f2d3014a3cc95116346eab4675817cf0c65f6d62
braney
  Tue Aug 18 11:12:35 2026 -0700
hgc: encode item detail text consistently, refs #38123

diff --git src/hg/hgc/hgc.h src/hg/hgc/hgc.h
index abda4b2f4a1..a4c0bd16077 100644
--- src/hg/hgc/hgc.h
+++ src/hg/hgc/hgc.h
@@ -1,626 +1,629 @@
 /* hgc - Human Genome Click processor - gets called when user clicks
  * on something in human tracks display. This file contains stuff
  * shared with other modules in hgc,  but not in other programs. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #ifndef HGC_H
 #define HGC_H
 
 #ifndef CART_H
 #include "cart.h"
 #endif
 
 #ifndef TRACKDB_H
 #include "trackDb.h"
 #endif
 
 #ifndef BED_H
 #include "bed.h"
 #endif
 
 #ifndef HDB_H
 #include "hdb.h"
 #endif
 
 #ifndef HPRINT_H
 #include "hPrint.h"
 #endif
 
 #ifndef CUSTOMTRACK_H
 #include "customTrack.h"
 #endif
 
 #ifndef WIKITRACK_H
 #include "wikiTrack.h"
 #endif
 
 #ifndef VARIOME_H
 #include "variome.h"
 #endif
 
 #ifndef BEDDETAIL_H
 #include "bedDetail.h"
 #endif
 
 #include "hgdpGeo.h"
 #include "dnaMotif.h"
 #include "togaClick.h"
 
 #include "featureBits.h"
 
 #include "snp125.h"
 
 
 extern struct cart *cart;	/* User's settings. */
 extern char *seqName;		/* Name of sequence we're working on. */
 extern int winStart, winEnd;    /* Bounds of sequence. */
 extern char *database;		/* Name of mySQL database. */
 extern char *organism;		/* Colloquial name of organism. */
 extern char *genome;		/* common name, e.g. Mouse, Human */
 extern char *scientificName;	/* Scientific name of organism. */
 extern struct hash *trackHash;	/* A hash of all tracks - trackDb valued */
 
 // A helper struct for allowing variable sized user defined tables. Each table
 // is encoded in one field of the bigBed with '|' as column separators and ';' as
 // field separators.
 struct embeddedTbl
 {
     struct embeddedTbl *next; // the next custom table
     char *field; // field name from bigBed, used as title when title is NULL
     char *title; // title of the table from trackDb, may be NULL
     char *encodedTbl; // contents of field in bigBed
 };
 
 void hgcStart(char *title);
 /* Print out header of web page with title.  Set
  * error handler to normal html error handler. */
 
 char *hgcPath();
 /* Return path of this CGI script. */
 
 char *hgcPathAndSettings();
 /* Return path with this CGI script and session state variable. */
 
 void hgcAnchorSomewhere(char *group, char *item, char *other, char *chrom);
 /* Generate an anchor that calls click processing program with item
  * and other parameters. */
 
 void hgcAnchorWindow(char *group, char *item, int thisWinStart,
         int thisWinEnd, char *other, char *chrom);
 /* Generate an anchor that calls click processing program with item
  * and other parameters, INCLUDING the ability to specify left and
  * right window positions different from the current window*/
 
 void hgcAnchor(char *group, char *item, char *other);
 /* Generate an anchor that calls click processing program with item
  * and other parameters. */
 
 struct trackDb *tdbForTableArg();
 /* get trackDb for track passed in table arg */
 
 void writeFramesetType();
 /* Write document type that shows a frame set, rather than regular HTML. */
 
 void htmlFramesetStart(char *title);
 /* Write DOCTYPE HTML and HEAD sections for framesets. */
 
 void alnModernStart(char *classicTitle);
 /* Begin an alignment page: modern single-page chrome when the modernAlignPage hg.conf flag is set
  * (showSomeAlignment then renders the modern body), else the classic <frameset>. */
 
