006/10/25 18:29:12  emj466
# new build directory
#
# Revision 1.1.1.2  2003/08/18 22:50:41  emj466
# no message
#
# Revision 1.1.1.1  2003/08/15 20:18:41  emj466
# initial load of dicty/build
#
# Revision 1.32  2003/05/27 18:22:46  shuai
# *** empty log message ***
#
# Revision 1.31  2003/04/23 20:41:26  shuai
# *** empty log message ***
#
# Revision 1.30  2002/12/02 18:30:28  shuai
# *** empty log message ***
#
# Revision 1.29  2002/11/20 21:12:27  shuai
# *** empty log message ***
#
# Revision 1.28  2002/11/14 21:33:18  kara
# changed the display so the generic gif is always used for the online
# journal link.
#
# Revision 1.27  2002/11/13 22:09:59  kara
# finished (hopefully) modifying the program to retrieve papers added in
# the last week.
#
# Revision 1.26  2002/11/13 18:54:09  shuai
# *** empty log message ***
#
# Revision 1.25  2002/11/13 17:45:27  kara
# added GetDate subroutine to get previous week's date
#
# Revision 1.24  2002/11/13 01:46:14  kara
# added two subroutines (references4date, displayAllRefsThisDate) to
# allow query and display of papers added within a range of dates
#
# Revision 1.23  2002/11/12 23:13:31  kara
# added note to curation summary page.
#
# Revision 1.22  2002/10/02 22:51:59  shuai
# *** empty log message ***
#
# Revision 1.21  2002/10/02 21:47:17  kara
# made some changes to HTML
#
# $Revision: 1.1 $
# $Source: /projects/dicty/build/source_files/db/lib/site_name/user/sdevGeneInfoUserPage.pm,v $
# $State: Exp $
# $Locker:  $             
#######################################################################
use strict;
use DBI;
use CGI qw/:all/;
use CGI::Carp qw(fatalsToBrowser);

use lib "/usr/local/dicty/www_dictybase/db/lib/dictyBase/Objects";
use GeneInfo;
use Reference;
use Locus;
use Feature;
use ConfigURLdictyBase;
use ConfigPathdictyBase;

use lib "/usr/local/dicty/www_dictybase/db/lib/common";
use Login qw (ConnectToDatabase);
use TextUtil qw (DeleteUnwantedChar);

use lib "/usr/local/dicty/www_dictybase/db/lib/dictyBase";
use dictyBaseObject;
use dictyBaseCentralMod qw(:formatPage :navigateInfo);

#######################################################################
#################### global variables #################################
#######################################################################

my $maxDisplayNo = 30;
my $dbh;
my $dblink; 
my $configUrl;
my $configPath;
my $downloadfile;
my $downloadUrl;

#######################################################################
sub new {      ############ constructor ###############################
#######################################################################
       
	my ($self, %args) = @_;

	$self = {};
	bless $self;

      	$self->{'_database'} = $args{'database'};
	$self->{'_help'}     = defined($args{'help'}) ? 
	                       $args{'help'} : "Gene_Info.html";
	$self->{'_locus'}     = $args{'locus'};
    	return $self;
}

sub help { $_[0]->{_help} }
sub database { $_[0]->{_database} }
sub title { $_[0]->{_title} }
sub locus { $_[0]->{_locus} }

######################################################################
sub DESTROY {   ############ destructor ##############################
######################################################################
    	if (defined $dbh) {
		$dbh->disconnect;
    	}
}

######################################################################
sub start{
######################################################################

    	my ($self) = @_;
	$configPath = ConfigPathdictyBase->new;
	$configUrl = ConfigURLdictyBase->new;
	$dblink = $configUrl->dblink($self->database);
	$self->setDownloadfile;
	my $locus = $self->{'_locus'};
	&DeleteUnwantedChar(\$locus);
	$self->{'_locus'} = $locus;
	if (!$self->locus) {
	    if((!param('topic')) && (!param('date'))) {
		$self->{'_title'} = "Gene Info Search";
		$self->printEntryForm;
	    }
	    elsif (param('date')) {
		$dbh = &ConnectToDatabase($self->database);
		$self->displayAllRefsThisDate;
	    }
	    else {
		$dbh = &ConnectToDatabase($self->database);
		$self->displayAllRefs4topics;
	    }
	    exit;
	}
	if ($self->locus =~ /\*/ || $self->locus =~ /\%/) {
	    $dbh = &ConnectToDatabase($self->database);
	    my @loci = $self->getGeneList;
	    if (@loci > 1) {
		$self->displayGeneList(@loci);
		exit;
	    }
	    elsif (!@loci) {
		$self->err_report("The locus/feature you entered is not found in database. Please correct it and try again.");
		exit;
	    }
	    else {
		$self->{'_locus'} = $loci[0];
	    }
	}
	elsif (!param('topic')) {
	    my $dictyBase = dictyBaseObject->new(database=>$self->database,
				     query=>$self->locus);
	    if ($dictyBase->isMultiple) {
		$dbh = &ConnectToDatabase($self->database);
		my @loci = $self->getGeneList;
		if (@loci == 1) {
		    $self->{'_locus'} = $loci[0];
		}
		else {
		    $self->displayGeneList(@loci);
		    exit;
		}
	    }
	    elsif ($dictyBase->locusName) { 
		$self->{'_locus'} = $dictyBase->locusName; 
	    }
	    elsif ($dictyBase->featureName) {
		$self->{'_locus'} = $dictyBase->featureName;
	    }
	    else {
		$self->err_report("The locus/feature you entered is not found in database. Please correct it and try again.");
		exit;
	    }
        }
	$dbh = &ConnectToDatabase($self->database);
	$self->{'_title'} = $self->locus." Literature Guide";
	my $giObject = GeneInfo->new(dbh=>$dbh,
				     locus=>$self->locus);
	if (param('topic')) {
	    $self->displayRef4topic($giObject);
	}
	#elsif (param('date')) {
	    #$self->displayAllRefsThisDate($giObject);
	#}
	elsif (param('type')) {
	    $self->displayLoci($giObject);
	}
	else {
	    $self->displaySummary($giObject);
	}
	exit;
	
}

#######################################################################
sub printEntryForm {
#######################################################################
        my ($self) = shift;

	&printStartPage($self->database, $self->title, $self->help);
	print center(table({-border=>3,
                        -cellpadding=>4,
                        -cellspacing=>4},
                       
                       Tr({-align=>'LEFT'},
                          [
                           td({-bgcolor=>"#b7d8e4",
                               -width=>350},
                              table({-border=>0},
                                    Tr({align=>'LEFT'},
                                       [
                                        td(start_form,
                                           "Enter locus name : ").
                                        td(textfield(-name=>'locus',
                                                     -size=>'15')),
                                        td(" ").td(submit, reset, end_form)
                                        ]))
                              )
                           ])));

	&printEndPage;
}

########################################################################
sub displaySummary {
########################################################################
    my ($self, $giObject) = @_;
    &printStartPage($self->database, $self->title, $self->help);
    print table({-border=>'0',
		 -width=>'100%'},   
Tr(td{-width=>'100%',
		       -colspan=>'2',
		       -valign=>'top'},
                       font({-size=>'+1'},
                       ("This page displays all the papers associated with ".$self->locus." in dictyBase, along with all the literature topics those papers address.  Click on a topic on the left to see the papers that address it."))).
Tr(td{-width=>'100%',
		       -colspan=>'2',
		       -valign=>'top'},
                (" ")).
		Tr(td({-width=>'30%',
		       -bgcolor=>'#d8d8d8',
		       -valign=>'top'},
		      $self->topicsSection($giObject)).
		   td({-width=>'70%',
		       -valign=>'top'},
		      table({-width=>'100%',
			     -border=>'0'},
			    
