#!/usr/bin/perl 
package sdevReferenceUserPage;

#######################################################################
##### Author :	Shuai Weng
##### Date   :  Feb. 2001
##### Description : This package contains all necessary methods for 
#####               displaying dictyBase curated paper to user. 
#####              
#######################################################################
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 Reference;
use GeneInfo;
use dictyBaseid;
use Community_annotation;
use TextSearch;
use ConfigURLdictyBase;

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

use lib "/usr/local/dicty/www_dictybase/db/lib/dictyBase";
use dictyBaseObject;
use FormatdictyBase qw(Divider75);
use dictyBaseCentralMod qw(:formatPage :getInfo :navigateInfo);


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

my $dbh;
my $dblink; 
my $configUrl;

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

	$self = {};
	bless $self;

      	$self->{'_database'} = $args{'database'};
	$self->{'_help'}     = defined($args{'help'}) ? 
	                       $args{'help'} : "Paper.html";
	$self->{'_refNo'}    = $args{'refNo'};
	$self->{'_pubmed'}   = $args{'pubmed'};
        $self->{'_ACEname'} = $args{'ACEname'};
    	return $self;
}

sub help { $_[0]->{_help} }
sub database { $_[0]->{_database} }
sub title { $_[0]->{_title} }
sub refNo { $_[0]->{_refNo} }
sub pubmed { $_[0]->{_pubmed} }

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

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

    	my ($self) = @_;
	$configUrl = ConfigURLdictyBase->new;
	$dblink = $configUrl->dblink($self->database);
	if (param('submit')) {
	    if (param('parameter') =~ /Papers in dictyBase/i) {
		$dbh = &ConnectToDatabase($self->database);
		$self->{'_title'} = "dictyBase Curated Papers";
		$self->paperSearch;
		exit;
	    }
	    elsif (param('parameter') =~ /Colleagues in dictyBase/i) {
		my $author = param('author');
		$author =~ s/^([^ ]+) .*$/$1/;
		print "location: ", $configUrl->dictyBaseCGIRoot, "$dblink/colleague/colleagueSearch?lname=$author\n";
		print "Content-type: text/html\n\n";
		exit;
	    }
	    else {
		my $author = param('author');
		$author =~ s/ /\+/g;
		print "location: ", $configUrl->ncbiUrlRoot2, "query?form=4&db=m&term=$author&dispmax=20&relentrezdate=No+Limit\n";
		print "Content-type: text/html\n\n";
		exit;
	    }
	}
	if (param('author')) {
	     $dbh = &ConnectToDatabase($self->database);
	     $self->{'_title'} = "dictyBase Curated Papers";
	     $self->paperSearch;
	     exit;
	}
	$dbh = &ConnectToDatabase($self->database);
	if ($self->{'_ACEname'}) {
	    my $refNo = $self->getRefNo4AceNm;
	    if (!$refNo) {
		my $aceNm = $self->{'_ACEname'};
		print "location: ", $configUrl->breadServerRoot, "cgi-bin/dbrun/SacchDB?find+AcePaper+$aceNm\n";
		print "Content-type: text/html\n\n";
		exit;	
	    }
	    $self->{'_refNo'} = $refNo;
	}
	if (!$self->refNo && !$self->pubmed) {
	    $self->{'_title'} = "Reference Search";
	    $self->printEntryForm;
	    exit;
	}   
	$self->{'_title'} = "dictyBase Curated Paper";
	my $refObject;
	if ($self->refNo) {
	    $refObject = Reference->new(dbh=>$dbh,
					reference_no=>$self->refNo);
	    if (!$refObject) {
		$self->err_report("The reference_no you entered (". $self->refNo.") is not found in database. Please correct it and try again.");
		exit;
	    }
	}
	else {
	    $refObject = Reference->new(dbh=>$dbh,
					pubmed=>$self->pubmed);
	    if (!$refObject->reference_no) {
		$self->err_report("The pubmed id you entered (". $self->pubmed.") is not found in database. Please correct it and try again.");
		exit;
	    }
	}
	if (!param('type')) {
	    $self->displayPaper($refObject);
	}
	else {
	    $self->displayCommentErratum($refObject);
	}
}