 struct psl *getAlignments(struct sqlConnection *conn, char *table, char *acc);
 /* get the list of alignments for the specified acc */
 
 void printAlignmentsSimple(struct psl *pslList, int startFirst, char *hgcCommand,
                            char *typeName, char *itemIn);
 /* Print list of mRNA alignments, don't add extra textual link when
  * doesn't honor hgcCommand. */
 
 void printAlignments(struct psl *pslList,
 		     int startFirst, char *hgcCommand, char *typeName, char *itemIn);
 /* Print list of mRNA alignments. */
 
 void printAlignmentsExtra(struct psl *pslList,
 		     int startFirst, char *hgcCommand, char *hgcCommandInWindow, char *typeName, char *itemIn);
 /* Print list of mRNA alignments with special "in window" alignment function. */
 
 void showSomeAlignment(struct psl *psl, bioSeq *oSeq,
 		       enum gfType qType, int qStart, int qEnd,
 		       char *qName, int cdsS, int cdsE);
 /* Display protein or DNA alignment in a frame. */
 
 void linkToOtherBrowserTitle(char *otherDb, char *chrom, int start, int end, char *title);
 /* Make anchor tag to open another browser window with a title. */
 
 void linkToOtherBrowser(char *otherDb, char *chrom, int start, int end);
 /* Make anchor tag to open another browser window. */
 
 void printEntrezGeneUrl(FILE *f, int geneid);
 /* Print URL for Entrez browser on a gene details page. */
 
     void printEntrezPubMedUidUrl(FILE *f, int pmid);
 /* Print URL for Entrez browser on a PubMed search. */
 
 void printSwissProtAccUrl(FILE *f, char *accession);
 /* Print URL for Swiss-Prot protein accession. */
 
 boolean clipToChrom(int *pStart, int *pEnd);
 /* Clip start/end coordinates to fit in chromosome. */
 
 void printCappedSequence(int start, int end, int extra);
 /* Print DNA from start to end including extra at either end.
  * Capitalize bits from start to end. */
 
 void printPos(char *chrom, int start, int end, char *strand, boolean featDna,
 	      char *item);
 /* Print position lines.  'strand' argument may be null. */
 
 void bedPrintPos(struct bed *bed, int bedSize, struct trackDb *tdb);
 /* Print first three fields of a bed type structure in
  * standard format. */
 
 void savePosInTextBox(char *chrom, int start, int end);
 /* Save basic position/database info in text box and hidden var.
    Positions becomes chrom:start-end*/
 
 void genericHeader(struct trackDb *tdb, char *item);
 /* Put up generic track info. */
 
 void genericBedClick(struct sqlConnection *conn, struct trackDb *tdb,
 		     char *item, int start, int bedSize);
 /* Handle click in generic BED track. */
 
 void printPosOnChrom(char *chrom, int start, int end, char *strand,
 		     boolean featDna, char *item);
 /* Print position lines referenced to chromosome. Strand argument may be NULL */
 
 void printTrackHtml(struct trackDb *tdb);
 /* If there's some html associated with track print it out. */
 
 void abbr(char *s, char *fluff);
 /* Cut out fluff from s. */
 
 void printTableHeaderName(char *name, char *clickName, char *url);
 /* creates a table to display a name vertically,
  * basically creates a column of letters */
 
 void printBacStsXRef(char *clone);
 /* Print out associated STS XRef information for BAC clone on BAC ends */
 /* tracks details pages. */
 
 /* ----Routines in other modules in the same directory---- */
 void genericWiggleClick(struct sqlConnection *conn, struct trackDb *tdb,
 	char *item, int start);
 /* Display details for WIGGLE tracks. */
 
 void genericBigWigClick(struct sqlConnection *conn, struct trackDb *tdb,
 	char *item, int start);
 /* Display details for BigWig  tracks. */
 
 void bigWigCustomClick(struct trackDb *tdb);
 /* Display details for BigWig custom tracks. */
 
 void genericBigBedClick(struct sqlConnection *conn, struct trackDb *tdb,
 		     char *item, int start, int end, int bedSize);
 
 void doPubsDetails(struct trackDb *tdb, char *item);
 /* Handle text2Genome track clicks in pubs.c */
 
