', # editorial
);
# retrieve a list of locus names and locus no. from the database
my %locusNo;
my $dbOff = 0;
if ($dbOff != 1) {
my $sqlGetLoci = ("SELECT locus_no, locus_name "
. "FROM CGM_DDB.locus");
my $sthGetLoci = $dbh->prepare($sqlGetLoci);
$sthGetLoci->execute();
while (my $array_ref = $sthGetLoci->fetchrow_arrayref) {
my $locus_no = $array_ref->[0];
my $locus_name = $array_ref->[1];
if (!defined $locusNo{$locus_name}) {
$locusNo{$locus_name} = $locus_no;
}
else {
$locusNo{$locus_name} .= ",$locus_no";
}
}
$sthGetLoci->finish();
}
# retrieve a list of alias names and locus no from the database.
if ($dbOff != 1) {
my $sqlGetLoci = ( "SELECT la.locus_no, a.alias_name "
. "FROM CGM_DDB.locus_alias la, CGM_DDB.alias a "
. "WHERE la.alias_no = a.alias_no ");
my $sthGetLoci = $dbh->prepare($sqlGetLoci);
$sthGetLoci->execute();
while (my $array_ref = $sthGetLoci->fetchrow_arrayref) {
my $locus_no = $array_ref->[0];
my $locus_name = $array_ref->[1];
if (!defined $locusNo{$locus_name}) {
$locusNo{$locus_name} = $locus_no;
}
else {
$locusNo{$locus_name} .= ",$locus_no";
}
}
$sthGetLoci->finish();
}
# translate ace_papers/references to dictyBase format
my %ace2oracle;
if ($dbOff != 1) {
my $sth
= $dbh->prepare("select unique(ACE_OBJECT), PRIMARY_KEY "
. "from CGM_DDB.ACELINK "
. "where ACE_CLASS = 'Paper' "
. "and TAB_NAME = 'REFERENCE'");
$sth->execute();
while (my $array_ref = $sth->fetchrow_arrayref) {
my $ace_paper_name = $array_ref->[0];
my $reference_no = $array_ref->[1];
$ace2oracle{$ace_paper_name} = $reference_no;
if ($reference_no eq "REFERENCE_NO") {
# print $ace_paper_name . "\t" . $reference_no . "\n";
}
}
$sth->finish();
}
my %paragraphs; # stores the paragraphs
my $paragraphCount = 0; # count of how many paragraphs read from flat file
my $aceParagraphCount = 0; # count of how many paragraphs read from flat file
my $duplicateCount = 0; # count of loci with identical paragraphs
my $badRefsCount = 0; # count of paragraphs not loaded because could not find
# a REFERENCE_NO for their ACE_paper_name (papers not yet loaded into Oracle?)
my $loadedParagraphsCount= 0; # count of paragraphs loaded into Oracle
my %paragraphUseCount; # number of times a given paragraph is used
# used to track identical paragraphs, word for word
my %identicalParagraphs; # lists all the loci that share the exact same
# paragraph text
my %primaryLoci; # lists all the primary loci for a given paragraph
# iterate through flat-file, locating paragraphs and associating them with
# loci
# Some browsers transmit line breaks as \r instead of the traditional
# \n. This will convert all \r line breaks to \n
$text =~ s/\r\n/\n/g;
$text =~ s/\r/\n/g;
foreach my $line (split(/\n/, $text)) {
$line .= "\n";
if ($line =~ /^\/\//) { next; }
if ($line =~
/^LongText : \"Gene Summary Paragraph for ([\w\-\'\,]+)\"/ ) {
$locusName = $1;
$locusName =~ tr/[a-z]/[A-Z]/;
$inParagraph = 1;