			    Tr(td(h4(a({-href=>$configUrl->dictyBaseCGIRoot."gene_page.pl?gene_name=".$self->locus},$self->locus).
					  " Literature Curation Summary"))).
			    Tr(td($self->summary($giObject)))
		      )
		   )
                )
	 );

    &printEndPage;
}

########################################################################
sub displayAllRefs4topics {
########################################################################
    my ($self) = @_;
    $self->{'_title'} = "References Associated with Literature Topic(s): ";
    
    my $giObject = GeneInfo->new(dbh=>$dbh);

    my $topicRefs = $self->references4topic($giObject);
 
    my $navigationBar = $self->displayNavigationBar;
   
    &printStartPage($self->database, $self->title, $self->help);

    print table({-width=>'100%',
		 -border=>'0'},
		Tr(td(&ResultNumber(totalHit=>$self->{'_end'},
				    showNum=>$maxDisplayNo,
				    beg=>param('beg')))).
		# Tr(td($navigationBar)).
                Tr(td(
		      table({-align=>'center',
			     -border=>'0',
			     -cellpadding=>'3',
			     -cellspacing=>'3',
			     -width=>'100%'},
			    Tr(th({-align=>'left',
				   -bgcolor=>'#a4abc2'},
				  "Reference").
			       th({-align=>'left',
				   -bgcolor=>'#a4abc2'},
				  "Genes Addressed")).
			    $topicRefs
		       ))).
		Tr(td($navigationBar))
	 ) ;
}

########################################################################
sub displayRef4topic {
########################################################################
    my ($self, $giObject) = @_;
    &printStartPage($self->database, $self->title, $self->help);
    my $topic;
    if (param('topic') =~ /^curated/i) {
	$topic = "Curated References";
    }
    elsif (param('topic') =~ /^not yet curated/i) {
	$topic = "References Not Yet Curated";
    }
    else { $topic = param('topic'); }
    my $topicRefs = $self->references4topic($giObject);
    my $navigationBar = $self->displayNavigationBar;
    print "<a name='top'>";
    print table({-border=>'0',
		 -width=>'100%'},   
		Tr(td({-width=>'30%',
		       -bgcolor=>'#d8d8d8',
		       -valign=>'top'},
		      $self->topicsSection($giObject)).
		   td({-width=>'70%',
		       -valign=>'top'},
		      table({-width=>'100%',
			     -border=>'0'},
			    $self->locusInfo.
			    Tr(td(h3(font({-color=>'red'},
					  $self->locus).
				  " - $topic"))).
			    Tr(td(&ResultNumber(totalHit=>$self->{'_end'},
						showNum=>$maxDisplayNo,
						beg=>param('beg')))).
			    # Tr(td($navigationBar)).
                            Tr(td(
				  table({-align=>'center',
					 -border=>'0',
					 -cellpadding=>'3',
					 -cellspacing=>'3',
					 -width=>'100%'},
					Tr(th({-align=>'left',
					       -bgcolor=>'#a4abc2'},
					      "Reference").
					   th({-align=>'left',
					       -bgcolor=>'#a4abc2'},
					      "Other Genes Addressed")).
					$topicRefs
				  )
			    )).
			    Tr(td($navigationBar))
		      )
		   )
                )
	 );
    print "<a name='bot'>";
    &printEndPage;
}

########################################################################
sub displayGeneList {
########################################################################
    my ($self, @loci) = @_;
    &printStartPage($self->database, $self->title, $self->help);
    my $num = @loci;
    print center(b("There are ".font({-color=>'red'}, $num)." loci found for locus name like ".font({-color=>'red'}, $self->locus)." in database")),p;
    my $return;
    foreach my $locus (@loci) {
	$return .= li(a({-href=>url."?locus=$locus"},
		     $locus));
    }
    print ul($return),p;

    &printEndPage;
}

########################################################################
sub displayLoci {
########################################################################
    my ($self, $giObject) = @_;
    &printStartPage($self->database, $self->title, $self->help);
    my $geneNum = $giObject->geneNum;
    print table({-align=>'center',
		 -valign=>'top',
	         -cellpadding=>'4'},
		 Tr(td({-bgcolor=>"#b7d8e4"},
			       a({-href=>url."?locus=".$self->locus},
				 $self->locus." Literature Topics")).
		    td({-bgcolor=>"#b7d8e4"},
			       a({-href=>$configUrl->dictyBaseCGIRoot."gene_page.pl?gene_name=".$self->locus},
			       $self->locus." Locus Info"))));
   
    print table({-align=>'center',
		 -valign=>'top'},
		 Tr(td(h2(font({-color=>'red'}, $geneNum)." other genes are mentioned in papers curated for ".$self->locus))));
    
    my $arrayRef4locus = $giObject->locusList;
    my $arrayRef4feat = $giObject->featureList;
    push (@$arrayRef4locus, @$arrayRef4feat);
    my $tableList; 
    my (@rows, @tables, @tableLabels, %geneLabel);
    my ($geneNo, $i, $colNum, $begGene, $preGene);
    my ($labelBeg, $labelEnd, $label);
    foreach my $rowRef (@$arrayRef4locus) {
	    my ($gene) = @$rowRef;
	    if (uc($gene) eq uc($self->locus)) { next; }
	    $i++;
	    $geneNo++;
	    $geneLabel{$geneNo} = $gene;
	    if ($i > 20) {
		$colNum++;
		unshift(@rows, td("${begGene}-${preGene}"));
		$tableList .= td(table({-align=>'center',
				        -valign=>'top',
				        -cellspacing=>'3',
					-cellpadding=>'3',
					-border=>'1'}, 
				       Tr({-align=>'center'},\@rows)));	
	
		undef @rows;
		$i = 1;
		$begGene = $gene;
	    }
	    if ($colNum == 5) {
		$labelBeg = $geneNo - 100;
		$labelEnd = $geneNo - 1;
		$label = "${labelBeg}-$labelEnd";
		push(@tableLabels, "${label}($geneLabel{$labelBeg}-$geneLabel{$labelEnd})");
		my $table= table({-align=>'center',
				  -valign=>'top'},
				 Tr(th({-colspan=>'5', 
					-bgcolor=>"#a4abc2",
					-align=>'center'},
				       font({-size=>'+1'}, $label))).
				 Tr($tableList));
		push(@tables, $table);
		undef $tableList;
		undef $colNum;
	    }
	    if ($i == 1) {
		$begGene = $gene;
	    }
	    push(@rows, td(a({-href=>$configUrl->dictyBaseCGIRoot."gene_page.pl?gene_name=$gene", -target=>'infowin'},$gene)));
	    $preGene = $gene;
    }
    unshift(@rows, td("${begGene}-${preGene}"));
    $tableList .= td({-align=>'center',
		      -valign=>'top'}, 
		     table({-align=>'center',
			    -valign=>'top',
			    -cellspacing=>'3',
			    -cellpadding=>'3',
			    -border=>'1'}, 
			   Tr({-align=>'center'},\@rows)));
	