 /* Handle click in generic bigBed track. */
 
 void bigBedCustomClick(struct trackDb *tdb);
 /* Display details for BigWig custom tracks. */
 
 void genericMafClick(struct sqlConnection *conn, struct trackDb *tdb,
 	char *item, int start);
 /* Display details for MAF tracks. */
 
 void genericAxtClick(struct sqlConnection *conn, struct trackDb *tdb,
 	char *item, int start, char *otherDb);
 /* Display details for AXT tracks. */
 
 void genericExpRatio(struct sqlConnection *conn, struct trackDb *tdb,
 	char *item, int start);
 /* Display details for expRatio tracks. */
 
 void rosettaDetails(struct trackDb *tdb, char *item);
 /* Set up details for rosetta. */
 
 void affyDetails(struct trackDb *tdb, char *item);
 /* Set up details for affy. */
 
 void gnfExpRatioDetails(struct trackDb *tdb, char *item);
 /* Put up details on some gnf track. */
 
 void loweExpRatioDetails(struct trackDb *tdb, char *item);
 /* Put up details on some lowe track. */
 
 void affyUclaDetails(struct trackDb *tdb, char *item);
 /* Set up details for affyUcla. */
 
 void cghNci60Details(struct trackDb *tdb, char *item);
 /* Set up details for cghNci60. */
 
 void nci60Details(struct trackDb *tdb, char *item);
 /* Set up details for nci60. */
 
 void doAffyHumanExon(struct trackDb *tdb, char *item);
 /* Details for affyHumanExon all exon arrays. */
 
 void doExpRatio(struct trackDb *tdb, char *item, struct customTrack *ct);
 /* Generic expression ratio deatils using microarrayGroups.ra file */
 /* and not the expRecord tables. */
 
 void getMsBedExpDetails(struct trackDb *tdb, char *expName, boolean all);
 /* Create tab-delimited output to download */
 
 void printPslFormat(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, char *subType);
 /*Handles click in Affy tracks and prints out alignment details with link*/
 /* to sequences if available in the database */
 
 void doAffy(struct trackDb *tdb, char *item, char *itemForUrl);
 /* Display alignment information for Affy tracks */
 
 void doScaffoldEcores(struct trackDb *tdb, char *item);
 /* Creates details page and gets the scaffold co-ordinates for unmapped */
 /* genomes for display and to use to create the correct outside link URL */
 
 struct customTrack *lookupCt(char *name);
 /* Return custom track for name, or NULL. */
 
 void doRnaSecStr(struct trackDb *tdb, char *itemName);
 /* Handle click on rnaSecStr type elements. */
 
 void motifHitSection(struct dnaSeq *seq, struct dnaMotif *motif);
 /* Print out section about motif. */
 
 void motifMultipleHitsSection(struct dnaSeq **seqs, int count, struct dnaMotif *motif, char *title);
 /* Print out section about motif, possibly with mutliple occurrences. */
 
 void motifLogoAndMatrix(struct dnaSeq **seqs, int count, struct dnaMotif *motif);
 /* Print out motif sequence logo and text (possibly with multiple occurences) */
 
 struct dnaMotif *loadDnaMotif(char *motifName, char *motifTable);
 /* Load dnaMotif from table. */
 
 void doTriangle(struct trackDb *tdb, char *item, char *motifTable);
 /* Display detailed info on a regulatory triangle item. */
 
 void doTransRegCode(struct trackDb *tdb, char *item, char *motifTable);
 /* Display detailed info on a transcriptional regulatory code item. */
 
 void doTransRegCodeProbe(struct trackDb *tdb, char *item,
 	char *codeTable, char *motifTable,
 	char *tfToConditionTable, char *conditionTable);
 /* Display detailed info on a CHIP/CHIP probe from transRegCode experiments. */
 
