dc23932b2dae91522d130c311ae3b28dbce488e6
braney
  Fri May 22 13:54:01 2015 -0700
add NCBI metadata to NCBI RefSeq track ( refs# 13673)

diff --git src/hg/lib/ncbiRefLink.c src/hg/lib/ncbiRefLink.c
new file mode 100644
index 0000000..d4329f5
--- /dev/null
+++ src/hg/lib/ncbiRefLink.c
@@ -0,0 +1,150 @@
+/* ncbiRefLink.c was originally generated by the autoSql program, which also 
+ * generated ncbiRefLink.h and ncbiRefLink.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 "ncbiRefLink.h"
+
+
+
+char *ncbiRefLinkCommaSepFieldNames = "id,gbKey,gene,dbXref,product";
+
+void ncbiRefLinkStaticLoad(char **row, struct ncbiRefLink *ret)
+/* Load a row from ncbiRefLink table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->id = row[0];
+ret->gbKey = row[1];
+ret->gene = row[2];
+ret->dbXref = row[3];
+ret->product = row[4];
+}
+
+struct ncbiRefLink *ncbiRefLinkLoad(char **row)
+/* Load a ncbiRefLink from row fetched with select * from ncbiRefLink
+ * from database.  Dispose of this with ncbiRefLinkFree(). */
+{
+struct ncbiRefLink *ret;
+
+AllocVar(ret);
+ret->id = cloneString(row[0]);
+ret->gbKey = cloneString(row[1]);
+ret->gene = cloneString(row[2]);
+ret->dbXref = cloneString(row[3]);
+ret->product = cloneString(row[4]);
+return ret;
+}
+
+struct ncbiRefLink *ncbiRefLinkLoadAll(char *fileName) 
+/* Load all ncbiRefLink from a whitespace-separated file.
+ * Dispose of this with ncbiRefLinkFreeList(). */
+{
+struct ncbiRefLink *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[5];
+
+while (lineFileRow(lf, row))
+    {
+    el = ncbiRefLinkLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct ncbiRefLink *ncbiRefLinkLoadAllByChar(char *fileName, char chopper) 
+/* Load all ncbiRefLink from a chopper separated file.
+ * Dispose of this with ncbiRefLinkFreeList(). */
+{
+struct ncbiRefLink *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[5];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = ncbiRefLinkLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct ncbiRefLink *ncbiRefLinkCommaIn(char **pS, struct ncbiRefLink *ret)
+/* Create a ncbiRefLink out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new ncbiRefLink */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->id = sqlStringComma(&s);
+ret->gbKey = sqlStringComma(&s);
+ret->gene = sqlStringComma(&s);
+ret->dbXref = sqlStringComma(&s);
+ret->product = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void ncbiRefLinkFree(struct ncbiRefLink **pEl)
+/* Free a single dynamically allocated ncbiRefLink such as created
+ * with ncbiRefLinkLoad(). */
+{
+struct ncbiRefLink *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->id);
+freeMem(el->gbKey);
+freeMem(el->gene);
+freeMem(el->dbXref);
+freeMem(el->product);
+freez(pEl);
+}
+
+void ncbiRefLinkFreeList(struct ncbiRefLink **pList)
+/* Free a list of dynamically allocated ncbiRefLink's */
+{
+struct ncbiRefLink *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    ncbiRefLinkFree(&el);
+    }
+*pList = NULL;
+}
+
+void ncbiRefLinkOutput(struct ncbiRefLink *el, FILE *f, char sep, char lastSep) 
+/* Print out ncbiRefLink.  Separate fields with sep. Follow last field with lastSep. */
+{
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->id);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->gbKey);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->gene);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->dbXref);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->product);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+