#######################################################################
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 Reference_no : ").
                                        td(textfield(-name=>'refNo',
                                                     -size=>'15'))]).
				    Tr({align=>'CENTER'},
				       [
					td(font({-color=>'red'}, b("OR")))]).
				    Tr({align=>'LEFT'},
                                       [
					td("Enter pubmed id : ").
					td(textfield(-name=>'pubmed',
                                                     -size=>'15'))]).
				    Tr({align=>'LEFT'},
                                       [
                                        td(submit, reset, end_form)
                                        ]))
                              )
                           ])));

	&printEndPage;
}

########################################################################
sub displayPaper {
########################################################################
    my ($self, $refObject) = @_;
    &printStartPage($self->database, $self->title, $self->help);
    $self->pageContents($refObject);
    print &Divider75;
    $self->citation($refObject);
    $self->abstract($refObject);
    $self->geneList($refObject);
    
    $self->communityAnnotation($refObject);

    $self->authorSearch($refObject);
    print &Divider75;
    $self->pageContents($refObject);
    &printEndPage;
}

########################################################################
sub displayCommentErratum {
########################################################################
    my ($self, $refObject) = @_;
   
    &printStartPage($self->database, $self->title, $self->help);
    $self->citation($refObject, "comment");
    my $list;
    foreach my $rowRef (@{$refObject->relatedRefArrayRef}) {
	my ($refNo, $pubtype) = @$rowRef;
	my $thisRefObject = Reference->new(dbh=>$dbh,
					   reference_no=>$refNo);
	my $citation = $self->citation($thisRefObject, "list");
	$list .= Tr(td({-width=>'90%',
			-valign=>'top'},
		       $citation).
		    td({-width=>'10%',
			-valign=>'top'},
		       $pubtype));
    }
    print table({-align=>'center',
		 -border=>'0',
		 -cellpadding=>'3',
		 -cellspacing=>'3',
		 -width=>'100%'},
		Tr({-bgcolor=>'#a4abc2'},
		   th({-align=>'left'},
		      "Reference").
		   th({-align=>'left'},
		      "Type")).
		$list
		);
    &printEndPage;
}

########################################################################
sub paperSearch {
########################################################################
    my ($self) = @_;
    my $arrayRef = $self->getRefInfoBYauthor(param('author'));
    if (@$arrayRef == 1) {
	my $rowRef = @$arrayRef[0];
	my ($refNo, $citation, $year) = @$rowRef;
	my $refObject = Reference->new(dbh=>$dbh,
				       reference_no=>$refNo);
	$self->displayPaper($refObject);
	exit;
    }
    &printStartPage($self->database, $self->title, $self->help);
    my @ref = reverse (@$arrayRef);
    my $num = @ref;
    my $tsObj = TextSearch->new(dbh=>$dbh,
				query=>param('author'));
    my $authorNum = $tsObj->authorNum;
    print center(b("There are ".font({-color=>'red'}, $authorNum)." authors associated with ".font({-color=>'red'}, $num)." papers found for author like ".font({-color=>'red'}, param('author'))." in database")),p;
    my $rows;
    foreach my $rowRef (@ref) {
	my ($refNo, $citation, $year) = @$rowRef;
	my $thisRefObj = Reference->new(dbh=>$dbh,
					reference_no=>$refNo);
	my $authorList = $thisRefObj->authorList;
	my $author = param('author');
	$author =~ s/[\*\%]//g;
	
	$authorList =~ s/($author)/<B style="color:black;background-color:#ffff66">$1<\/b>/gi;
	$citation = $self->citation($thisRefObj, "reflist");
	
	$rows .= Tr(td($authorList).
		    td($citation));
    }
    print table({-align=>'center',
		 -border=>'3'},
		Tr({-align=>'center'},
		   th("Author(s)").
		   th("Citation")).
		$rows),p;
    &printEndPage;
}

########################################################################
sub citation {
########################################################################
    my ($self, $refObject, $type) = @_;
    my $citation;
    if ($type =~ /(list|comment)/i) {
	$citation = $refObject->formatedCitation4erratum;
    }
    elsif ($type) {
	$citation = $refObject->formatedCitation;
    }
    else {
	$citation = $refObject->formatedCitationWithFullAuthor;
    }
    ###
    if (!$type) {
	print table({-align=>'center',
		     -border=>'0',
		     -cellpadding=>'3',
		     -cellspacing=>'3',
		     -width=>'550'},
		    Tr(td(font({-size=>'+1'}, $citation))));
    }
    elsif ($type =~ /comment/i){
	print table({-align=>'center',
		     -border=>'0',
		     -cellpadding=>'3',
		     -cellspacing=>'3',
		     -width=>'100%'},
		    Tr(th({-valign=>'top',
			   -bgcolor=>"#a4abc2"},
			  "Comments".br"& Errata".br."relevant to:").
		       td(font({-size=>'+1'}, $citation))));
    }
    else { return $citation; }
}