 void doPeakClusters(struct trackDb *tdb, char *item);
 /* Display detailed info about a cluster of peaks from other tracks. */
 
 void doPeakClusterListItemsAssayed();
 /* Put up a page that shows all experiments associated with a cluster track. */
 
 void doFactorSource(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, int end);
 /* Display detailed info about a cluster of peaks from other tracks. */
 
 void doFlyreg(struct trackDb *tdb, char *item);
 /* flyreg.org: Drosophila DNase I Footprint db. */
 
 void dbRIP(struct trackDb *tdb, char *item, char *itemForUrl);
 /* Put up dbRIP track info */
 
 void doCgapSage(struct trackDb *tdb, char *itemName);
 /* CGAP SAGE details. */
 
 char* getEntrezNucleotideUrl(char *accession);
 /* get URL for Entrez browser on a nucleotide. free resulting string */
 
 void printEntrezNucleotideUrl(FILE *f, char *accession);
 /* Print URL for Entrez browser on a nucleotide. */
 
 void printEntrezProteinUrl(FILE *f, char *accession);
 /* Print URL for Entrez browser on a protein. */
 
 void printCcdsForMappedGene(struct sqlConnection *conn, char *acc,
                             char *mapTable);
 /* Print out CCDS links a gene mapped via a cddsGeneMap table  */
 
 int getImageId(struct sqlConnection *conn, char *acc);
 /* get the image id for a clone, or 0 if none */
 
 char *getRefSeqSummary(struct sqlConnection *conn, char *acc);
 /* RefSeq summary or NULL if not available; free result */
 
 char *getRefSeqCdsCompleteness(struct sqlConnection *conn, char *acc);
 /* get description of RefSeq CDS completeness or NULL if not available */
 
 char *kgIdToSpId(struct sqlConnection *conn, char* kgId);
 /* get the swissprot id for a known genes id; resulting string should be
  * freed */
 
 char *hgTracksPathAndSettings();
 /* Return path with hgTracks CGI path and session state variable. */
 
 void medlineLinkedTermLine(char *title, char *text, char *search, char *keyword);
 /* Produce something that shows up on the browser as
  *     TITLE: value
  * with the value hyperlinked to medline using a specified search term. */
 
 void medlineLinkedLine(char *title, char *text, char *search);
 /* Produce something that shows up on the browser as
  *     TITLE: value
  * with the value hyperlinked to medline. */
 
 void hgcAnchorPosition(char *group, char *item);
 /* Generate an anchor that calls click processing program with item
  * and group parameters. */
 
 void geneShowPosAndLinks(char *geneName, char *pepName, struct trackDb *tdb,
 			 char *pepTable, char *pepClick,
 			 char *mrnaClick, char *genomicClick, char *mrnaDescription);
 /* Show parts of gene common to everything. If pepTable is not null,
  * it's the old table name, but will check gbSeq first. */
 
 bool loweLabClick(char *track, char *item, struct trackDb *tdb);
 /* check if we have one of the lowelab tracks */
 
 void showTxInfo(char *geneName, struct trackDb *tdb, char *txInfoTable);
 /* Print out stuff from txInfo table. */
 
 void showCdsEvidence(char *geneName, struct trackDb *tdb, char *evTable);
 /* Print out stuff from cdsEvidence table. */
 
 void doWikiTrack(char *itemName, char *chrom, int winStart, int winEnd);
 /* handle item clicks on wikiTrack - may create new items */
 
 void doCreateWikiItem(char *itemName, char *chrom, int winStart, int winEnd);
 /* handle create item clicks for wikiTrack */
 
 void doAddWikiComments(char *itemName, char *chrom, int winStart, int winEnd);
 /* handle add comment item clicks for wikiTrack */
 
 void doDeleteWikiItem(char *itemName, char *chrom, int winStart, int winEnd);
 /* handle delete item clicks for wikiTrack */
 
 void offerLogin(int id, char *loginType, char *table);
 /* display login prompts to the wiki when user isn't already logged in */
 