    my $labelBeg = $labelEnd + 1;
    my $label = "${labelBeg}-$geneNo";
    push(@tableLabels, "${label}($geneLabel{$labelBeg}-$geneLabel{$geneNo})");
    my $table= table({-align=>'center',
		      -valign=>'top'},
		     Tr(th({-colspan=>'5', 
			    -bgcolor=>"#a4abc2",
			    -align=>'center'},
			   font({-size=>'+1'}, $label))).
		     Tr($tableList));
    push(@tables, $table);
    my $popup = table({-align=>'center'},
		      Tr(td(b(font({-size=>'+1'}, "Jump to: "))).
			 td(start_form).
			 td(popup_menu(-name=>'jumpItem',
				       -"values"=>\@tableLabels,
				       -onchange=>'jump(this)')).
			 td(end_form)));
    for(my $i = 0; $i <= @tables; $i++) {
	print "<a name='$tableLabels[$i]'>";
	if ($geneNum > 100) {
	    print $popup;
	}
	print $tables[$i];
    }
 
    my $maxCuratedDate = $giObject->maxCuratedDate;
    my $maxPubmedSearchDate = $giObject->maxPubmedSearchDate;

    print br.br.table({-align=>'center'},
		      Tr(td(b("Date of last curation:")).
			 td($maxCuratedDate).
			 td(b("Date of last PubMed Search:")).
			 td($maxPubmedSearchDate)
			 ));
   
   &printEndPage;
}

########################################################################
sub locusInfo {
########################################################################
    my ($self) = @_;
    return Tr(td(table({-align=>'right',
			  -border=>'0',
			  -cellpadding=>'4'},
			 Tr(td({-bgcolor=>'#b7d8e4',
				-align=>'right'},
			       a({-href=>$configUrl->dictyBaseCGIRoot."gene_page.pl?gene_name=".$self->locus},
				$self->locus." Locus Info")))
			 )));

}


########################################################################
sub topicsSection {
########################################################################
    my ($self, $giObject) = @_;
    return table({-width=>'100%',
		  -cellpadding=>'0',
		  -cellspacing=>'0'},
		 Tr(td({-bgcolor=>'#d8d8d8',
			-align=>'left',
			-valign=>'center'},
		       h4(a({-href=>$configUrl->dictyBaseCGIRoot."gene_page.pl?gene_name=".$self->locus}, $self->locus).
			  font({-color=>'black'}, " LITERATURE TOPICS".br."(formerly Gene Info)")
		       ))).
		 $self->geneticsCellBiol($giObject).
		 $self->nucleicAcidInfo($giObject).
		 $self->proteinInfo($giObject).
		 $self->relatedGenesProteins($giObject).
		 $self->researchAids($giObject).
		 $self->curatedLiterature($giObject).
		 $self->additionalInfo($giObject)
	    );
   

 
}

########################################################################
sub geneticsCellBiol {
########################################################################
    my ($self, $giObject) = @_;
    my $returnTopics = $self->topicEntry($giObject->hasCellularLocation,
					 "Cellular Location");
    $returnTopics .= $self->topicEntry($giObject->hasCellCyclePhaseInvolved,
				       "Cell Cycle Phase Involved");
    $returnTopics .= $self->topicEntry($giObject->hasFunctionProcess,
				       "Function/Process");
    $returnTopics .= $self->topicEntry($giObject->hasGeneticInteractions,
				       "Genetic Interactions");
    $returnTopics .= $self->topicEntry($giObject->hasMutantsPhenotypes,
				       "Mutants/Phenotypes");
    $returnTopics .= $self->topicEntry($giObject->hasRegulationOf,
				       "Regulation of");
    $returnTopics .= $self->topicEntry($giObject->hasRegulatoryRole,
				       "Regulatory Role");
    if ($returnTopics) {
	$returnTopics = Tr(td({-bgcolor=>"#a4abc2"},
			   b("Genetics/Cell Biology"))).ul($returnTopics);
    }
    return $returnTopics;
}

########################################################################
sub nucleicAcidInfo {
########################################################################
    my ($self, $giObject) = @_;
    my $returnTopics = $self->topicEntry($giObject->hasDnaRnaSequenceFeatures,
					 "DNA/RNA Sequence Features");
    $returnTopics .= $self->topicEntry($giObject->hasMapping,
				       "Mapping");
    $returnTopics .= $self->topicEntry($giObject->hasRnaLevelsAndProcessing,
				       "RNA Levels and Processing");
    $returnTopics .= $self->topicEntry($giObject->hasTranscription,
				       "Transcription");
    $returnTopics .= $self->topicEntry($giObject->hasTranslationalRegulation,
				       "Translational Regulation");
    if ($returnTopics) {
	$returnTopics = Tr(td({-bgcolor=>"#a4abc2"},
			   b("Nucleic Acid Information"))).ul($returnTopics);
    }
    return $returnTopics;
}

########################################################################
sub proteinInfo {
########################################################################
    my ($self, $giObject) = @_;
    my $returnTopics = 
	$self->topicEntry($giObject->hasProteinNucleicAcidInteractions,
			  "Protein-Nucleic Acid Interactions");
    $returnTopics .= $self->topicEntry(
			$giObject->hasProteinPhysicalProperties,
			"Protein Physical Properties");
    $returnTopics .= $self->topicEntry(
		        $giObject->hasProteinProcessingRegulation,
			"Protein Processing/Regulation");
    $returnTopics .= $self->topicEntry(
			$giObject->hasProteinProteinInteractions,
			"Protein-protein Interactions");
    $returnTopics .= $self->topicEntry(
			$giObject->hasProteinNucleicAcidStructure,
			"Protein/Nucleic Acid Structure");
    $returnTopics .= $self->topicEntry(
			$giObject->hasSubstratesLigandsCofactors,
			"Substrates/Ligands/Cofactors");
    $returnTopics .= $self->topicEntry(
			$giObject->hasProteinSequenceFeatures, 
			"Protein Sequence Features");
    if ($returnTopics) {
	$returnTopics = Tr(td({-bgcolor=>"#a4abc2"},
			   b("Protein Information"))).ul($returnTopics);
    }
    return $returnTopics;
}

########################################################################
sub relatedGenesProteins {
########################################################################
    my ($self, $giObject) = @_;
    my $returnTopics = $self->topicEntry($giObject->hasDiseaseGeneRelated,
					 "Disease Gene Related");
    $returnTopics .= $self->topicEntry(
		        $giObject->hasNonFungalRelatedGenesProteins, 
			"Non-Fungal Related Genes/Proteins");
    $returnTopics .= $self->topicEntry(
			$giObject->hasFungalRelatedGenesProteins, 
                        "Fungal Related Genes/Proteins");    
    if ($returnTopics) {
	$returnTopics = Tr(td({-bgcolor=>"#a4abc2"},
			   b("Related Genes/Proteins"))).ul($returnTopics);
    }
    return $returnTopics;
}