########################################################################
sub abstract {
########################################################################
    my ($self, $refObject) = @_;
    my $abstract = $refObject->abstract;
    my $status = $refObject->status;
    my $pubtypeArrayRef = $refObject->pubtypeArrayRef;
    my $source = $refObject->ref_source;
    my $pubmed = $refObject->pubmed;
    my $colspanNum = 4; 
    my $abstractContent = td({-align=>'right'}, 
			     font({-size=>'-1'}, 
				  b("Status:"))).
			  td({-align=>'left'},
			     font({-size=>'-1'},
				  $status));

    #replace 'YPD' with 'Pubmed' as ref_source
    if ($source eq 'YPD') {
	$source = 'PubMed';
    }

    if ($$pubtypeArrayRef[0]) {
	my $pubtype;
	foreach my $rowRef (@$pubtypeArrayRef) {
	    my ($type) = @$rowRef;
	    $pubtype .= $type."|";
	}
	$pubtype =~ s/\|$//;
	$colspanNum += 2;
	$abstractContent .= td({-align=>'right'}, 
			       font({-size=>'-1'}, 
				    b("Type:"))).
			    td({-align=>'left'},
			       font({-size=>'-1'},
				    $pubtype));
    }
    $abstractContent .= td({-align=>'right'}, 
			   font({-size=>'-1'}, 
				b("Source:"))).
			td({-align=>'left'},
			   font({-size=>'-1'},
				$source));
    if ($pubmed) {
	$colspanNum += 2;
	$abstractContent .= td({-align=>'right'}, 
			       font({-size=>'-1'}, 
				    b("PubMed ID:"))).
			    td({-align=>'left'},
			       font({-size=>'-1'},
				    $pubmed));
    }
    $abstractContent = Tr($abstractContent);
    if ($abstract) { 
	print "<a name=abstract>";
	$abstractContent = Tr(td({-colspan=>"$colspanNum"}, 
			      b("Abstract:").$abstract)).$abstractContent;
    }
    print table({-align=>'center',
		 -border=>'0',
		 -cellpadding=>'3',
		 -cellspacing=>'3',
		 -width=>'600'},
		$abstractContent);

}

########################################################################
sub geneList {
########################################################################
    my ($self, $refObject) = @_;
    my @lociList = $self->getCuratedGeneList($refObject);
    my (%loci, @loci);
    foreach my $row (@lociList) {
	my ($locus, $locusNo) = split(/:/, $row);
	$loci{$locus}++;
	push(@loci, $locus);
    }
    my @TMPnotYetCuratedLoci = $self->getNotYetCuratedGeneList($refObject);
    my @notYetCuratedLoci;
    foreach my $row (@TMPnotYetCuratedLoci) {
	my ($locus, $locusNo) = split(/:/, $row);
	if (!$loci{$locus}) { 
	    push(@notYetCuratedLoci, $locus);
	}
    }
    print &Divider75;
    if (!@loci && !@notYetCuratedLoci) { return; }
    print "<a name=summary>";
    my %foundTopicGene;
    $self->topic4Gene(\%foundTopicGene, $refObject);
    if (@loci > 20) {
	my $num = @loci;
	print center(b("There are ".font({-color=>'red', -size=>'+1'}, $num)." different genes addressed in this paper."));
	my @tableLabels;
	for (my $i = 0; $i <= $#loci; $i += 10) {
	    my $endIndex = $i + 9;
	    if ($endIndex > $#loci) { $endIndex = $#loci; }
	    my $beg = $i+1;
	    my $end = $endIndex + 1;
	    my $label = "#$beg-$end($loci[$i]-$loci[$endIndex])";
	    push(@tableLabels, "$label");
        }
	my $popup = table({-align=>'center'},
		      Tr(td(b("Jump toSummary Chart for: ")).
			 td(start_form).
			 td(popup_menu(-name=>'jumpItem',
				       -"values"=>\@tableLabels,
				       -onchange=>'jump(this)')).
			 td(end_form)));
	print $popup, &Divider75;
	$self->note;
	my $j = 0;
	for (my $i = 0; $i <= $#loci; $i += 10) {
	    $j++;
	    if ($j == 4 || $j == 7 || $j == 10) {
		print $popup;
		$self->note;
	    }
	    my $endIndex = $i + 9;
	    if ($endIndex > $#loci) { $endIndex = $#loci; }
	    my @displayLoci = @loci[$i..$endIndex];
	    my $beg = $i+1;
	    my $end = $endIndex + 1;
	    my $label = "#$beg-$end($loci[$i]-$loci[$endIndex])";
	    $self->geneTable(\@displayLoci, \%foundTopicGene, $label);
        }
    }
    elsif (@loci > 10) {
	my $num = @loci;
	my $jumpLink = 
	            Tr(td({-width=>'50%',
		           -align=>'center'}, 
			  a({-href=>"#1-10($loci[0]-$loci[9])"}, 
			    "#1-10").
			  " ($loci[0]-$loci[9])").
		       td({-width=>'50%',
                           -align=>'center'}, 
			  a({-href=>"#11-$num($loci[10]-$loci[$#loci])"}, 
			    "#11-$num").
			  " ($loci[10]-$loci[$#loci])"));

