src/hg/hgGene/hgGene.h 1.50

Index: src/hg/hgGene/hgGene.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgGene/hgGene.h,v
retrieving revision 1.49
retrieving revision 1.50
diff -b -B -U 1000000 -r1.49 -r1.50
--- src/hg/hgGene/hgGene.h	23 Feb 2010 20:35:37 -0000	1.49
+++ src/hg/hgGene/hgGene.h	23 Feb 2010 23:03:37 -0000	1.50
@@ -1,281 +1,281 @@
 /* hgGene.h - important structures and interfaces between
  * modules of the gene details viewer. */
 
 #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. */
     };
 
 struct section *sectionNew(struct hash *sectionRa, char *name);
 /* Create a section loading all common parts but the methods 
  * sectionRa. */
 
 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 *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 *gadSection(struct sqlConnection *conn, 
 	struct hash *sectionRa);
 /* Create GAD 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. */
 
 #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. */
 
 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 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 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(struct sqlConnection *conn);
+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 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 *curProtId;		/* Current protein Id. */
 extern char *curGeneName;		/* Biological name of gene. */
 extern char *curGeneChrom;	/* Chromosome current gene is on. */
 struct genePred *curGenePred;	/* Current gene prediction structure. */
 extern int curGeneStart,curGeneEnd;	/* Position in chromosome. */
 struct sqlConnection *spConn;	/* Connection to SwissProt database. */
 extern char *swissProtAcc;	/* SwissProt accession (may be NULL). */
 
 #define KG_UNKNOWN 0
 #define KG_I       1
 #define KG_II      2
 #define KG_III     3
 extern int kgVersion;           /* KG version */