25a1ed58b2f9fc2d9ad7fdbe9117f0b2f47253f3
fanhsu
  Tue Nov 9 16:38:23 2010 -0800
Update for RGD Genes, Redmine issue #29.
diff --git src/hg/hgGene/hgGene.h src/hg/hgGene/hgGene.h
index 13364cc..c92e6b7 100644
--- src/hg/hgGene/hgGene.h
+++ src/hg/hgGene/hgGene.h
@@ -30,52 +30,57 @@
 
     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. */
     };
 
 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 *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. */
@@ -100,30 +105,34 @@
 	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 *ctdRgdGene2Section(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. */
@@ -163,30 +172,35 @@
 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 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);