	print table({-width=>'600', 
		     -align=>'center'},
		    Tr(th({-colspan=>'2',
			   -align=>'center'}, 
			  b("There are ".font({-color=>'red', -size=>'+1'}, $num)." different genes addressed in this paper. Jump to Summary Chart for: "))).$jumpLink), &Divider75;
	
	my @firstLoci = @loci[0..9];
	my @secondLoci = @loci[10..$#loci];
	my $label1 = "#1-10($loci[0]-$loci[9])";
	my $label2 = "#11-$num($loci[10]-$loci[$#loci])";
	$self->geneTable(\@firstLoci, \%foundTopicGene, $label1);
	$self->note;
	$self->geneTable(\@secondLoci, \%foundTopicGene, $label2);
	print p, table({-width=>'600', 
			-align=>'center'},
		       Tr(th({-colspan=>'2',
			      -align=>'center'}, 
			     b("Jump to Summary Chart for: "))).
		       $jumpLink);
    }
    elsif (@loci >= 1) {
	$self->geneTable(\@loci, \%foundTopicGene);
    }
    if (@notYetCuratedLoci) {
        my $genelist;
	foreach my $locus (@notYetCuratedLoci) {
	    $genelist .= a({-href=>$configUrl->dictyBaseCGIRoot."gene_page.pl?gene_name=$locus",
			    -target=>'infowin'},
			   $locus)." | ";
	}
	if (@notYetCuratedLoci == 1) {
	    print p, center(b("There is one 'not yet curated' gene for this paper. ". $genelist));
	}
	else {
	    print p, center(b("There are ".@notYetCuratedLoci." 'not yet curated' genes for this paper. ".$genelist));
        }
    }

}

########################################################################
sub note {
########################################################################
    print table(
		Tr(
		   td({-align=>'left',
		       -width=>'100%'},
		      ul(li("To find other papers on a gene and topic, click in the appropriate box.").
			 li("To go to the Locus page for a gene, click on the gene name."))
		  )));
}

