/* hgGene.h - important structures and interfaces between * modules of the gene details viewer. */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef CART_H #include "cart.h" #endif #ifndef JKSQL_H #include "jksql.h" #endif #ifndef GENEPRED_H #include "genePred.h" #endif #ifndef HPRINT_H #include "hPrint.h" #endif struct section /* A section of the details page - put in the page * index. */ { struct section *next; char *name; /* Symbolic name. */ char *shortLabel; /* Short human readable label - 2 words or less. */ char *longLabel; /* Long human readable label. */ double priority; /* Order of section. */ struct hash *settings; /* Settings hash from section.ra. */ boolean (*exists)(struct section *section, struct sqlConnection *conn, char *geneId); /* Return TRUE if this section needs to be printed. */ void (*print)(struct section *section, struct sqlConnection *conn, char *geneId); /* Print section given connection to genome database. */ /* Some section-specific data. */ char *raFile; /* Ra file to load additional info from. */ void *items; /* Some list of items. */ /* Some FlyBase specific stuff. */ char *flyBaseTable; /* Which table to use. */ char *rgdGeneTable; /* Which table to use. */ void *extras; // Contains any section specific stuff int checkTime; // Time to check existence (for performance tuning) */ int printTime; // Time to print (for performance tuning) */ }; struct section *sectionNew(struct hash *sectionRa, char *name); /* Create a section loading all common parts but the methods * sectionRa. */ struct section *gencodeSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create gencode section. */ struct section *linksSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create links section. */ struct section *otherOrgsSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create other organisms section. */ struct section *sequenceSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create sequence section. */ struct section *swissProtCommentsSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create SwissProt comments section. */ struct section *rgdGeneRawSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create rgdGeneRaw section */ struct section *flyBaseRolesSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create FlyBase roles section. */ struct section *flyBasePhenotypesSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create FlyBase Phenotypesroles section. */ struct section *flyBaseSynonymsSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create FlyBase synonyms section. */ struct section *bdgpExprInSituSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create BDGP Expression in situ image links section. */ struct section *goSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create GO annotations section. */ struct section *infoSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create UCSC KG Model Info section. */ struct section *methodSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create UCSC KG Method section. */ struct section *pseudoGeneSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create pseudoGene section. */ struct section *mrnaDescriptionsSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create mrnaDescriptions section. */ struct section *microarraySection(struct sqlConnection *conn, struct hash *sectionRa); /* Create microarray section. */ struct section *altSpliceSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create altSplice section. */ struct section *ctdSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create CTD section. */ struct section *primersSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create primers section. */ struct section *ctdRgdGene2Section(struct sqlConnection *conn, struct hash *sectionRa); /* Create CTD section. */ struct section *gadSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create GAD section. */ struct section *malaCardsSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create malaCards section. */ struct section *domainsSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create domains section. */ struct section *pathwaysSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create pathways section. */ struct section *rnaStructureSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create rnaStructure section. */ struct section *localizationSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create Localization section. */ struct section *transRegCodeMotifSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create dnaBindMotif section. */ struct section *synonymSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create synonym (aka Other Names) section. */ struct section *geneReviewsSection(struct sqlConnection *conn, struct hash *sectionRa); /* create geneReviews section - print out GeneReviews for this gene. */ #define HGG_GENE_ALLELES "geneAlleles" struct section *allelesSection(struct sqlConnection *conn, struct hash *sectionRa); // Create Common Gene Haplotype Alleles section. void prGRShortKg(struct sqlConnection *conn, char *itemName); /* print GeneReviews short label associated to this refGene item */ struct section *gtexSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create GTEx gene expression section. */ #ifdef EXAMPLE struct section *xyzSection(struct sqlConnection *conn, struct hash *sectionRa); /* Create xyz section. */ #endif /* EXAMPLE */ /* -------- Helper functions ---------- */ char *getGeneName(char *id, struct sqlConnection *conn); /* Return gene name associated with ID. Freemem * this when done. */ char *getSwissProtAcc(struct sqlConnection *conn, struct sqlConnection *spConn, char *geneId); /* Look up SwissProt id. Return NULL if not found. FreeMem