 void outputJavaScript();
 /* java script functions used in the create item form */
 
 void doVariome (char *wikiItemId, char *chrom, int winStart, int winEnd);
 /* handle item clicks on variome - may create new items */
 
 void displayVariomeItem (struct variome *item, char *userName);
 /* given an already fetched item, get the item description from
  *      the wiki.  Put up edit form(s) if userName is not NULL
  * separate from wikiTrack for form field differences and help
  */
 
 void doCreateVariomeItem (char *itemName, char *chrom, int winStart, int winEnd);
 /* handle create item clicks for variome */
 
 void doAddVariomeComments(char *wikiItemId, char *chrom, int winStart, int winEnd);
 /* handle add comment item clicks for Variome Track */
 
 void doDeleteVariomeItem(char *wikiItemId, char *chrom, int winStart, int winEnd);
 /* handle delete item clicks for Variome Track */
 
 void printWikiVariomeForm (struct bedDetail *item);
 /* print the wiki annotation form for the variome track */
 
 void customMafClick(struct sqlConnection *conn,
 	struct sqlConnection *conn2, struct trackDb *tdb);
 /* handle clicks on a custom maf */
 
 void doBigEncodePeak(struct trackDb *tdb, struct customTrack *cti, char *item);
 /*  details for encodePeak type tracks.  */
 
 void doEncodePeak(struct trackDb *tdb, struct customTrack *cti, char *item);
 /*  details for encodePeak type tracks.  */
 
 void doEncodeFiveC(struct sqlConnection *conn, struct trackDb *tdb);
 /* Print details for 5C track */
 
 void doPeptideMapping(struct sqlConnection *conn, struct trackDb *tdb, char *item);
 /* Print details for a peptideMapping track.  */
 
 void doHgdpGeo(struct trackDb *tdb, char *item);
 /* Show details page for HGDP SNP with population allele frequencies
  * plotted on a world map. */
 
 void hgdpGeoImg(struct hgdpGeo *geo);
 /* Generate image as PNG, PDF, EPS: world map with pie charts for population allele frequencies. */
 
 char *hgdpPngFilePath(char *rsId);
 /* Return the stable PNG trash-cached image path for rsId. */
 
 void hgdpGeoFreqTable(struct hgdpGeo *geo);
 /* Print an HTML table of populations and allele frequencies. */
 
 void printOtherSnpMappings(char *table, char *name, int start,
 			   struct sqlConnection *conn, int rowOffset, struct trackDb *tdb);
 /* If this SNP (from any bed4+ table) is not uniquely mapped, print the other mappings. */
 
 void printCustomUrl(struct trackDb *tdb, char *itemName, boolean encode);
 /* Wrapper to call printCustomUrlWithLabel using the url setting in trackDb */
 
 void printCustomUrlWithFields(struct trackDb *tdb, char *itemName, char *itemLabel, boolean encode,                                                      struct slPair *fields);
 /* Wrapper to call printCustomUrlWithLabel with additional fields to substitute */
 
 void printOtherCustomUrl(struct trackDb *tdb, char *itemName, char* urlSetting, boolean encode);
 /* Wrapper to call printCustomUrlWithLabel to use another url setting other than url in trackDb e.g. url2, this allows the use of multiple urls for a track
  *  to be set in trackDb. */
 
 void printIdOrLinks(struct asColumn *col, struct hash *fieldToUrl, struct trackDb *tdb, char *idList);
 /* if trackDb does not contain a "urls" entry for current column name, just print idList as it is.
  *  * Otherwise treat idList as a comma-sep list of IDs and print one row per id, with a link to url,
  *   * ($$ in url is OK, wildcards like $P, $p, are also OK)
  *    * */
 
 void printDbSnpRsUrl(char *rsId, char *labelFormat, ...)
 /* Print a link to dbSNP's report page for an rs[0-9]+ ID. */
 #ifdef __GNUC__
 __attribute__((format(printf, 2, 3)))
 #endif
     ;
 