########################################################################
sub geneTable {
########################################################################
    my ($self, $lociRef, $foundTopicGeneRef, $label) = @_;
    my $subtitle = "Genes addressed in this paper ";
    if ($label) {
	print "<a name=$label>";
	$label =~ s/^([^\(]+)\(.+$/$1/;
	if ($label =~ /^#([0-9]+)-([0-9]+)$/) {
	    if ($1 == $2) { $label = "#$1"; }
	}
	$subtitle .= "($label)";
    }
    my $geneNum = @$lociRef;
    my $tableHeader;
    my %foundLocus;
    foreach my $locus (@$lociRef) {
	$tableHeader .= th({-rowspan=>'2',
			    -align=>'center',
			    -valign=>'center',
			    -bgcolor=>'#b7d8e4'},
			   a({-href=>$configUrl->dictyBaseCGIRoot."gene_page.pl?gene_name=$locus",
			      -target=>'infowin'}, $locus));
	$foundLocus{$locus}++;
    }
    my $geneTable;
    my %foundTopic;
    foreach my $key (sort (keys %$foundTopicGeneRef)) {
	my ($topic, $locus) = split(/:/, $key);
	my $linkTopic = $topic;
	$linkTopic =~ s/ /\+/g;
	if ($foundLocus{$locus} && !$foundTopic{$topic}) {
	    $foundTopic{$topic}++;
	    my $tableCell = td({-width=>"20%"},
			       $topic);
	    foreach my $gene (@$lociRef) {
		if ($$foundTopicGeneRef{"$topic:$gene"}) {
		    $tableCell .= td({-width=>"10%",
				      -align=>'center'},
				     a({-href=>$configUrl->dictyBaseCGIRoot."$dblink/reference/geneinfo.pl?locus=$gene&topic=$linkTopic",
				        -target=>'infowin'},
				       "X"));
		}
		else {
		    $tableCell .= td({-width=>"10%"}, br);
		}
	    }
	    $geneTable .= Tr($tableCell);
	}
    }
    print p,
          table({-align=>'center',
	         -border=>'1',
		 -cellpadding=>'4',
		 -cellspacing=>'2',
		 -width=>"100%"},
		 Tr(td({-rowspan=>'2'}).
		    th({-align=>'center',
			-colspan=>"$geneNum",
			-align=>'center',
			-bgcolor=>'#a4abc2'},
		       $subtitle)).
		 Tr($tableHeader).
		 Tr(th({-align=>'center',
			-bgcolor=>'#a4abc2'},
		       "Topics in this paper")).
		 $geneTable
	  );

}

########################################################################
sub authorSearch {
########################################################################
    my ($self, $refObject) = @_;
    my $authorList = $refObject->authorList;
    my @author = split(/\, /, $authorList);
    if ($author[$#author] =~ /et al/i) {
	pop @author;
    }
    my $authorPopup = popup_menu(-name=>'author',
				 -"values"=>\@author);
    my @parameter = ("Papers in dictyBase", "Colleagues in dictyBase", "PubMed");
    my $paraPopup = popup_menu(-name=>'parameter',
				 -"values"=>\@parameter);
    print "<a name=author>";
    print start_form, table({-align=>'center',
			     -width=>'600',
			     -border=>'0',
			     -cellpadding=>'3',
			     -cellspacing=>'3'},
			    Tr(th({-align=>'left',
				   -bgcolor=>'#a4abc2'},
				  "&nbsp;Author Searches")).
			    Tr(td({-bgcolor=>'#d8d8d8'},
				  table({-border=>'0',
					 -cellpadding=>'0',
					 -cellspacing=>'0'},
					Tr(td({-colspan=>'3'}, "To find contact information or other publications by the authors of this paper, follow these three steps:".br.br)).
					Tr(td("(1) Choose an author,").
					   td("(2) Choose a search parameter,&nbsp;&nbsp;&nbsp;&nbsp;").
					   td("(3) Click to implement.")).

					Tr(td($authorPopup).
					   td($paraPopup).
					   td(submit(-name=>'submit',
						     -value=>'Search!')))
					)))

			    ), end_form;
}

########################################################################
sub topic4Gene {
########################################################################
    my ($self, $foundTopicGeneRef, $refObject) = @_;
   
    foreach my $rowRef (@{$refObject->locusTopicArrayRef}) {
	my ($topic, $locusNm) = @$rowRef;
	uc($locusNm);
	$$foundTopicGeneRef{"$topic:$locusNm"}++;
    }
    foreach my $rowRef (@{$refObject->featureTopicArrayRef}) {
	my ($topic, $featNm) = @$rowRef;
	uc($featNm);
	$$foundTopicGeneRef{"$topic:$featNm"}++;
    }
}

########################################################################
sub getRefNo4AceNm {
########################################################################
    my ($self) = @_;
    my $refNo = Reference->GetReferenceNoBYaceNm(dbh=>$dbh,
				    ACEname=>$self->{'_ACEname'});
    return $refNo;
}

########################################################################
sub getCuratedGeneList {
########################################################################
    my ($self, $refObj) = @_;
    my @loci = $refObj->getCuratedLoci;
    my @feats = $refObj->getCuratedFeatures;
    push (@loci, @feats);
    return @loci;
}

########################################################################
sub getNotYetCuratedGeneList {
########################################################################
    my ($self, $refObj) = @_;
    my @loci = $refObj->getNotYetLoci;
    my @feats = $refObj->getNotYetFeatures;
    push (@loci, @feats);
    return @loci;
}