########################################################################
sub researchAids {
########################################################################
    my ($self, $giObject) = @_;
    my $returnTopics = $self->topicEntry($giObject->hasAlias,
					  "Alias");
    $returnTopics .= $self->topicEntry($giObject->hasOtherFeatures, 
					   "Other Features");
    $returnTopics .= $self->topicEntry($giObject->hasStrainsConstructs, 
					   "Strains/Constructs");
    $returnTopics .= $self->topicEntry($giObject->hasTechniquesAndReagents,
					   "Techniques and Reagents");
    $returnTopics .= $self->topicEntry($giObject->hasGenomeWideAnalysis, 
					   "Genome-wide Analysis");
    if ($returnTopics) {
	$returnTopics = Tr(td({-bgcolor=>"#a4abc2"},
			   b("Research Aids"))).ul($returnTopics);
    }
    return $returnTopics;
}

########################################################################
sub curatedLiterature {
########################################################################
    my ($self, $giObject) = @_;
    my $returnTopics = $self->topicEntry($giObject->hasSelectedReview, 
					  "Selected Review");
    $returnTopics .= $self->topicEntry($giObject->hasReviews,
					   "Reviews");
    $returnTopics .= $self->topicEntry($giObject->hasCurated, 
			   "List of all Curated References", "curated");
    if ($returnTopics) {
	$returnTopics = Tr(td({-bgcolor=>"#a4abc2"},
			   b("Curated Literature"))).ul($returnTopics);
    }
    return $returnTopics;
}

########################################################################
sub additionalInfo {
########################################################################
    my ($self, $giObject) = @_;
    my $returnTopics = $self->topicEntry($giObject->hasNotYetCurated,
					 "References Not Yet Curated", 
					 "not yet curated");
    $returnTopics .= $self->topicEntry($giObject->hasArchivedLiterature,
				       "Archived Literature");
    $returnTopics .= $self->topicEntry(1, "Literature Curation Summary");
    $returnTopics .= $self->geneSummaryParagraph($giObject);    
    $returnTopics .= $self->pubmedSearch;
    if ($returnTopics) {
	$returnTopics = Tr(td({-bgcolor=>"#a4abc2"},
			   b("Additional Information"))).ul($returnTopics);
    }
    return $returnTopics;
}

########################################################################
sub topicEntry {
########################################################################
    my ($self, $foundTopic, $listTopic, $linkTopic) = @_;
    if (!$foundTopic) { return;}
    if (!$linkTopic) { $linkTopic = $listTopic; }
    my $locus = $self->locus;
    if (!param('topic') && $listTopic =~ /Literature Curation Summary/i) {
	return Tr(td(li(img({-border=>'0',
			     -src=>$configUrl->breadServerRoot.'images/right.gif'}).font({-color=>'red'},
			    "Literature Curation Summary"))));		
    }
    elsif (param('topic') =~ /^$linkTopic/i) {
	$linkTopic =~ s/ /\+/g;
	return Tr(td(li(img({-border=>'0',
			     -src=>$configUrl->breadServerRoot.'images/right.gif'}).font({-color=>'red'},
			    "$listTopic"))));		
    }
    else {
	$linkTopic =~ s/ /\+/g;
	if ($listTopic =~ /Literature Curation Summary/i) {
	    return Tr(td(li(a({-href=>url."?locus=$locus"}, $listTopic))));
	}
	else {
	    return Tr(td(li(a({-href=>url."?locus=$locus&topic=$linkTopic"}, "$listTopic"))));
	}
    }
}

########################################################################
sub summary {
########################################################################
    my ($self, $giObject) = @_;
    my $allRefs = $self->references4topic($giObject, "all");
    my $navigationBar = $self->displayNavigationBar;
    my $curatedRefNum = $giObject->curatedRefNum;
    my $notYetCuratedRefNum = $giObject->notYetCuratedRefNum;
    my $communityAnnotatedRefNum = $giObject->communityAnnotatedRefNum;
    
    my $communityAnnotationRefNumRow;

    if ($communityAnnotatedRefNum) {
	
	my $locusObj = Locus->new(dbh=>$dbh,
				  locus_name=>$self->locus);
	
	my $dictyBaseid = $locusObj->dictyBaseid || $locusObj->dictyBaseidList;

	my $communityUrl = $configUrl->dictyBaseCGIRoot."$dblink/DisplayCommuAnno?dictyBaseid=$dictyBaseid";

	$communityAnnotationRefNumRow =
	    Tr(td(a({-href=>$communityUrl,
		     -target=>'infowin'},
		    img({-src=>$configUrl->dictyBaseImages."star.gif",
		         -border=>0}))." ".
		  b("References selected for Community Annotation")));
    }

    if (!$curatedRefNum && !$notYetCuratedRefNum) {
	return b("No reference found for ".font({-color=>'red'}, $self->locus)." in database in this moment.");
    }
    return table({-width=>'100%',
		  -align=>'right',
		  -border=>'0'},
		 Tr(td(b("Curated References for ".
			 $self->locus.": ").
		       a({-href=>url."?locus=".$self->locus.
			  "&topic=curated"}, 
			 $curatedRefNum))).
		 Tr(td(b("References Not Yet Curated: ").
		       a({-href=>url."?locus=".$self->locus.
			  "&topic=not+yet+curated"}, $notYetCuratedRefNum))).
		 Tr(td($self->selectedReview($giObject))).
		 $communityAnnotationRefNumRow.
		 Tr(td(hr)).
## all refs here
		Tr(td(
		table({-width=>'100%',
		 -border=>'0'},
		Tr(td(&ResultNumber(totalHit=>$self->{'_end'},
				    showNum=>$maxDisplayNo,
				    beg=>param('beg')))).
		# Tr(td($navigationBar)).
                Tr(td(
		      table({-align=>'center',
			     -border=>'0',
			     -cellpadding=>'3',
			     -cellspacing=>'3',
			     -width=>'100%'},
			    Tr(th({-align=>'left',
				   -bgcolor=>'#a4abc2'},
				  "Reference").
			       th({-align=>'left',
				   -bgcolor=>'#a4abc2'},
				  "Genes Addressed")).
			    $allRefs
		       ))).
		Tr(td($navigationBar))
	 ) ))
##########
		 
	   );	 
}

########################################################################
sub selectedReview {
########################################################################
    my ($self, $giObject) = @_;
    my $minCuratedDate = $giObject->minCuratedDate;
    my $maxCuratedDate = $giObject->maxCuratedDate;
    my $otherGeneNum = $giObject->geneNum;
    my $maxPubmedSearchDate = $giObject->maxPubmedSearchDate;
    if (!$giObject->hasSelectedReview) { 
	return 
	       Tr(td(b("Number of Other Genes referred to in ".$self->locus." Literature: ").a({-href=>url."?locus=".$self->locus."&type=other"}, $otherGeneNum))).
               #Tr(td("&nbsp;")).
               Tr(td(b("Date of last curation: ").$maxCuratedDate)).
	       Tr(td(b("Date of last PubMed Search: ").$maxPubmedSearchDate));
    }
    my $arrayRef = $giObject->selectedReviewRef;
    my $rowRef = @$arrayRef[0];
    my ($refNo, $citation, $year) = @$rowRef;
    my ($citation, $refObject) = $self->citation($refNo);
#    my $note = " The literature for this gene has been reviewed in the reference(s) listed under Selected Review. Due to the extensive literature available for this gene, only references published since $minCuratedDate have been curated. Earlier references can be found under ".
#		a({-href=>url."?locus=".$self->locus."&topic=Archived+Literature", target=>'infowin'}, "Archive of older references").
#		    " and older reviews can be found under the ".
#		    a({-href=>url."?locus=".$self->locus."&topic=Reviews", target=>'infowin'}, "Reviews")." topic.";