 void doBamDetails(struct trackDb *tdb, char *item);
 /* Show details of an alignment from a BAM file. */
 
 void doVcfTabixDetails(struct trackDb *tdb, char *item);
 /* Show details of an alignment from a VCF file compressed and indexed by tabix. */
 
 void doVcfTabixDetailsExt(struct trackDb *tdb, char *item, struct featureBits **pFbList, int start, int end);
 /* Show details of an alignment from a VCF file compressed and indexed by tabix. */
 
 void doVcfDetails(struct trackDb *tdb, char *item);
 /* Show details of an alignment from an uncompressed VCF file. */
 
 void doVcfDetailsExt(struct trackDb *tdb, char *item, struct featureBits **pFbList, int start, int end);
 /* Show details of an alignment from an uncompressed VCF file. */
 
 void doBarChartDetails(struct trackDb *tdb, char *item);
 /* Details of barChart item */
 
 void doMyVariantsDetails(struct customTrack *ct, char *itemIdString);
 /* Show details of a myVariants item. */
 
 void doBedDetail(struct trackDb *tdb, struct customTrack *ct, char *itemName);
 /* generate the detail page for a custom track of bedDetail type */
 
 void doPgSnp(struct trackDb *tdb, char *itemName, struct customTrack *ct);
 /* print detail page for personal genome track (pgSnp) */
 
 void doGvf(struct trackDb *tdb, char *item);
 /* Show details for variants represented as GVF, stored in a bed8Attrs table */
 
 void doGeneReviews(struct trackDb *tdb, char *itemName);
 /* generate the detail page for geneReviews */
 
 void prGeneReviews(struct sqlConnection *conn, char *itemName);
 /* print GeneReviews associated to this item */
 
 void prGRShortRefGene(struct sqlConnection *conn, char *itemName);
 /* print GeneReviews short label associated to this refGene item */
 
 void doLrg(struct trackDb *tdb, char *item);
 /* Locus Reference Genomic (LRG) info. */
 
 void doLrgTranscriptPsl(struct trackDb *tdb, char *item);
 /* Locus Reference Genomic (LRG) transcript mapping and sequences. */
 
 void htcLrgCdna(char *item);
 /* Serve up LRG transcript cdna seq */
 
 void doPeptideAtlas(struct trackDb *tdb, char *item);
 /* Details for PeptideAtlas peptide mapping */
 
 void doGtexGeneExpr(struct trackDb *tdb, char *item);
 /* Details of GTEX gene expression item */
 
 void doGtexEqtlDetails(struct trackDb *tdb, char *item);
 /* Details of GTEx eQTL item */
 
 void printSnp125Function(struct trackDb *tdb, struct snp125 *snp);
 /* If the user has selected a gene track for functional annotation,
  * report how this SNP relates to any nearby genes. */
 
 void printSnp153Function(struct trackDb *tdb, struct snp125 *snp);
 /* If the user has selected a gene track for functional annotation,
  * report how this SNP relates to any nearby genes. */
 
 void doBigDbSnp(struct trackDb *tdb, char *rsId);
 /* Show details for bigDbSnp item. */
 
 void printAddWbr(char *text, int distance);
 /* a crazy hack for firefox/mozilla that is unable to break long words in tables
  * We need to add a <wbr> tag every x characters in the text to make text breakable.
  */
 
 void printIframe(struct trackDb *tdb, char *itemName);
 /* print an iframe with the URL specified in trackDb (iframeUrl), can have
  * the standard codes in it (like $$ for itemName, etc) */
 
 char *getIdInUrl(struct trackDb *tdb, char *itemName);
 /* If we have an idInUrlSql tag, look up itemName in that, else just
  * return itemName. */
 
 // trackDb setting prefix for JS visualization scripts on details pages.
 // Format: detailsScript.<plotType>.<fieldName> <jsonConfig>
 // Parsed in both bigBedClick.c (to build JSON + load JS) and hgc.c (to skip fields from table).
 #define DETAILS_SCRIPT_PREFIX "detailsScript.*"
 