########################################################################
sub getRefInfoBYauthor {
########################################################################
    my ($self, $author) = @_;
    $author = "\U$author"; 
    $author =~ s/\*/\%/g;
    if ($author !~ /\%/) {
	$author = $author."\%";
    }
    my $arrayRef = Reference->GetRefInfoArrayRefBYauthor(dbh=>$dbh,
					       author=>$author);
    return $arrayRef;
}


########################################################################
sub pageContents {
########################################################################
    my ($self, $refObject) = @_;
    my $pageContent = a({-href=>'#author'}, "Author Search")." | ";
    my $locusArrayRef = $refObject->locusArrayRef;
    my $featureArrayRef = $refObject->featureArrayRef;
    if ($$locusArrayRef[0]->[0] || $$featureArrayRef[0]->[0]) {
	$pageContent = a({-href=>'#summary'}, "Summary Chart").
	    " | ".$pageContent;
    }
    if ($refObject->abstract) {
	$pageContent = a({-href=>'#abstract'}, "Abstract").
		      " | ".$pageContent;
    }
    if ($refObject->dictyBaseidForCommunityAnnotatedRef) {
	$pageContent .= a({-href=>'#CA'},
			  "Community Annotation").
			a({-href=>'#CA'},
			  img({-src=>$configUrl->dictyBaseImages."star.gif",
			       -border=>0}));
    }
			   
    $pageContent = "Page Contents: ".$pageContent;
    print table({-align=>'center'}, 
		    Tr(td($pageContent)));
    
}

########################################################################
sub communityAnnotation {
########################################################################
    my ($self, $refObject) = @_;

    if (!$refObject->dictyBaseidForCommunityAnnotatedRef) { return; }

    my @dictyBaseid = split(/\|/, $refObject->dictyBaseidForCommunityAnnotatedRef);

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

    my $rows;

    foreach my $dictyBaseid (@dictyBaseid) {

	my $dictyBaseidObj = dictyBaseid->new(dbh=>$dbh,
				  dictyBaseid=>$dictyBaseid);

	my $featNm = $dictyBaseidObj->feature_name;
	
	my $showNm = $dictyBaseidObj->locus_name;

	if ($dictyBaseidObj->feature_name) { 

	    if ($showNm) { $showNm .= "/"; }

	    $showNm .= $dictyBaseidObj->feature_name;

	}
	
	my $arrayRef = 
	    Community_annotation->CommunityAnnotationArrayRef(dbh=>$dbh,
							      dictyBaseid=>$dictyBaseid);
	
	my $list;

	foreach my $rowRef (@$arrayRef) {

	    my ($community_annotation_no, $annotation_set_no, 
		$topic, $other) = @$rowRef;

	    my $anchor = $topic;

	    $anchor =~ s/^([^ ]+) .+$/$1/;
	    $anchor =~ s/[,;]$//;

	    $list .= a({-href=>$communityUrl.$dictyBaseid."#$anchor",
		        -target=>'infowin'},
		       $topic)." | ";
	    
	}
	$list =~ s/ \| $//;

	$rows .= Tr(td({-align=>'center'},
		       a({-href=>$locusUrl.$dictyBaseid,
			  -target=>'infowin'},
			 $showNm)).
		    td($list));
    }

    print &Divider75;

    print table({-width=>'100%',
		 -border=>0,
		 -cellspacing=>3,
		 -cellpadding=>4},
		Tr(th({-align=>'left',
		       -colspan=>2},
		      a({-name=>'CA'},
			img({-src=>$configUrl->dictyBaseImages."star.gif",
			     -border=>0})).
		      font({-size=>'+1'},
			   "This reference has been selected for Community Annotations on the genes and topics listed in the table below."))).
		Tr(td(font({-color=>'red'},
			   "NOTE: ")."Community annotations are submitted by members of the Dictyostelium community.".a({-href=>$configUrl->dictyBaseCGIRoot."$dblink/communityAnnotation"},
														"Click here")." to submit a Community Annotation."))),br;


    print table({-width=>'100%',
		 -border=>1,
		 -cellspacing=>3,
		 -cellpadding=>4},
		Tr(th({-bgcolor=>"#a4abc2"}, "Gene/ORF").
		   th({-bgcolor=>"#a4abc2"}, "Topic")).
		$rows),p;

    print &Divider75;

}


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

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

    if (defined $dbh) {
	$dbh->disconnect;
    }
    exit;
}


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