    my $note = " Due to extensive literature available for this gene, not all references have been curated. dictyBase considers information published one year or more prior to the ".a({-href=>url."?locus=".$self->locus."&topic=Reviews", target=>'infowin'}, "Selected Review")." to be covered by that review. Therefore, many references published before the review will not be curated to a specific Literature Topic. Instead, these papers will be listed in ".a({-href=>url."?locus=".$self->locus."&topic=Archived+Literature", target=>'infowin'}, "Archived Literature.");

    my $return = #Tr(td(b(u("Selected Review:")))).
	   #Tr(td(blockquote($citation))).
	   Tr(td(blockquote(b("Note:").$note)));
    if ($otherGeneNum >= 1) {
	$return .= Tr(td(b("Number of Other Genes referred to in ".$self->locus." Literature: ").font({-color=>'red'}, a({-href=>url."?locus=".$self->locus."&type=other"},$otherGeneNum))));
    }
    $return .=  Tr(td(b("Date of last curation: ").$maxCuratedDate)).
           Tr(td(b("Date of last PubMed Search: ").$maxPubmedSearchDate));
    return $return;
}

########################################################################
sub references4topic {
########################################################################
    my ($self, $giObject, $all) = @_;

    my $arrayRef;
    if ($all) {
	$arrayRef = $giObject->topicInfo;
    }
    elsif (param('topic') =~ /\:/) {
	my @topic = split(/\:/, param('topic'));
	foreach my $topic (@topic) {
	    $self->{'_title'} .= $topic.", ";
	    if (!$arrayRef) {
		$arrayRef = $giObject->topicInfo($topic);
	    }
	    else {
		my $thisArrayRef =  $giObject->topicInfo($topic);
		push(@$arrayRef, @$thisArrayRef);
	    }
	}
	$self->{'_title'} =~ s/, $//;
    }
    else {
	if (!$self->locus) {
	    $self->{'_title'} .= param('topic');
	}
	$arrayRef = $giObject->topicInfo(param('topic'));
    }
    
    my $end = @$arrayRef;
    my (@refs, %tmp); 
    if (param('sortedBy') =~ /citation/i) {
	foreach my $rowRef (@$arrayRef) {
	    my ($refNo, $citation, $year, $pubmed, $journal) = @$rowRef;
	    $tmp{$citation} = $refNo."\t".$year."\t".$pubmed."\t".$journal;
	}
	foreach my $citation (sort (keys %tmp) ) {
	    my ($refNo, $year, $pubmed, $journal) = 
		split(/\t/, $tmp{$citation});
	    my @row = ($refNo, $citation, $year);
	    my $rowRef = \@row;
	    push(@refs, $rowRef);
	}
    }
    elsif (!$self->locus) {
	my @tmpRefs;
	foreach my $rowRef (@$arrayRef) {
	    my ($refNo, $citation, $year, $pubmed, $journal) = @$rowRef;
	    if ($tmp{$year}) { $tmp{$year} .= "::"; }
	    $tmp{$year} .= $refNo."\t".$citation."\t".$pubmed."\t".$journal;
	}
	foreach my $year (sort{$a<=>$b} (keys %tmp) ) {
	    my @entry = split(/::/, $tmp{$year});
	    foreach my $entry (@entry) {
		my ($refNo, $citation, $pubmed, $journal) = 
		    split(/\t/, $entry);
		my @row = ($refNo, $citation, $year, $pubmed, $journal);
		my $rowRef = \@row;
		push(@tmpRefs, $rowRef);
	    }
	}
	@refs = reverse (@tmpRefs);
    }
    else {
	@refs = reverse (@$arrayRef);
    }
   
    my $returnList;
    my $bgcolor;
    my $beg = param('beg');
    if (!$beg) { $beg = 1; }
    my $matchYear;
    if (param('navigateList') =~ /^Year ([0-9]+)$/i) {
	$matchYear = $1;
    }
    if (!param('id')) {
	open(OUT, ">$downloadfile") ||
	    die "Can't open '$downloadfile' for writing:$!\n";
	print OUT "Citation\tLoci\n\n";
    }
    my $searchFor = param('searchFor');
    my $filterBy = param('filterBy');
    my ($num, $skipRow, $stop, $matchNum);
    my @navigationList;
    my %year;
    
    my ($locusNm4RefNoHashRef, $featNm4RefNoHashRef, $url4RefNoHashRef);
    my ($relatedRefInfo4RefNoHashRef, $webSupplementUrl4RefNOHashRef);

    if (!$self->locus && @refs > 100) {
	$locusNm4RefNoHashRef = $giObject->getLocusNm4RefNoHashRef;
	$featNm4RefNoHashRef = $giObject->getFeatNm4RefNoHashRef;
	$url4RefNoHashRef = $giObject->getUrl4RefNoHashRef;
	$relatedRefInfo4RefNoHashRef 
	    = $giObject->getRelatedRefInfo4RefNoHashRef;
	$webSupplementUrl4RefNOHashRef 
	    = $giObject->getWebSupplementUrl4RefNoHashRef;
    }

    my %foundRef;
    foreach my $rowRef (@refs) {    
	my ($refNo, $ORIcitation, $year, $pubmed, $journal) = @$rowRef;
	if ($foundRef{$refNo}) { 
	    $end--;
	    next;
	}
	$foundRef{$refNo}++;
	$year{$year}++;
	if ($matchYear && $matchYear < $year) { 
	    $skipRow++;
	    next;
	}
	if ($filterBy) {
	    if ($searchFor =~ /citation/i && 
		$ORIcitation !~ /$filterBy/i) { 
		next; 
	    }
	    elsif ($searchFor =~ /year/i && 
		   $year !~ /$filterBy/i) {
		next;
	    }
	  