$aceParagraphCount++;
next;
}
# translate ACE-style initials into Oracle user-names
if (($line =~ m/(\d{4}-\d{1,2}-\d{1,2}) (\w+)/)
&& (defined $curators{$2})) {
$line =~ s/(\d{4}-\d{1,2}-\d{1,2}) (\w+)/$1 $curators{$2}/
}
if ($line =~ /\*\*\*LongTextEnd\*\*\*/) {
$paragraph =~ s/\n{2,}//g;
$paragraph =~ s/[\n +]/ /g;
$inParagraph = 0;
my $locusNo = $locusNo{$locusName};
# keep track of how many other loci use the current paragraph
if (defined $paragraphUseCount{$paragraph}) {
my $originalLocusName = $paragraphUseCount{$paragraph};
# $primaryLoci{$originalLocusName}{$locusNo} = 1;
foreach my $individualLocusNo(split(/,/, $locusNo)) {
$primaryLoci{$originalLocusName}{$individualLocusNo} = 1;
}
if (defined $identicalParagraphs{$paragraphUseCount{$paragraph}}) {
$identicalParagraphs{$originalLocusName} .= "," . $locusNo;
}
else {
$identicalParagraphs{$originalLocusName} = $locusNo;
}
$duplicateCount++;
}
else {
$paragraphs{$locusName} = $paragraph;
$paragraphUseCount{$paragraph} = $locusName;
foreach my $individualLocusNo(split(/,/, $locusNo)) {
$primaryLoci{$locusName}{$individualLocusNo} = 1;
}
}
$locusName = "";
$paragraph = "";
$paragraphCount++;
}
if ($inParagraph == 1) {
$paragraph .= $line;
}
}
my $noDCStampCount = 0;
my %phraseCategoryFull = reverse %phraseCategories;
my %badRefs;
# enables flushing of standard out without a \n character;
$|=1;
# find the longest phrase, and the loci whose paragraph contains that
# longest phrase
my $maxPhraseLength = 0;
my $maxPhraseLocus = "";
parag:
foreach my $locus (sort keys %paragraphs) {
my %secondaryLoci;
my $paragraph = $paragraphs{$locus};
my $locusNo = $locusNo{$locus}; # translate locus_name to a locus_no
my $date;
my $curator;
my $noDCStamp = 0;
if ($paragraph =~ /((\d{4}-\d{1,2}-\d{1,2}) (\w+))/) {
$date = $2;
$curator = $3;
# remove the date/curator stamp from the raw-text
$paragraph =~ s/$1//;
}
else {
$noDCStampCount++;
$noDCStamp = 1;
}
# Correcting any variants of "Homolog" to "related_genes"
$paragraph =~ s/\<(\/*)Homologs*/\<$1related_genes/g;
$paragraph =~ s/\<(\/*)homologs*/\<$1related_genes/g;
# do not allow consecutive tags separated by a comma without a space
$paragraph =~ s/\>,\, \/) {
if (defined $ace2oracle{$1}) {
my $ref_no = $ace2oracle{$1};
$paragraph =~ s/\<$1\>/\/g;
}
else {
# look for references that cannot be translated into
# Oracle reference numbers
$badRefsCount++;
if (defined $badRefs{$1}) {
$badRefs{$1} .= ",$locus";
}
else {
$badRefs{$1} = $locus;
}
die ("Unable to parse paragraph because it contains "
. "the following ACE paper reference that is not "
. "yet loaded into Oracle: " . $1 . "\n"
);
next parag;
}
}
# mark off locus names in the text
my $poss_locusName = $word;
if ($word =~ m/^\(*((\<[a-zA-Z\_\ ]*\>)*([A-Za-z\-\,\'0-9]+)\)*)/) {
$poss_locusName = $3;
$poss_locusName =~ s/^\W//; # remove leading whitespace
$poss_locusName =~ s/[,\.]$//; # remove trailing , or .
