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/lib/hgnc.c src/hg/lib/hgnc.c
new file mode 100644
index 0000000..f770cc7
--- /dev/null
+++ src/hg/lib/hgnc.c
@@ -0,0 +1,435 @@
+/* hgnc.c was originally generated by the autoSql program, which also 
+ * generated hgnc.h and hgnc.sql.  This module links the database and
+ * the RAM representation of objects. */
+
+#include "common.h"
+#include "linefile.h"
+#include "dystring.h"
+#include "jksql.h"
+#include "hgnc.h"
+
+
+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. */
+{
+
+ret->hgncId = row[0];
+ret->symbol = row[1];
+ret->name = row[2];
+ret->status = row[3];
+ret->locusType = row[4];
+ret->locusGroup = row[5];
+ret->prvSymbols = row[6];
+ret->prvNames = row[7];
+ret->synonyms = row[8];
+ret->nameSyns = row[9];
+ret->chrom = row[10];
+ret->dateApprv = row[11];
+ret->dateMod = row[12];
+ret->dateSymChange = row[13];
+ret->dateNmChange = row[14];
+ret->accession = row[15];
+ret->enzymeIds = row[16];
+ret->entrezId = row[17];
+ret->ensId = row[18];
+ret->mgdId = row[19];
+ret->miscDbs = row[20];
+ret->miscIds = row[21];
+ret->pubMed = row[22];
+ret->refSeqIds = row[23];
+ret->geneFamilyNm = row[24];
+ret->geneFamilyDesc = row[25];
+ret->recType = row[26];
+ret->primaryId = row[27];
+ret->secondaryId = row[28];
+ret->ccdsId = row[29];
+ret->vegaId = row[30];
+ret->locusDbs = row[31];
+ret->gdbMapped = row[32];
+ret->entrezMapped = row[33];
+ret->omimMapped = row[34];
+ret->refSeqMapped = row[35];
+ret->uniProtMapped = row[36];
+ret->ensMapped = row[37];
+ret->ucscMapped = row[38];
+ret->mgiMapped = row[39];
+ret->rgdMapped = row[40];
+}
+
+struct hgnc *hgncLoadWithNull(char **row)
+/* Load a hgnc from row fetched with select * from hgnc
+ * from database.  Dispose of this with hgncFree(). */
+{
+struct hgnc *ret;
+
+AllocVar(ret);
+ret->hgncId = cloneString(row[0]);
+ret->symbol = cloneString(row[1]);
+ret->name = cloneString(row[2]);
+ret->status = cloneString(row[3]);
+ret->locusType = cloneString(row[4]);
+ret->locusGroup = cloneString(row[5]);
+ret->prvSymbols = cloneString(row[6]);
+ret->prvNames = cloneString(row[7]);
+ret->synonyms = cloneString(row[8]);
+ret->nameSyns = cloneString(row[9]);
+ret->chrom = cloneString(row[10]);
+ret->dateApprv = cloneString(row[11]);
+ret->dateMod = cloneString(row[12]);
+ret->dateSymChange = cloneString(row[13]);
+ret->dateNmChange = cloneString(row[14]);
+ret->accession = cloneString(row[15]);
+ret->enzymeIds = cloneString(row[16]);
+ret->entrezId = cloneString(row[17]);
+ret->ensId = cloneString(row[18]);
+ret->mgdId = cloneString(row[19]);
+ret->miscDbs = cloneString(row[20]);
+ret->miscIds = cloneString(row[21]);
+ret->pubMed = cloneString(row[22]);
+ret->refSeqIds = cloneString(row[23]);
+ret->geneFamilyNm = cloneString(row[24]);
+ret->geneFamilyDesc = cloneString(row[25]);
+ret->recType = cloneString(row[26]);
+ret->primaryId = cloneString(row[27]);
+ret->secondaryId = cloneString(row[28]);
+ret->ccdsId = cloneString(row[29]);
+ret->vegaId = cloneString(row[30]);
+ret->locusDbs = cloneString(row[31]);
+ret->gdbMapped = cloneString(row[32]);
+ret->entrezMapped = cloneString(row[33]);
+ret->omimMapped = cloneString(row[34]);
+ret->refSeqMapped = cloneString(row[35]);
+ret->uniProtMapped = cloneString(row[36]);
+ret->ensMapped = cloneString(row[37]);
+ret->ucscMapped = cloneString(row[38]);
+ret->mgiMapped = cloneString(row[39]);
+ret->rgdMapped = cloneString(row[40]);
+return ret;
+}
+
+struct hgnc *hgncLoadAll(char *fileName) 
+/* Load all hgnc from a whitespace-separated file.
+ * Dispose of this with hgncFreeList(). */
+{
+struct hgnc *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[41];
+
+while (lineFileRow(lf, row))
+    {
+    el = hgncLoadWithNull(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct hgnc *hgncLoadAllByChar(char *fileName, char chopper) 
+/* Load all hgnc from a chopper separated file.