        }
	my ($citation, $locusList, $featureList);
	if (!$self->locus && @refs > 100) {
	    my $urls = $$url4RefNoHashRef{$refNo};
	    my $relatedRefInfo = $$relatedRefInfo4RefNoHashRef{$refNo};
	    my $webSuppUrl = $$webSupplementUrl4RefNOHashRef{$refNo};
	    $citation = $self->citation2($refNo, $ORIcitation, $pubmed, 
					 $journal, $urls, 
					 $relatedRefInfo, $webSuppUrl);
	    $locusList = $$locusNm4RefNoHashRef{$refNo};
	    $featureList = $$featNm4RefNoHashRef{$refNo};
	}
	else {
	    my $refObject;
	    ($citation, $refObject) = $self->citation($refNo);
	    foreach my $rowRef (@{$refObject->locusArrayRef}) {
		my ($locusNm) = @$rowRef;
		$locusList .= $locusNm."\t";
	    }
	    $locusList =~ s/\t$//;
	    foreach my $rowRef (@{$refObject->featureArrayRef}) {
		my ($featNm) = @$rowRef;
		$featureList .= $featNm."\t";
	    }
	    $featureList =~ s/\t$//;
	}
	my $loci;
        if ($locusList && $featureList) { 
	    $loci = $locusList."\t".$featureList;
	}
	elsif ($locusList) { $loci = $locusList; }
	elsif ($featureList) { $loci = $featureList; }
	$loci =~ s/^\t//;
	$loci =~ s/\t$//;
	my @loci = split(/\t/, $loci);
	if (!param('id')) {
	    print OUT "$ORIcitation\t@loci\n";
	}
	$num++;
	if ($num < $beg) { next; }
	if ($num >= $beg + $maxDisplayNo && !param('id')) {
	    if (!$stop) { $stop = $num - 1; }
	    next;
	}
	elsif ($num >= $beg + $maxDisplayNo && param('id')) { 
	    if (!$stop) {$stop = $num - 1;}
	    next;
	}
	my $listLoci;
	my $i;
	foreach my $locus (@loci) {
	    if ($self->locus && $self->locus =~ /^$locus$/i) { 
		next;
	    }
	    $i++;
	    if ($i > 15) { last; }
	    if ($i == 15) {
		$listLoci .= " |".a({-href=>$configUrl->dictyBaseCGIRoot."$dblink/reference/reference.pl?refNo=$refNo#summary", -target=>'infowin'}, font({-color=>'red'}, "MORE"));
	    }
	    else {
		$listLoci .= " |".a({-href=>$configUrl->dictyBaseCGIRoot."gene_page.pl?gene_name=$locus", -target=>'infowin'}, $locus);
	    }
	}
	$listLoci =~ s/^\|//;
	if (!$listLoci) { $listLoci = br; }
	if (!$bgcolor) { 
	    $returnList .= Tr(td({-width=>"70%",
				  -valign=>"top"},
				 $citation).
			      td({-width=>"30%",
				  -valign=>"top"},
				 $listLoci));
	    $bgcolor = "#d8d8d8";
	}
	else {
	    $returnList .= Tr({-bgcolor=>"$bgcolor"},
			      td({-width=>"70%",
				  -valign=>"top"},
				 $citation).
			      td({-width=>"30%",
				  -valign=>"top"},
				 $listLoci));
	    $bgcolor = "";
	}
	$matchNum++;
    }
    $self->{'_end'} = $end;
    if (!param('id')) { close(OUT); }
    foreach my $year (sort {$a<=>$b;} keys %year ) {
	push(@navigationList, "Year $year");
    }
    $self->{'_skipRow'} = $skipRow;
    $self->{'_stop'} = $stop;
    $self->{'_matchNum'} = $matchNum;
    $self->{'_navigationList'} = \@navigationList;
    return $returnList ;
}

########################################################################
sub citation {
########################################################################
    my ($self, $refNo) = @_;
    my $refObject = Reference->new(dbh=>$dbh,
				   reference_no=>$refNo);
    my $citation;
    if (param('topic') =~ /not yet curated/i) {
	$citation = $refObject->formatedCitation4notYetTopic;
    }
    else {
	$citation = $refObject->formatedCitation;
    } 
    return ($citation, $refObject);
}

########################################################################
sub citation2 {
########################################################################
    my ($self, $refNo, $citation, $pubmed, $journal, $urls, 
	$relatedRefInfo, $webSuppUrl) = @_;
    $citation =~ s/^([^0-9]+\([0-9]{4}\))(.+)$/<b>$1<\/b>$2/;
    $citation =~ s/^([^0-9]+\([0-9]{4}\))$/<b>$1<\/b> personal communication/;
    $citation .= br;
    my $image = "dictyBaserefsml.gif";
    $citation .= a({-href=>$configUrl->dictyBaseCGIRoot."$dblink/reference/reference.pl?refNo=$refNo",
		           -target=>'infowin'},
			  img({-src=>$configUrl->dictyBaseImages."$image",
			       -border=>'0',
			       -alt=>"dictyBase Papers Entry"}));
    if ($pubmed) {
	$citation .= "&nbsp;&nbsp;".a({-href=>$configUrl->ncbiUrlRoot."query.fcgi?cmd=Retrieve&db=PubMed&list_uids=${pubmed}&dopt=Abstract",
		      -target=>'infowin'},
			  img({-src=>$configUrl->dictyBaseImages."pubmedrefsml.gif",
			       -border=>'0',
			       -alt=>"Pubmed Entry"}))."&nbsp;&nbsp;";
    }
    if ($urls) { 
	#KD: no longer using the specific gifs for specfic journals; just
        #    using one generic gif
	#my $journalGif = $journal; 
	#$journalGif =~ s/ /\./g;
	#$journalGif .= ".gif";
	#if (! -e $configPath->gifDir."$journalGif") { 
	#    $journalGif = "Generic.gif"; 
	#}
	my $journalGif = "full_text.gif";
    
	$citation .= a({-href=>"$urls",
		        -target=>'infowin'},
		       img({-src=>$configUrl->dictyBaseImages."$journalGif",
			    -border=>'0',
			    -alt=>"online article1"}))."&nbsp;&nbsp;";
    }
    if ($webSuppUrl) {
	$citation .= a({-href=>"$webSuppUrl",
		        -target=>'infowin'},
		       img({-src=>$configUrl->dictyBaseImages."webSupplement.gif",
			    -border=>'0',
			    -alt=>"Web Supplement"}));

    }
    if ($relatedRefInfo) {
	$citation .= a({-href=>$configUrl->dictyBaseCGIRoot."$dblink/reference/reference.pl?refNo=".$refNo."&type=other",
		        -target=>'infowin'},
		       img({-src=>$configUrl->dictyBaseImages."C&E.gif",
			    -border=>'0',
			    -alt=>"dictyBase Curated Comments & Errata"}));

    }
    return $citation;
}

########################################################################
sub geneSummaryParagraph {
########################################################################
    my ($self, $giObject) = @_;
    my $found;
    my $locus = $self->locus;
    my $paragraphNo = $giObject->paragraphNo();

    if (defined $giObject->paragraphNo) {
	$found = 1;
    }
    else {
	undef $found;
    }

    if (!$found) { return; }	
    return 
	   Tr(td(a({-href=>$configUrl->dictyBaseCGIRoot."$dblink/locus.pl?locusNo=".$giObject->locusNo."#summaryParagraph",
    		    -target=>'infowin'},
		   $self->locus." Gene Summary Paragraph")));
}

########################################################################
sub pubmedSearch {
########################################################################
    my ($self) = @_;
    return Tr(td(a({-href=>$configUrl->ncbiUrlRoot."query.fcgi?cmd=search&db=PubMed&term=%28".$self->locus."%5bTEXT%3anoexp%5d%20AND%20Dictyostelium%20discoideum%5bALL%5d%29",
		    -target=>'infowin'},
		   "PubMed Search"))).
           Tr(td(a({-href=>$configUrl->ncbiUrlRoot."query.fcgi?cmd=search&db=PubMed&term=%28".$self->locus."%5bALL%5d%20AND%20Dictyostelium%20discoideum%5bALL%5d%29",
		    -target=>'infowin'},
		   "Expanded PubMed Search")));
}

########################################################################
sub displayNavigationBarNew {
########################################################################
    my ($self)= @_;
    my $end = $self->{'_end'};
    if ($end <= $maxDisplayNo) { return;}
    my $beg = param('beg');
    my $matchNum = $self->{'_matchNum'};
    my $stop = $self->{'_stop'};
    my $skipRow = $self->{'_skipRow'};
    if (!$stop) { $stop = $end;}
    if ($beg < $skipRow + 1) { 
    	$beg = $skipRow + 1; 
    }
    if ($stop < $skipRow + 30) {
    	$stop += $skipRow + 1;
    }
    my $navigationBar;
       