$poss_locusName =~ s/p$//i; # remove trailing p or P
my $poss_locusNameUC = $poss_locusName;
$poss_locusNameUC =~ tr/[a-z]/[A-Z]/;
if (
(defined $locusNo{$poss_locusNameUC})
&&
($paragraph !~ /\$poss_locusName<\/locus>/)
) {
# get the list of locus_no's corresponding to this locus
# name
my $locusNo = $locusNo{$poss_locusNameUC};
my $locusNoTmp = "";
# locus_name maps to multiple loci, don't embed a single
# locus number into the tag, use a hash symbol
# (The hash symbol tells the paragraph render function
# to do a search by locus_name)
if ($locusNo =~ /,/) {
$locusNoTmp = "#";
}
else {
$locusNoTmp = $locusNo;
}
(my $firstLocusNo, undef) = split(/,/, $locusNo);
if (defined $primaryLoci{$locus}{$firstLocusNo}) {
$paragraph =~ s/(\W)$poss_locusName([\Wp])/$1\$poss_locusName<\/locus>$2/g;
}
else {
if (!defined $secondaryLoci{$locusNo}) {
$paragraph =~ s/(\W)$poss_locusName([\Wp])/$1\$poss_locusName<\/locus>$2/g;
foreach my $locusNo (split(/,/, $locusNo)) {
$secondaryLoci{$locusNo} = 1;
}
}
else {
}
}
}
# locate new primary loci
elsif ($word =~ /locus01:(\S+)/) {
my $locusNo = $1;
my $primaryLocusName = $paragraphUseCount{$paragraph};
my $otherPrimaryLoci =
$identicalParagraphs{$primaryLocusName};
if ($otherPrimaryLoci !~ /$locusNo/) {
$identicalParagraphs{$primaryLocusName} = ", $locusNo";
}
}
}
$poss_locusName = "";
}
# location tags - convert to 'cellular_component'
$paragraph =~ s/\<(\/*)location/\<$1cellular_component/g;
$paragraph =~ s/\n\n/\/g; # try to locate paragraph breaks
$paragraph =~ s/\n/ /g; # remove forced line breaks
$paragraph =~ s/(\)*$//; # remove trailing tags
$paragraph =~ s/^(\)*//; # remove leading tags
$paragraph =~ s/\\//g; # remove multiple tags
# tag corections
$paragraph =~ s/\>,\, \//g; # remove tags
$paragraph =~ s/\<\/name\>//g; # remove tags
# replace phrase categories with 2-letter phrase category abbreviations
foreach my $phraseCategory (sort keys %phraseCategories) {
my $abbrev = $phraseCategories{$phraseCategory};
$paragraph =~ s/\<$phraseCategory\>/\/g;
$paragraph =~ s/\<\/$phraseCategory\>/\<\/PC_$abbrev\>/g;
}
# remove spaces from phrases that have one or more spaces between the
# last start phrase category tag and the first word of the phrase
$paragraph =~ s/\ +(\w)/\$2/g;
# insert a space between ending and starting phrase category markers
$paragraph =~ s/\<\/PC_(\w\w)\>\/\<\/PC_$1\> \/g;
# remove spaces from between start pharse category tags
$paragraph =~ s/\\W+\/\\/g;
$paragraph =~ s/\<\/*name\>//g; # remove and tags
# $paragraph =~ s/\<\/*i\>//g; # remove and tags
# $paragraph =~ s/\<\/*b\>//g; # remove and tags
# attempt to locate the end of a phrase if it is not terminated by
# an end phrase category tag
$paragraph =~ s/[\.\s+](\)/\<\/PC_ZZ\> $1/g;
# put each phrase on its own line, each phrase is prefixed with %
$paragraph =~ s/(\<\/PC_\w\w\>) +(\)/$1\n\%\%\%\t$2/g;
# look for phrases that are separated by a and place that tag
# inside previous phrase, and then break the phrases onto separate
# lines
# $paragraph =~ s/(\<\/PC_\w\w\>)
(\)/$1\n\%\%\%\t$2/g;
$paragraph =~ s/(\<\/PC_\w\w\>)*
(\)/$1\n\%\%\%\t$2/g;
# locate the first phrase of the paragraph and place it on its own
# line, prefixed with a % symbol
$paragraph =~ s/^ *(\)/\%\%\%\t$1/;
# remove spaces between > and ) symbols
$paragraph =~ s/\>\W+\)/\>\)/g;
# look for paragraphs whose loci we cannot identify locus_no for
if (defined $locusNo) {
}
else {
$locusNo = "***** $locus *****";
}
# retrieve a list of all other loci that share an identical paragraph
# with the current paragraph
my $otherPrimaryLoci = "";
if (defined $identicalParagraphs{$locus}) {
$otherPrimaryLoci = "," . $identicalParagraphs{$locus};
}
# this line adds a list of primary loci to the line
$paragraph =~ s/\%\%\%/\%\%\%\t$locusNo$otherPrimaryLoci/g;
# remove any remaining end-phrase category tags
$paragraph =~ s/\<\/PC_\w\w\>//g;
# insert a tab between start phrase category tags and the first word
# of the phrase
$paragraph =~ s/(\)(\w)/$1\t$2/g;
# insert a tab between start phrase category tag and the first tag
# provided that the second tag:
# (is not a phrase category tag/does not start with P)
$paragraph =~ s/(\)\s*(\<[^P])/$1\t$2/g;
# strip off the angle-bracks and PC_ prefix of the start phrase
# category tag
$paragraph =~ s/\/$1,/g;
$paragraph =~ s/\s*$//g; # remove trailing spaces
$paragraphCount--;
# error check: ensure that the first phrase is marked off with a
# phrase category
if ($paragraph !~ /^\%\%\%\W+\d+\W\w+\W/) {
die ("The submitted paragraph does not start with a valid "
. "phrase category tag (2).\n"
);
}
#### CREATE PARAGRAPH & PHRASE OBJECTS and LOAD INTO THE DATABASE ####
my $paragraph_obj = ParagraphDS->new(dbh=>$dbh);
