e3e21c453e6963fddd0f1c32a1d6a4b9bab685e2
hiram
  Thu Feb 4 14:57:18 2016 -0800
first pass as display of metadata for NCBI RefSeq track, needs improvement refs #13673

diff --git src/hg/lib/ncbiRefSeqLink.c src/hg/lib/ncbiRefSeqLink.c
new file mode 100644
index 0000000..36a8f16
--- /dev/null
+++ src/hg/lib/ncbiRefSeqLink.c
@@ -0,0 +1,254 @@
+/* ncbiRefSeqLink.c was originally generated by the autoSql program, which also 
+ * generated ncbiRefSeqLink.h and ncbiRefSeqLink.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 "ncbiRefSeqLink.h"
+
+
+
+char *ncbiRefSeqLinkCommaSepFieldNames = "id,status,name,product,mrnaAcc,protAcc,locusLinkId,omimId,hgnc,genbank,pseudo,gbkey,source,gene_biotype,gene_synonym,ncrna_class,note,description";
+
+void ncbiRefSeqLinkStaticLoad(char **row, struct ncbiRefSeqLink *ret)
+/* Load a row from ncbiRefSeqLink table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->id = row[0];
+ret->status = row[1];
+ret->name = row[2];
+ret->product = row[3];
+ret->mrnaAcc = row[4];
+ret->protAcc = row[5];
+ret->locusLinkId = row[6];
+ret->omimId = row[7];
+ret->hgnc = row[8];
+ret->genbank = row[9];
+ret->pseudo = row[10];
+ret->gbkey = row[11];
+ret->source = row[12];
+ret->gene_biotype = row[13];
+ret->gene_synonym = row[14];
+ret->ncrna_class = row[15];
+ret->note = row[16];
+ret->description = row[17];
+}
+
+struct ncbiRefSeqLink *ncbiRefSeqLinkLoad(char **row)
+/* Load a ncbiRefSeqLink from row fetched with select * from ncbiRefSeqLink
+ * from database.  Dispose of this with ncbiRefSeqLinkFree(). */
+{
+struct ncbiRefSeqLink *ret;
+
+AllocVar(ret);
+ret->id = cloneString(row[0]);
+ret->status = cloneString(row[1]);
+ret->name = cloneString(row[2]);
+ret->product = cloneString(row[3]);
+ret->mrnaAcc = cloneString(row[4]);
+ret->protAcc = cloneString(row[5]);
+ret->locusLinkId = cloneString(row[6]);
+ret->omimId = cloneString(row[7]);
+ret->hgnc = cloneString(row[8]);
+ret->genbank = cloneString(row[9]);
+ret->pseudo = cloneString(row[10]);
+ret->gbkey = cloneString(row[11]);
+ret->source = cloneString(row[12]);
+ret->gene_biotype = cloneString(row[13]);
+ret->gene_synonym = cloneString(row[14]);
+ret->ncrna_class = cloneString(row[15]);
+ret->note = cloneString(row[16]);
+ret->description = cloneString(row[17]);
+return ret;
+}
+
+struct ncbiRefSeqLink *ncbiRefSeqLinkLoadAll(char *fileName) 
+/* Load all ncbiRefSeqLink from a whitespace-separated file.
+ * Dispose of this with ncbiRefSeqLinkFreeList(). */
+{
+struct ncbiRefSeqLink *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[18];
+
+while (lineFileRow(lf, row))
+    {
+    el = ncbiRefSeqLinkLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct ncbiRefSeqLink *ncbiRefSeqLinkLoadAllByChar(char *fileName, char chopper) 
+/* Load all ncbiRefSeqLink from a chopper separated file.
+ * Dispose of this with ncbiRefSeqLinkFreeList(). */
+{
+struct ncbiRefSeqLink *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[18];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = ncbiRefSeqLinkLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct ncbiRefSeqLink *ncbiRefSeqLinkCommaIn(char **pS, struct ncbiRefSeqLink *ret)
+/* Create a ncbiRefSeqLink out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new ncbiRefSeqLink */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->id = sqlStringComma(&s);
+ret->status = sqlStringComma(&s);
+ret->name = sqlStringComma(&s);
+ret->product = sqlStringComma(&s);
+ret->mrnaAcc = sqlStringComma(&s);
+ret->protAcc = sqlStringComma(&s);
+ret->locusLinkId = sqlStringComma(&s);
+ret->omimId = sqlStringComma(&s);
+ret->hgnc = sqlStringComma(&s);
+ret->genbank = sqlStringComma(&s);
+ret->pseudo = sqlStringComma(&s);
+ret->gbkey = sqlStringComma(&s);
+ret->source = sqlStringComma(&s);
+ret->gene_biotype = sqlStringComma(&s);
+ret->gene_synonym = sqlStringComma(&s);
+ret->ncrna_class = sqlStringComma(&s);
+ret->note = sqlStringComma(&s);
+ret->description = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void ncbiRefSeqLinkFree(struct ncbiRefSeqLink **pEl)
+/* Free a single dynamically allocated ncbiRefSeqLink such as created
+ * with ncbiRefSeqLinkLoad(). */
+{
+struct ncbiRefSeqLink *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->id);
+freeMem(el->status);
+freeMem(el->name);
+freeMem(el->product);
+freeMem(el->mrnaAcc);
+freeMem(el->protAcc);
+freeMem(el->locusLinkId);
+freeMem(el->omimId);
+freeMem(el->hgnc);
+freeMem(el->genbank);
+freeMem(el->pseudo);
+freeMem(el->gbkey);
+freeMem(el->source);
+freeMem(el->gene_biotype);
+freeMem(el->gene_synonym);
+freeMem(el->ncrna_class);
+freeMem(el->note);
+freeMem(el->description);
+freez(pEl);
+}
+
+void ncbiRefSeqLinkFreeList(struct ncbiRefSeqLink **pList)
+/* Free a list of dynamically allocated ncbiRefSeqLink's */
+{
+struct ncbiRefSeqLink *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    ncbiRefSeqLinkFree(&el);
+    }
+*pList = NULL;
+}
+
+void ncbiRefSeqLinkOutput(struct ncbiRefSeqLink *el, FILE *f, char sep, char lastSep) 
+/* Print out ncbiRefSeqLink.  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->status);
+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->product);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->mrnaAcc);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->protAcc);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->locusLinkId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->omimId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->hgnc);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->genbank);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->pseudo);
+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->source);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->gene_biotype);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->gene_synonym);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->ncrna_class);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->note);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->description);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+