#    if (!$beg) { $beg = 1; }
#    my ($prevBeg, $nextBeg);
#    if ($end > $stop+1) {
#	$nextBeg = $stop-1;
#    }
#    if ($beg > 1) {
#	$prevBeg = $beg - 28;
#	if ($prevBeg < 1) { $prevBeg = 1;}
#    }
    my $id = param('id');
    if (!$id) { $id = $$; }
#    my $filterBy = param('filterBy');
#    my $sortedBy = param('sortedBy');
#    my $searchFor = param('searchFor');
#    my $navigationListRef = $self->{'_navigationList'};
#    my @listItem = @$navigationListRef;
#    my @sortColumn = ("Citation", "Year");
    my $topic = param('topic');
    $topic =~ s/ /\+/g;
    my $url = url."?locus=".$self->locus."&topic=$topic&id=$id";
#    my $nextPrevUrl = $url;
#    if ($filterBy) {
#	$filterBy =~ s/ /\+/g;
#	$searchFor =~ s/ /\+/g;
#	$nextPrevUrl .= "&searchFor=$searchFor&filterBy=$filterBy";	    
#    }
#    elsif ($sortedBy) {
#	$sortedBy =~ s/ /\+/g;
#	$nextPrevUrl .= "&sortedBy=$sortedBy";
#    }
#    $navigationBar =  &navigationBar(database=>$self->database,
#				     url=>$url,
#				     nextPrevUrl=>$nextPrevUrl,
#				     beg=>$beg,
#				     nextBeg=>$nextBeg,
#				     prevBeg=>$prevBeg,
#				     downloadfile=>"geneinfo.$id.xls",
#				     navigateListRef=>\@listItem,
#				     sortListRef=>\@sortColumn,
#				     pos=>'top'), br;
#
    
    $navigationBar = &ResultPageList(url=>$url,
				     totalHit=>$self->{'_end'},
				     beg=>$beg,
				     showNum=>$maxDisplayNo);

    return $navigationBar;
}


########################################################################
sub displayNavigationBar {
########################################################################
    my ($self)= @_;
    my $end = $self->{'_end'};
    if ($end <= $maxDisplayNo) { return;}
    my $beg = param('beg');
    my $matchNum = $self->{'_matchNum'};
    my $stop = $self->{'_stop'};
    my $skipRow = $self->{'_skipRow'};
    if (!$stop) { $stop = $end;}
    if ($beg < $skipRow + 1) { 
    	$beg = $skipRow + 1; 
    }
    if ($stop < $skipRow + 30) {
    	$stop += $skipRow + 1;
    }
    my $navigationBar;
       
    if (!$beg) { $beg = 1; }
    my ($prevBeg, $nextBeg);
    if ($end > $stop+1) {
	$nextBeg = $stop+1;
    }
    if ($beg > 1) {
	$prevBeg = $beg - $maxDisplayNo;
	if ($prevBeg < 1) { $prevBeg = 1;}
    }
    my $id = param('id');
    if (!$id) { $id = $$; }
    my $filterBy = param('filterBy');
    my $sortedBy = param('sortedBy');
    my $searchFor = param('searchFor');
    my $navigationListRef = $self->{'_navigationList'};
    my @listItem = @$navigationListRef;
    my @sortColumn = ("Citation", "Year");
    my $topic = param('topic');
    $topic =~ s/ /\+/g;
    my $url = url."?locus=".$self->locus."&topic=$topic&id=$id";
    if (param('date')) {
	$url .= "&date=1";
    }
    my $nextPrevUrl = $url;
    if ($filterBy) {
	$filterBy =~ s/ /\+/g;
	$searchFor =~ s/ /\+/g;
	$nextPrevUrl .= "&searchFor=$searchFor&filterBy=$filterBy";	    
    }
    elsif ($sortedBy) {
	$sortedBy =~ s/ /\+/g;
	$nextPrevUrl .= "&sortedBy=$sortedBy";
    }
    $navigationBar =  &ResultPageList(url=>$url,
				     totalHit=>$self->{'_end'},
				     beg=>$beg,
				     showNum=>$maxDisplayNo).
	              &navigationBar(database=>$self->database,
				     url=>$url,
				     nextPrevUrl=>$nextPrevUrl,
				     beg=>$beg,
				     nextBeg=>$nextBeg,
				     prevBeg=>$prevBeg,
				     downloadfile=>"geneinfo.$id.xls",
				     navigateListRef=>\@listItem,
				     sortListRef=>\@sortColumn,
				     pos=>'top'), br;
    
    return $navigationBar;
}

########################################################################
sub setDownloadfile {
########################################################################
    my ($self) = @_;
    if (!param('id')) {
	$downloadfile = $configPath->tmpDir."geneinfo.$$.xls";
	$downloadUrl = $configUrl->dictyBaseHtmlTmp."geneinfo.$$.xls";
    }
    else {
	$downloadfile = $configPath->tmpDir."geneinfo.".param('id').".xls";
	$downloadUrl = $configUrl->dictyBaseHtmlTmp."geneinfo.".param('id').".xls";
    }
}

########################################################################
sub getGeneList {
########################################################################
    my ($self) = @_;

    my $locus = $self->{'_locus'};
    $locus =~ s/\*/\%/g;

    my $locusArrayRef = Locus->GetLocusArrayRefBYname(dbh=>$dbh,
						      locus_name=>$locus);
    my @loci;
    foreach my $rowRef (@$locusArrayRef) {
	my ($locusNm) = @$rowRef;
	push(@loci, $locusNm);
    }
    my $featArrayRef = Feature->GetFeatureArrayRefBYname(dbh=>$dbh,
					      feature_name=>$locus);
    foreach my $rowRef (@$featArrayRef) {
	my ($featNm) = @$rowRef;
	push(@loci, $featNm);
    }
    return @loci;
}

########################################################################
sub err_report {
########################################################################
    my ($self, $err) = @_;

    &printStartPage($self->database, $self->title, $self->help);
   
    print b($err);
    
    &printEndPage;

#    $dbh->disconnect;
    exit;
}
########################################################################
sub displayAllRefsThisDate {
########################################################################
## display references published within a time frame.  KD
    my ($self) = @_;
    $self->{'_title'} = "References Added to dictyBase This Week";
    
    my $giObject = GeneInfo->new(dbh=>$dbh);

    my $dateRefs = $self->references4date($giObject);
 
    my $navigationBar = $self->displayNavigationBar;
   
    &printStartPage($self->database, $self->title, $self->help);

    print table({-width=>'100%',
		 -border=>'0'},
		Tr(td($navigationBar)).
                Tr(td(
		      table({-align=>'center',
			     -border=>'0',
			     -cellpadding=>'3',
			     -cellspacing=>'3',
			     -width=>'100%'},
			    Tr(th({-align=>'left',
				   -bgcolor=>'#a4abc2'},
				  "Reference").
			       th({-align=>'left',
				   -bgcolor=>'#a4abc2'},
				  "Genes Addressed")).
			    $dateRefs
		       ))).
		Tr(td($navigationBar))
	 ) ;
}
########################################################################
sub references4date {
########################################################################
    ## KD added to find references added in a range of dates
    my ($self, $giObject) = @_;
    my $arrayRef;
    $arrayRef = $giObject->dateInfo;
    my $end = @$arrayRef;
    