this when done. * spConn is existing SwissProt database conn. May be NULL. */ char *genomeSetting(char *name); /* Return genome setting value. Aborts if setting not found. */ char *genomeOptionalSetting(char *name); /* Returns genome setting value or NULL if not found. */ struct hash *readRa(char *rootName, struct hash **retHashOfHash); /* Read in ra in root, root/org, and root/org/database. */ int gpRangeIntersection(struct genePred *gp, int start, int end); /* Return number of bases range start,end shares with genePred. */ boolean checkDatabases(char *databases); /* Check all databases in space delimited string exist. */ boolean isFly(); /* Return true if organism is D. melanogaster. */ boolean isRgdGene(struct sqlConnection *conn); /* Return true if the gene set is RGD Genes. */ char *getRgdGeneUniProtAcc(char *genId, struct sqlConnection *conn); char *getFlyBaseId(struct sqlConnection *conn, char *geneId); /* Return flyBase ID of gene if any. */ void showSeqFromTable(struct sqlConnection *conn, char *geneId, char *geneName, char *table); /* Show some sequence from given table. */ void printPrimer3Anchor(char *table, char *itemName, char *chrom, int start, int end); /* Print primer3 sequence export anchor. */ void printGenomicSeqLink(struct sqlConnection *conn, char *geneId, char *chrom, int start, int end); /* Figure out known genes table, position of gene, link it. */ void printProteinSeqLink(struct sqlConnection *conn, char *geneId); /* Print out link to fetch protein. */ void printMrnaSeqLink(struct sqlConnection *conn, char *geneId); /* Print out link to fetch mRNA. */ char *descriptionString(char *id, struct sqlConnection *conn); /* return description as it would be printed in html, can free after use */ char *aliasString(char *id, struct sqlConnection *conn); /* return alias string as it would be printed in html, can free after use */ /* -------- CGI Command Variables ---------- */ #define hggDoPrefix "hgg_do_" /* Prefix for all commands. */ #define hggDoKgMethod "hgg_do_kgMethod" #define hggDoWikiTrack "hgg_do_wikiTrack" #define hggDoWikiAddComment "hgg_do_wikiAddComment" #define hggDoGetMrnaSeq "hgg_do_getMrnaSeq" #define hggDoGetProteinSeq "hgg_do_getProteinSeq" #define hggDoRnaFoldDisplay "hgg_do_rnaFoldDisplay" #define hggDoOtherProteinSeq "hgg_do_otherProteinSeq" #define hggDoOtherProteinAli "hgg_do_otherProteinAli" #define hggDoTxInfoDescription "hgg_do_txInfoDescription" #define hggAjaxSection "ajaxSection" #define geneCgi "../cgi-bin/hgGene" /* -------- Commands ---------- */ void doKgMethod(); /* Present KG Method, Credits, and Data Use Restrictions. */ void doWikiTrack(struct sqlConnection *conn); /* Put up wiki track editing controls */ void doTxInfoDescription(); /* Put up info on fields in txInfo table. */ void doGetMrnaSeq(struct sqlConnection *conn, char *geneId, char *geneName); /* Get mRNA sequence in a simple page. */ void doGetProteinSeq(struct sqlConnection *conn, char *geneId, char *geneName); /* Get mRNA sequence in a simple page. */ void doOtherProteinSeq(struct sqlConnection *conn, char *homologName); /* Put up page that displays protein sequence from other organism. */ void doOtherProteinAli(struct sqlConnection *conn, char *localId, char *localName); /* Put up page that shows alignment between this protein sequence * and other species. */ void doRnaFoldDisplay(struct sqlConnection *conn, char *geneId, char *geneName); /* Display mRNA sequence folding. */ void doSamT02(char *proteinId, char *database); /* show SAM-T02 sub-section */ /* -------- CGI Data Variables ---------- */ #define hggOrg "org" /* Organism we're working on. */ #define hggDb "db" /* Database we're working on. */ #define hggPrefix "hgg_" /* Prefix to all 'local' cart vars. */ #define hggGene "hgg_gene" /* Main gene id. */ #define hggProt "hgg_prot" /* Main protein id. */ #define hggChrom "hgg_chrom" /* Chromosome gene is on. */ #define hggStart "hgg_start" /* Start position. */ #define hggType "hgg_type" /* Table name */ #define hggEnd "hgg_end" /* End position. */ #define hggItem "hgg_item" /* Gene item, used for ccdsGene */ #define hggExpRatioColors "hgg_expRatioColors" /* Expression Ratio coloring. */ #define hggMrnaFoldRegion "hgg_mrnaFoldRegion" /* Which region in mRNA to show. */ #define hggMrnaFoldPs "hgg_mrnaFoldPs" /* PostScript file. */ #define hggOtherId "hgg_otherId" /* Other organism gene id. */ #define hggOtherPepTable "hgg_otherPepTable" /* Other organism peptide table. */ /* -------- Global Variables --------*/ extern struct cart *cart; /* This holds cgi and other variables between clicks. */ extern struct hash *oldCart; /* Old cart hash. */ extern char *database; /* Name of genome database - hg15, mm3, or the like. */ extern char *genome; /* Name of genome - mouse, human, etc. */ extern char *curGeneId; /* Current Gene Id. */ extern char *curAlignId; /* Current Align Id. */ extern char *curProtId; /* Current protein Id. */ extern char *curGeneName; /* Biological name of gene. */ extern char *curGeneChrom; /* Chromosome current gene is on. */ extern struct genePred *curGenePred; /* Current gene prediction structure. */ extern boolean isGencode; /* is this based on the Gencode models */ extern boolean isGencode2; /* is this based on the Gencode models and use ensembl id as primary id */ extern int curGeneStart,curGeneEnd; /* Position in chromosome. */ extern struct sqlConnection *spConn; /* Connection to SwissProt database. */ extern char *swissProtAcc; /* SwissProt accession (may be NULL). */ extern struct trackDb *globalTdb; /* The trackDb structure for the table containing the current item. */ #define KG_UNKNOWN 0 #define KG_I 1 #define KG_II 2 #define KG_III 3 extern int kgVersion; /* KG version */