# If there is no curator or date stamp, then just use today's date
# and the current curator as a default curator/date stamp.
if ($noDCStamp == 1) {
$curator = $self->user;
(my $DAY, my $MONTH, my $YEAR) = (localtime)[3,4,5];
if ($MONTH < 10) { $MONTH = "0" . $MONTH; }
if ($DAY < 10) { $DAY = "0" . $DAY; }
$date = ($YEAR+1900) . "-" . ($MONTH+1) . "-" . $DAY;
}
$paragraph_obj->setWrittenBy($curator);
$paragraph_obj->setDateWritten($date);
my $phraseCount = 0;
foreach my $phrase (split(/\n/, $paragraph)) {
(undef, my $locusNo, my $phraseCatAbbrev, my $phraseText)
= split(/\t/, $phrase);
foreach my $primaryLocus (split(/,/, $locusNo)) {
if ((!defined $secondaryLoci{$primaryLocus}) &&
(!defined $forcePrimaryLocus))
{
$paragraph_obj->setPrimaryLoci($primaryLocus);
}
}
if (defined $forcePrimaryLocus) {
$paragraph_obj->setPrimaryLoci($forcePrimaryLocus);
}
my $new_phrase
= $paragraph_obj->insertPhrase(new_phrase_text=>$phraseText,
new_phrase_order=>9999);
$phraseCatAbbrev =~ s/ +//g;
foreach my $phraseCat (split(/,/, $phraseCatAbbrev)) {
my $phraseCatFull = $phraseCategoryFull{$phraseCat};
$phraseCatFull =~ s/_/ /g;
$new_phrase->setPhraseCategory($phraseCatFull);
}
$phraseCount++;
}
$loadedParagraphsCount++;
return $paragraph_obj;
}
}
########################################################################
sub printEMailBugReport {
########################################################################
my ($self, $message) = @_;
##########################
my @buttons = ();
push(@buttons, ("E-Mail"
. ("\tSend bug report.")));
my $options
= $self->buttons("Select an action", \@buttons);
##########################
my $query = new CGI;
my @names = $query->param();
my $cgiFieldValues = "";
foreach my $pName (@names) {
$cgiFieldValues .= $pName . " = \"" . param($pName) . "\"\n";
}
my $output = "";
$output .= (p
"To correct this error, use the BACK button on your browser "
. "and make the appropriate corrections."
. p
. "If you do not understand or know how to correct the error "
. "above, this error may require the attention of an dictyBase "
. " programmer. "
. "The form below may be useful in reporting this problem: "
);
my $userEmail = lc($hiddenVars{'user'}) . $domain;
$output .= (startform .
table(Tr(td(
"Programmer's E-mail address: "
).
td(
textfield(-name=>"To",
-size=>75,
-value=>$programmerEmail)
)
).
Tr(td(
"Your e-mail address: "
).
td(
textfield(-name=>"From",
-size=>75,
-value=>$userEmail
)
)
).
Tr(td({-valign=>"top"},
"Your comments").
td(
textarea({-name=>'comments',
-cols=>78,
-wrap=>"yes",
-rows=>10})
)
).
Tr(td({-valign=>"top"},
"Error Message").
td(
textarea({-name=>'error',
-value=>$message,
-cols=>78,
-wrap=>"yes",
-rows=>5})
)
).
Tr(td({-valign=>"top"},
"Script Data").
td(
textarea({-name=>'cgiFields',
-value=>$cgiFieldValues,
-wrap=>"yes",
-cols=>78,
-rows=>5})
)
)
).
