/* 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 "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. */ 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 doVcfDetails(struct trackDb *tdb, char *item); /* Show details of an alignment from an uncompressed VCF file. */ void doBarChartDetails(struct trackDb *tdb, char *item); /* Details of barChart item */ void doMakeItemsDetails(struct customTrack *ct, char *itemIdString); /* Show details of a makeItems 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(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 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. */ void printFieldLabel(char *entry); /* print the field label, the first column in the table, as a . Allow a * longer description after a |-char, as some fields are not easy to * understand. */ 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   */ { return isEmpty(val) ? " " : 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. */ 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