5976dc3dee86013c695d4ecfc69f44e3ec6b002d
cline
  Tue Jan 17 16:17:50 2012 -0800
Updated the HGNC object so that it contains all the fields from the HGNC standard download tables
diff --git src/hg/inc/hgnc.h src/hg/inc/hgnc.h
new file mode 100644
index 0000000..d10de9f
--- /dev/null
+++ src/hg/inc/hgnc.h
@@ -0,0 +1,101 @@
+/* hgnc.h was originally generated by the autoSql program, which also 
+ * generated hgnc.c and hgnc.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef HGNC_H
+#define HGNC_H
+
+#define HGNC_NUM_COLS 41
+
+struct hgnc
+/* A cross-reference table between HUGO Gene Nomenclature Committee (HGNC) IDs and other database IDs. */
+    {
+    struct hgnc *next;  /* Next in singly linked list. */
+    char *hgncId;	/* HGNC ID */
+    char *symbol;	/* Approved Symbol */
+    char *name;	/* Approved Name */
+    char *status;	/* Status */
+    char *locusType;	/* Locus Type */
+    char *locusGroup;	/* Locus Group */
+    char *prvSymbols;	/* Previous Symbols */
+    char *prvNames;	/* Previous Names */
+    char *synonyms;	/* Synonyms */
+    char *nameSyns;	/* Name synonyms */
+    char *chrom;	/* Reference sequence chromosome or scaffold */
+    char *dateApprv;	/* Date Approved */
+    char *dateMod;	/* Date Modified */
+    char *dateSymChange;	/* Date Symbol Changed */
+    char *dateNmChange;	/* Date Name Changed */
+    char *accession;	/* Accession Numbers */
+    char *enzymeIds;	/* Enzyme IDs */
+    char *entrezId;	/* Entrez Gene ID */
+    char *ensId;	/* Ensembl Gene ID */
+    char *mgdId;	/* MGD ID */
+    char *miscDbs;	/* Misc Database Links */
+    char *miscIds;	/* Misc Database IDs */
+    char *pubMed;	/* Pubmed IDs */
+    char *refSeqIds;	/* RefSeq IDs */
+    char *geneFamilyNm;	/* Gene Family Name */
+    char *geneFamilyDesc;	/* Gene Family Description */
+    char *recType;	/* Record Type */
+    char *primaryId;	/* Primary ID */
+    char *secondaryId;	/* Secondary ID */
+    char *ccdsId;	/* CCDS ID */
+    char *vegaId;	/* Vega ID */
+    char *locusDbs;	/* Locus-Specific Databases */
+    char *gdbMapped;	/* GDB ID (mapped data) */
+    char *entrezMapped;	/* Entrez Gene ID (mapped data) */
+    char *omimMapped;	/* OMIM ID (mapped data) */
+    char *refSeqMapped;	/* RefSeq (mapped data) */
+    char *uniProtMapped;	/* UniProt ID (mapped data) */
+    char *ensMapped;	/* ENSEMLB ID (mapped data) */
+    char *ucscMapped;	/* UCSC ID (mapped data) */
+    char *mgiMapped;	/* MGD ID (mapped data) */
+    char *rgdMapped;	/* Rat genome database ID (mapped data) */
+    };
+
+void hgncStaticLoadWithNull(char **row, struct hgnc *ret);
+/* Load a row from hgnc table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+
+struct hgnc *hgncLoadWithNull(char **row);
+/* Load a hgnc from row fetched with select * from hgnc
+ * from database.  Dispose of this with hgncFree(). */
+
+struct hgnc *hgncLoadAll(char *fileName);
+/* Load all hgnc from whitespace-separated file.
+ * Dispose of this with hgncFreeList(). */
+
+struct hgnc *hgncLoadAllByChar(char *fileName, char chopper);
+/* Load all hgnc from chopper separated file.
+ * Dispose of this with hgncFreeList(). */
+
+#define hgncLoadAllByTab(a) hgncLoadAllByChar(a, '\t');
+/* Load all hgnc from tab separated file.
+ * Dispose of this with hgncFreeList(). */
+
+struct hgnc *hgncCommaIn(char **pS, struct hgnc *ret);
+/* Create a hgnc out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new hgnc */
+
+void hgncFree(struct hgnc **pEl);
+/* Free a single dynamically allocated hgnc such as created
+ * with hgncLoad(). */
+
+void hgncFreeList(struct hgnc **pList);
+/* Free a list of dynamically allocated hgnc's */
+
+void hgncOutput(struct hgnc *el, FILE *f, char sep, char lastSep);
+/* Print out hgnc.  Separate fields with sep. Follow last field with lastSep. */
+
+#define hgncTabOut(el,f) hgncOutput(el,f,'\t','\n');
+/* Print out hgnc as a line in a tab-separated file. */
+
+#define hgncCommaOut(el,f) hgncOutput(el,f,',',',');
+/* Print out hgnc as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+#endif /* HGNC_H */
+