$self->embedHiddenFields() .
br.
submit({-name=>'submit',
-value=>"Report Problem",
}
) .
endform
);
return $output;
}
########################################################################
sub emailBugReport {
########################################################################
my ($self) = @_;
my $destEMail = param('To');
my $origEMail = param('From');
my $comments = param('comments');
my $errorMsg = param('error');
my $cgiFields = param('cgiFields');
my $output = "";
eval {
open (MAIL, "|/usr/lib/sendmail -oi -t");
my $mailHeaders =
("From: $origEMail\n"
. "To: $destEMail\n"
. "Subject: $self->{'_database'} Paragraph Curation Page "
. "-- problem report\n");
print MAIL $mailHeaders;
my $separator = "==========================================\n";
print MAIL ("This message was generated by a user who encountered an "
. "error while using the Paragraph Curation script. It "
. "was most likely generated during a database commit "
. "operation. \n\n");
print MAIL $separator;
print MAIL ("The user has provided the following comments:\n\n"
. $comments . "\n\n"
);
print MAIL $separator;
print MAIL ("The script generated the following error message:\n\n"
. $errorMsg . "\n\n"
);
print MAIL $separator;
print MAIL ("The following data was passed to the script:\n\n"
. $cgiFields . "\n\n"
);
print MAIL $separator;
print MAIL ("This is the end of the problem report message, generated "
. "on " . (scalar localtime) . "\n\n");
close(MAIL);
$output .= "Your bug report has been sent to " . $destEMail . p;
};
if ($@) {
my $errorMessage = $@;
$output .= "An error was encountered while e-mailing your bug report.";
$output .= p. code($@) . p;
$output .= ("Your bug report was not sent. Please contact a "
. "programmer via other means."
. p);
}
return $output;
}
########################################################################
sub mergePhrase {
########################################################################
my ($self, %args) = @_;
my $mergeType = $args{'type'};
my $paragraphNo = $args{'paragraphNo'};
my $currPhraseNo = $args{'currPhraseNo'};
my $phrase1Obj;
my $phrase2Obj;
my $phrase1No;
my $phrase2No;
my $paragraphObj = ParagraphDS->new(dbh=>$dbh,
paragraphNo=>$paragraphNo);
if ($mergeType eq "previous") {
$phrase2No = $currPhraseNo;
$phrase2Obj = PhraseDS->new(dbh=>$dbh,
phrase_no=>$phrase2No
);
$phrase1Obj = $paragraphObj->getPhrase($phrase2Obj->getPhraseOrder() - 1);
$phrase1Obj = $paragraphObj->getPhrase(0);
$phrase1No = $phrase1Obj->getPhraseNo();
}
else {
$phrase1No = $currPhraseNo;
$phrase1Obj = PhraseDS->new(dbh=>$dbh,
phrase_no=>$phrase1No
);
$phrase2Obj = $paragraphObj->getPhrase($phrase1Obj->getPhraseOrder() + 1);
$phrase2No = $phrase2Obj->getPhraseNo();
}
$phrase1Obj->setPhraseText($phrase1Obj->getPhraseText()
. " "
. $phrase2Obj->getPhraseText());
# merge phrase categories
my $phrase2PCRef = $phrase2Obj->getPhraseCategories();
my %phrase2PC = %$phrase2PCRef;
foreach my $p2PC (sort keys %phrase2PC) {
$phrase1Obj->setPhraseCategory($p2PC);
}
# delete the phrase from the paragraph object
$paragraphObj->updatePhrase($phrase1Obj,
$phrase1Obj->getPhraseOrder());
$paragraphObj->deletePhrase($phrase2Obj->getPhraseNo);
my $output = "";
# commit the changes to the database.
eval {
$paragraphObj->update();
$dbh->commit();
# $dbh->rollback();
$output .= $self->blueTitleBar("Messages: ");
$output .= ("The phrase has been succesully merged."
." All phrase data has been updated and committed into "
." the database."