+char *hubEncode(struct trackDb *tdb, char *text);
+/* Return text escaped for HTML if it belongs to a track hub, otherwise return it unchanged. */
+
 void printFieldLabel(char *entry);
 /* print the field label, the first column in the table, as a <td>. Allow a
  * longer description after a |-char, as some fields are not easy to
  * understand. */
 
 void printFieldLabelWithId(char *entry, char *fieldName);
 /* Like printFieldLabel but adds id="bfld_<fieldName>" to the <tr> element,
  * so JavaScript can find the row by field name. */
 
 struct slPair* getExtraFields(struct trackDb *tdb, char **fields, int fieldCount);
 /* return the extra field names and their values as a list of slPairs */
 
 struct slPair *getFields(struct trackDb *tdb, char **fields);
 /* return field names and their values as a list of slPairs.  */
 
 void printEmbeddedTable(struct trackDb *tdb, struct embeddedTbl *embeddedTblList,
                         struct dyString *tableLabelsDy);
 /* Pretty print a '|' and ';' encoded table or a JSON encoded table from a bigBed field.
  * The JSON encoded tables get passed through as json so hgc.js can build them instead,
  * which preserves the table order */
 
 void getExtraTableFields(struct trackDb *tdb, struct slName **retFieldNames, struct embeddedTbl **retEmbeddedTblList, struct hash *fieldsToEmbeddedTbl);
 /* Parse the trackDb field "extraTableFields" into the field names and titles specified,
  * and fill out a hash keyed on the bigBed field name (which may be in an external file
  * and not in the bigBed itself) to a helper struct for storing user defined tables. */
 
 int extraFieldsPrintAs(struct trackDb *tdb,struct sqlResult *sr,char **fields,int fieldCount, struct asObject *as);
 // Any extra bed or bigBed fields (defined in as and occurring after N in bed N + types.
 // sr may be null for bigBeds.
 // Returns number of extra fields actually printed.
 
 int extraFieldsPrint(struct trackDb *tdb,struct sqlResult *sr,char **fields,int fieldCount);
 // Any extra bed or bigBed fields (defined in as and occurring after N in bed N + types.
 // sr may be null for bigBeds.
 // Returns number of extra fields actually printed.
 
 struct slPair *parseDetailsTablUrls(struct trackDb *tdb);
 /* Parse detailsUrls setting string into an slPair list of {offset column name, fileOrUrl} */
 
 char *readOneLineMaybeBgzip(char *fileOrUrl, bits64 offset, bits64 len);
 /* If fileOrUrl is bgzip-compressed and indexed, then use htslib's bgzf functions to
  * retrieve uncompressed data from offset; otherwise (plain text) use udc. If len is 0,
  * read up to next '\n' delimiter. */
 
 #define NUCCORE_SEARCH "https://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore&cmd=search&term="
 
 void doJRepeat (struct trackDb *tdb, char *repeat);
 void doBigRmskRepeat (struct trackDb *tdb, char *repeat);
 /* New RepeatMasker Visualization defined in joinedRmskClick.c */
 
 INLINE char* strOrNbsp(char* val)
 /* return val if not empty otherwise HTML entity &nbsp; */
 {
 return isEmpty(val) ? "&nbsp;" : val;
 }
 
 void doInteractDetails(struct trackDb *tdb, char *item);
 /* Details of interaction item */
 
 void doParDetails(struct trackDb *tdb, char *name);
 /* show details of a PAR item. */
 
 void doLorax(struct trackDb *tdb, char *item);
 /* Display the Lorax multi-tree viewer. */
 
 void doQuickLiftChain(struct trackDb *tdb, char *item);
 /* Deal with click on quickLift chain track.*/
 
 struct psl *getPslAndSeq(struct trackDb *tdb, char *chromName, struct bigBedInterval *bb, 
     unsigned seqTypeField, DNA **retSeq, char **retCdsStr);
 /* Read in psl and query sequence out of a bbiInverval on a give chromosome */
 #endif