    ## code for navigation bar
    my (@refs, %tmp); 
    if (param('sortedBy') =~ /citation/i) {
	foreach my $rowRef (@$arrayRef) {
	    my ($refNo, $citation, $year, $pubmed, $journal) = @$rowRef;
	    $tmp{$citation} = $refNo."\t".$year."\t".$pubmed."\t".$journal;
	}
	foreach my $citation (sort (keys %tmp) ) {
	    my ($refNo, $year, $pubmed, $journal) = 
		split(/\t/, $tmp{$citation});
	    my @row = ($refNo, $citation, $year);
	    my $rowRef = \@row;
	    push(@refs, $rowRef);
	}
    }
    elsif (!$self->locus) {
	my @tmpRefs;
	foreach my $rowRef (@$arrayRef) {
	    my ($refNo, $citation, $year, $pubmed, $journal) = @$rowRef;
	    if ($tmp{$year}) { $tmp{$year} .= "::"; }
	    $tmp{$year} .= $refNo."\t".$citation."\t".$pubmed."\t".$journal;
	}
	foreach my $year (sort{$a<=>$b} (keys %tmp) ) {
	    my @entry = split(/::/, $tmp{$year});
	    foreach my $entry (@entry) {
		my ($refNo, $citation, $pubmed, $journal) = 
		    split(/\t/, $entry);
		my @row = ($refNo, $citation, $year, $pubmed, $journal);
		my $rowRef = \@row;
		push(@tmpRefs, $rowRef);
	    }
	}
	@refs = reverse (@tmpRefs);
    }
    else {
	@refs = reverse (@$arrayRef);
    }
   
    my $returnList;
    my $bgcolor;
    my $beg = param('beg');
    if (!$beg) { $beg = 1; }
    my $matchYear;
    if (param('navigateList') =~ /^Year ([0-9]+)$/i) {
	$matchYear = $1;
    }
    if (!param('id')) {
	open(OUT, ">$downloadfile") ||
	    die "Can't open '$downloadfile' for writing:$!\n";
	print OUT "Citation\tLoci\n\n";
    }
    my $searchFor = param('searchFor');
    my $filterBy = param('filterBy');
    my ($num, $skipRow, $stop, $matchNum);
    my @navigationList;
    my %year;
    
    my ($locusNm4RefNoHashRef, $featNm4RefNoHashRef, $url4RefNoHashRef);
    my ($relatedRefInfo4RefNoHashRef, $webSupplementUrl4RefNOHashRef);

    if (!$self->locus && @refs > 100) {
	$locusNm4RefNoHashRef = $giObject->getLocusNm4RefNoHashRef;
	$featNm4RefNoHashRef = $giObject->getFeatNm4RefNoHashRef;
	$url4RefNoHashRef = $giObject->getUrl4RefNoHashRef;
	$relatedRefInfo4RefNoHashRef 
	    = $giObject->getRelatedRefInfo4RefNoHashRef;
	$webSupplementUrl4RefNOHashRef 
	    = $giObject->getWebSupplementUrl4RefNoHashRef;
    }

    my %foundRef;
    foreach my $rowRef (@refs) {    
	my ($refNo, $ORIcitation, $year, $pubmed, $journal) = @$rowRef;
	if ($foundRef{$refNo}) { 
	    $end--;
	    next;
	}
	$foundRef{$refNo}++;
	$year{$year}++;
	if ($matchYear && $matchYear < $year) { 
	    $skipRow++;
	    next;
	}
	if ($filterBy) {
	    if ($searchFor =~ /citation/i && 
		$ORIcitation !~ /$filterBy/i) { 
		next; 
	    }
	    elsif ($searchFor =~ /year/i && 
		   $year !~ /$filterBy/i) {
		next;
	    }
	  
        }
	my ($citation, $locusList, $featureList);
	if (!$self->locus && @refs > 100) {
	    my $urls = $$url4RefNoHashRef{$refNo};
	    my $relatedRefInfo = $$relatedRefInfo4RefNoHashRef{$refNo};
	    my $webSuppUrl = $$webSupplementUrl4RefNOHashRef{$refNo};
	    $citation = $self->citation2($refNo, $ORIcitation, $pubmed, 
					 $journal, $urls, 
					 $relatedRefInfo, $webSuppUrl);
	    $locusList = $$locusNm4RefNoHashRef{$refNo};
	    $featureList = $$featNm4RefNoHashRef{$refNo};
	}
	else {
	    my $refObject;
	    ($citation, $refObject) = $self->citation($refNo);
	    foreach my $rowRef (@{$refObject->locusArrayRef}) {
		my ($locusNm) = @$rowRef;
		$locusList .= $locusNm."\t";
	    }
	    $locusList =~ s/\t$//;
	    foreach my $rowRef (@{$refObject->featureArrayRef}) {
		my ($featNm) = @$rowRef;
		$featureList .= $featNm."\t";
	    }
	    $featureList =~ s/\t$//;
	}
	my $loci;
        if ($locusList && $featureList) { 
	    $loci = $locusList."\t".$featureList;
	}
	elsif ($locusList) { $loci = $locusList; }
	elsif ($featureList) { $loci = $featureList; }
	$loci =~ s/^\t//;
	$loci =~ s/\t$//;
	my @loci = split(/\t/, $loci);
	if (!param('id')) {
	    print OUT "$ORIcitation\t@loci\n";
	}
	$num++;
	if ($num < $beg) { next; }
	if ($num >= $beg + $maxDisplayNo && !param('id')) {
	    if (!$stop) { $stop = $num - 1; }
	    next;
	}
	elsif ($num >= $beg + $maxDisplayNo && param('id')) { 
	    if (!$stop) {$stop = $num - 1;}
	    next;
	}
	my $listLoci;
	my $i;
	foreach my $locus (@loci) {
	    if ($self->locus && $self->locus =~ /^$locus$/i) { 
		next;
	    }
	    $i++;
	    if ($i > 15) { last; }
	    if ($i == 15) {
		$listLoci .= " |".a({-href=>$configUrl->dictyBaseCGIRoot."$dblink/reference/reference.pl?refNo=$refNo#summary", -target=>'infowin'}, font({-color=>'red'}, "MORE"));
	    }
	    else {
		$listLoci .= " |".a({-href=>$configUrl->dictyBaseCGIRoot."gene_page.pl?gene_name=$locus", -target=>'infowin'}, $locus);
	    }
	}
	$listLoci =~ s/^\|//;
	if (!$listLoci) { $listLoci = br; }
	if (!$bgcolor) { 
	    $returnList .= Tr(td({-width=>"70%",
				  -valign=>"top"},
				 $citation).
			      td({-width=>"30%",
				  -valign=>"top"},
				 $listLoci));
	    $bgcolor = "#d8d8d8";
	}
	else {
	    $returnList .= Tr({-bgcolor=>"$bgcolor"},
			      td({-width=>"70%",
				  -valign=>"top"},
				 $citation).
			      td({-width=>"30%",
				  -valign=>"top"},
				 $listLoci));
	    $bgcolor = "";
	}
	$matchNum++;
    }
    $self->{'_end'} = $end;
    if (!param('id')) { close(OUT); }
    foreach my $year (sort {$a<=>$b;} keys %year ) {
	push(@navigationList, "Year $year");
    }
    $self->{'_skipRow'} = $skipRow;
    $self->{'_stop'} = $stop;
    $self->{'_matchNum'} = $matchNum;
    $self->{'_navigationList'} = \@navigationList;
    return $returnList ;
}

########################################################################
1;
########################################################################