cfb63bd22072217bc504665d8abeb5f81587c8d7
hiram
  Thu Sep 15 18:09:14 2016 -0700
better to call chromXref as chromAlias and now is a three column table with primary key refs #18027

diff --git src/hg/lib/chromAlias.c src/hg/lib/chromAlias.c
new file mode 100644
index 0000000..d8a466d
--- /dev/null
+++ src/hg/lib/chromAlias.c
@@ -0,0 +1,164 @@
+/* chromAlias.c was originally generated by the autoSql program, which also 
+ * generated chromAlias.h and chromAlias.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 "chromAlias.h"
+
+
+
+char *chromAliasCommaSepFieldNames = "alias,chrom,source";
+
+void chromAliasStaticLoad(char **row, struct chromAlias *ret)
+/* Load a row from chromAlias table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->alias = row[0];
+ret->chrom = row[1];
+ret->source = row[2];
+}
+
+struct chromAlias *chromAliasLoad(char **row)
+/* Load a chromAlias from row fetched with select * from chromAlias
+ * from database.  Dispose of this with chromAliasFree(). */
+{
+struct chromAlias *ret;
+
+AllocVar(ret);
+ret->alias = cloneString(row[0]);
+ret->chrom = cloneString(row[1]);
+ret->source = cloneString(row[2]);
+return ret;
+}
+
+struct chromAlias *chromAliasLoadAll(char *fileName) 
+/* Load all chromAlias from a whitespace-separated file.
+ * Dispose of this with chromAliasFreeList(). */
+{
+struct chromAlias *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[3];
+
+while (lineFileRow(lf, row))
+    {
+    el = chromAliasLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct chromAlias *chromAliasLoadAllByChar(char *fileName, char chopper) 
+/* Load all chromAlias from a chopper separated file.
+ * Dispose of this with chromAliasFreeList(). */
+{
+struct chromAlias *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[3];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = chromAliasLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct chromAlias *chromAliasCommaIn(char **pS, struct chromAlias *ret)
+/* Create a chromAlias out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new chromAlias */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->alias = sqlStringComma(&s);
+ret->chrom = sqlStringComma(&s);
+ret->source = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void chromAliasFree(struct chromAlias **pEl)
+/* Free a single dynamically allocated chromAlias such as created
+ * with chromAliasLoad(). */
+{
+struct chromAlias *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->alias);
+freeMem(el->chrom);
+freeMem(el->source);
+freez(pEl);
+}
+
+void chromAliasFreeList(struct chromAlias **pList)
+/* Free a list of dynamically allocated chromAlias's */
+{
+struct chromAlias *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    chromAliasFree(&el);
+    }
+*pList = NULL;
+}
+
+void chromAliasOutput(struct chromAlias *el, FILE *f, char sep, char lastSep) 
+/* Print out chromAlias.  Separate fields with sep. Follow last field with lastSep. */
+{
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->alias);
+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->source);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+void chromAliasJsonOutput(struct chromAlias *el, FILE *f) 
+/* Print out chromAlias in JSON format. */
+{
+fputc('{',f);
+fputc('"',f);
+fprintf(f,"alias");
+fputc('"',f);
+fputc(':',f);
+fputc('"',f);
+fprintf(f, "%s", el->alias);
+fputc('"',f);
+fputc(',',f);
+fputc('"',f);
+fprintf(f,"chrom");
+fputc('"',f);
+fputc(':',f);
+fputc('"',f);
+fprintf(f, "%s", el->chrom);
+fputc('"',f);
+fputc(',',f);
+fputc('"',f);
+fprintf(f,"source");
+fputc('"',f);
+fputc(':',f);
+fputc('"',f);
+fprintf(f, "%s", el->source);
+fputc('"',f);
+fputc('}',f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+