+ * Dispose of this with hgncFreeList(). */
+{
+struct hgnc *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[41];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = hgncLoadWithNull(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+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 */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->hgncId = sqlStringComma(&s);
+ret->symbol = sqlStringComma(&s);
+ret->name = sqlStringComma(&s);
+ret->status = sqlStringComma(&s);
+ret->locusType = sqlStringComma(&s);
+ret->locusGroup = sqlStringComma(&s);
+ret->prvSymbols = sqlStringComma(&s);
+ret->prvNames = sqlStringComma(&s);
+ret->synonyms = sqlStringComma(&s);
+ret->nameSyns = sqlStringComma(&s);
+ret->chrom = sqlStringComma(&s);
+ret->dateApprv = sqlStringComma(&s);
+ret->dateMod = sqlStringComma(&s);
+ret->dateSymChange = sqlStringComma(&s);
+ret->dateNmChange = sqlStringComma(&s);
+ret->accession = sqlStringComma(&s);
+ret->enzymeIds = sqlStringComma(&s);
+ret->entrezId = sqlStringComma(&s);
+ret->ensId = sqlStringComma(&s);
+ret->mgdId = sqlStringComma(&s);
+ret->miscDbs = sqlStringComma(&s);
+ret->miscIds = sqlStringComma(&s);
+ret->pubMed = sqlStringComma(&s);
+ret->refSeqIds = sqlStringComma(&s);
+ret->geneFamilyNm = sqlStringComma(&s);
+ret->geneFamilyDesc = sqlStringComma(&s);
+ret->recType = sqlStringComma(&s);
+ret->primaryId = sqlStringComma(&s);
+ret->secondaryId = sqlStringComma(&s);
+ret->ccdsId = sqlStringComma(&s);
+ret->vegaId = sqlStringComma(&s);
+ret->locusDbs = sqlStringComma(&s);
+ret->gdbMapped = sqlStringComma(&s);
+ret->entrezMapped = sqlStringComma(&s);
+ret->omimMapped = sqlStringComma(&s);
+ret->refSeqMapped = sqlStringComma(&s);
+ret->uniProtMapped = sqlStringComma(&s);
+ret->ensMapped = sqlStringComma(&s);
+ret->ucscMapped = sqlStringComma(&s);
+ret->mgiMapped = sqlStringComma(&s);
+ret->rgdMapped = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void hgncFree(struct hgnc **pEl)
+/* Free a single dynamically allocated hgnc such as created
+ * with hgncLoad(). */
+{
+struct hgnc *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->hgncId);
+freeMem(el->symbol);
+freeMem(el->name);
+freeMem(el->status);
+freeMem(el->locusType);
+freeMem(el->locusGroup);
+freeMem(el->prvSymbols);
+freeMem(el->prvNames);
+freeMem(el->synonyms);
+freeMem(el->nameSyns);
+freeMem(el->chrom);
+freeMem(el->dateApprv);
+freeMem(el->dateMod);
+freeMem(el->dateSymChange);
+freeMem(el->dateNmChange);
+freeMem(el->accession);
+freeMem(el->enzymeIds);
+freeMem(el->entrezId);
+freeMem(el->ensId);
+freeMem(el->mgdId);
+freeMem(el->miscDbs);
+freeMem(el->miscIds);
+freeMem(el->pubMed);
+freeMem(el->refSeqIds);
+freeMem(el->geneFamilyNm);
+freeMem(el->geneFamilyDesc);
+freeMem(el->recType);
+freeMem(el->primaryId);
+freeMem(el->secondaryId);
+freeMem(el->ccdsId);
+freeMem(el->vegaId);
+freeMem(el->locusDbs);
+freeMem(el->gdbMapped);
+freeMem(el->entrezMapped);
+freeMem(el->omimMapped);
+freeMem(el->refSeqMapped);
+freeMem(el->uniProtMapped);
+freeMem(el->ensMapped);
+freeMem(el->ucscMapped);
+freeMem(el->mgiMapped);
+freeMem(el->rgdMapped);
+freez(pEl);
+}
+
+void hgncFreeList(struct hgnc **pList)
+/* Free a list of dynamically allocated hgnc's */
+{
+struct hgnc *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    hgncFree(&el);
+    }
+*pList = NULL;
+}
+
+void hgncOutput(struct hgnc *el, FILE *f, char sep, char lastSep) 
+/* Print out hgnc.  Separate fields with sep. Follow last field with lastSep. */
+{
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->hgncId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->symbol);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->name);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->status);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->locusType);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->locusGroup);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->prvSymbols);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->prvNames);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->synonyms);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->nameSyns);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->chrom);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->dateApprv);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->dateMod);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->dateSymChange);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->dateNmChange);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->accession);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->enzymeIds);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->entrezId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->ensId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->mgdId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->miscDbs);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->miscIds);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->pubMed);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->refSeqIds);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->geneFamilyNm);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->geneFamilyDesc);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->recType);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->primaryId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->secondaryId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->ccdsId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->vegaId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->locusDbs);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->gdbMapped);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->entrezMapped);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->omimMapped);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->refSeqMapped);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->uniProtMapped);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->ensMapped);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->ucscMapped);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->mgiMapped);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->rgdMapped);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+