.p);
$output.= $self->printEditPhrase(
phraseObj=>$phrase1Obj,
paragraphObj=>$paragraphObj
);
};
if ($@) {
my $errorMessage = $@;
$output .= $self->blueTitleBar("Error Encountered: ");
$output .= code($errorMessage);
$output .= p;
$output .= $self->blueTitleBar("What to do next: ");
$output .= $self->printEMailBugReport($errorMessage
. "\n\n" . "");
$output .= $self->printEditPhrase(
phrase_no=>$currPhraseNo,
paragraph_no=>$paragraphNo
);
}
return $output;
}
########################################################################
sub splitPhrase {
########################################################################
my ($self, %args) = @_;
my $paragraphNo = $args{'paragraphNo'};
my $phraseNo = $args{'phraseNo'};
my $phraseObj = PhraseDS->new(dbh=>$dbh,
phrase_no=>$phraseNo);
my $paragraphObj = ParagraphDS->new(dbh=>$dbh,
paragraphNo=>$paragraphNo);
my $phraseText = param('phraseText');
if ($phraseText !~ m/\w*\|\|\|\w*/) {
die "Unable to determine where this phrase should be split";
}
my ($oldPhraseText, @newPhraseTexts) = split(/\|\|\|/, $phraseText);
$phraseObj->setPhraseText($oldPhraseText);
my $oldPhraseOrder = $phraseObj->getPhraseOrder();
$paragraphObj->updatePhrase($phraseObj,
$oldPhraseOrder);
my $splitPhraseInsertPosition = $oldPhraseOrder + 1;
# retrieve phrase categories
my $pcRef = $phraseObj->getPhraseCategories();
my %existingPhraseCategories = %$pcRef;
foreach my $newPhraseText(@newPhraseTexts) {
# print "Working on phrase: $newPhraseText", br;
my $newPhraseObj = PhraseDS->new(dbh=>$dbh);
$newPhraseObj->setPhraseText($newPhraseText);
# print "The phrase contains this text: " . $newPhraseObj->getPhraseText() . br;
$newPhraseObj->validate();
# print "Phrase validated.", br;
foreach my $phraseCategory (sort keys %existingPhraseCategories) {
$newPhraseObj->setPhraseCategory($phraseCategory);
}
# print "Attempting to insert the phrase in to the paragraph.", br;
$paragraphObj->insertPhrase
(new_phrase_object=>$newPhraseObj,
new_phrase_order=>$splitPhraseInsertPosition++);
# print "The phrase insertion was successful.", br;
}
my $output = "";
# commit the changes to the database.
eval {
# print "Updating the paragraph object.", br;
$paragraphObj->update();
# print "Update of paragraph completed.", br;
$dbh->commit();
# $dbh->rollback();
$output .= $self->blueTitleBar("Messages: ");
$output .= ("The phrase has been succesully split. "
. "All phrase data has been updated and committed into "
. "the database."
.p);
$output.= $self->printEditPhrase(
phraseObj=>$phraseObj,
paragraphObj=>$paragraphObj
);
};
if ($@) {
my $errorMessage = $@;
$output .= $self->blueTitleBar("Error Encountered: ");
$output .= code($errorMessage);
$output .= p;
$output .= $self->blueTitleBar("What to do next: ");
$output .= $self->printEMailBugReport($errorMessage
. "\n\n" . "");
$output .= $self->printEditPhrase(
phrase_no=>$phraseNo,
paragraph_no=>$paragraphNo
);
}
return $output;
}
########################################################################
sub printParagraphReferences {
########################################################################
my ($self, %args) = @_;
my $paragraphNo = $args{'paragraphNo'};
$self->{'_title'} = (uc($self->database) . " Paragraph References");
my $paragraphObj;
if (defined $paragraphNo) {
$paragraphObj = ParagraphDS->new(dbh=>$dbh,
paragraphNo=>$paragraphNo);
}
else {
return;
}
#### DUPLICATED CODE FROM ParagraphUI.pm::displayParagraph()
my $referenceListRef = $paragraphObj->getReferences();
my @referenceList = @$referenceListRef;
my $references = "";
my $refno = 1;
my @bgcolor = ("#FFFFFF", "#F5F5F5");
my %references;
foreach my $ref (@referenceList) {
my $refObj;
my $reference_no;
if ($ref =~ /RF:(\d+)/) {
$reference_no = $1;
$refObj = Reference->new(dbh=>$dbh,
reference_no=>$reference_no);
$references{$reference_no} = 1;
}
elsif ($ref =~ /PM:(\d+)/) {
my $pubmed_id = $1;
$refObj = Reference->new(dbh=>$dbh,
pubmed=>$pubmed_id);
$reference_no = $refObj->reference_no();
if (defined $references{$reference_no}) {
# don't print a reference line for this value if it has already
# been displayed previously (i.e. it was found as a REF_NO
# value, and now the same reference is listed a second time
# as a PUBMED id)
next;
}
}
my $currBgcolor = (($refno % 2) == 1) ? $bgcolor[1] : $bgcolor[0];
$references .= Tr(td({bgcolor=>$currBgcolor,
valign=>"top",
align=>"left"},
"$refno)"),
td({bgcolor=>$currBgcolor},
a(
{name=>"$reference_no"}
).
$refObj->formatedCitation()
)
);
$refno++;
}
$references = (b("Summary References:") .
table({border=>0},
$references
)
);
#### END OF DUPLICATED CODE FROM ParagraphUI.pm::displayParagraph()
return $references;
}
########################################################################
1;
########################################################################