4c1d2a0a761f1afc9da81243357e462ae14c3756
braney
  Thu Dec 15 14:49:26 2022 -0800
add assembly aliasing to hub connection

diff --git src/hg/inc/asmAlias.h src/hg/inc/asmAlias.h
new file mode 100644
index 0000000..e65706b
--- /dev/null
+++ src/hg/inc/asmAlias.h
@@ -0,0 +1,82 @@
+/* asmAlias.h was originally generated by the autoSql program, which also 
+ * generated asmAlias.c and asmAlias.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef ASMALIAS_H
+#define ASMALIAS_H
+
+#include "jksql.h"
+#define ASMALIAS_NUM_COLS 2
+
+extern char *asmAliasCommaSepFieldNames;
+
+struct asmAlias
+/* correspondence of assembly identifiers to UCSC database or GenArk hub equivalents */
+    {
+    struct asmAlias *next;  /* Next in singly linked list. */
+    char *alias;	/* external assembly name */
+    char *browser;	/* UCSC genome browser equivalent */
+    };
+
+void asmAliasStaticLoad(char **row, struct asmAlias *ret);
+/* Load a row from asmAlias table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+
+struct asmAlias *asmAliasLoadByQuery(struct sqlConnection *conn, char *query);
+/* Load all asmAlias from table that satisfy the query given.  
+ * Where query is of the form 'select * from example where something=something'
+ * or 'select example.* from example, anotherTable where example.something = 
+ * anotherTable.something'.
+ * Dispose of this with asmAliasFreeList(). */
+
+void asmAliasSaveToDb(struct sqlConnection *conn, struct asmAlias *el, char *tableName, int updateSize);
+/* Save asmAlias as a row to the table specified by tableName. 
+ * As blob fields may be arbitrary size updateSize specifies the approx size
+ * of a string that would contain the entire query. Arrays of native types are
+ * converted to comma separated strings and loaded as such, User defined types are
+ * inserted as NULL. This function automatically escapes quoted strings for mysql. */
+
+struct asmAlias *asmAliasLoad(char **row);
+/* Load a asmAlias from row fetched with select * from asmAlias
+ * from database.  Dispose of this with asmAliasFree(). */
+
+struct asmAlias *asmAliasLoadAll(char *fileName);
+/* Load all asmAlias from whitespace-separated file.
+ * Dispose of this with asmAliasFreeList(). */
+
+struct asmAlias *asmAliasLoadAllByChar(char *fileName, char chopper);
+/* Load all asmAlias from chopper separated file.
+ * Dispose of this with asmAliasFreeList(). */
+
+#define asmAliasLoadAllByTab(a) asmAliasLoadAllByChar(a, '\t');
+/* Load all asmAlias from tab separated file.
+ * Dispose of this with asmAliasFreeList(). */
+
+struct asmAlias *asmAliasCommaIn(char **pS, struct asmAlias *ret);
+/* Create a asmAlias out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new asmAlias */
+
+void asmAliasFree(struct asmAlias **pEl);
+/* Free a single dynamically allocated asmAlias such as created
+ * with asmAliasLoad(). */
+
+void asmAliasFreeList(struct asmAlias **pList);
+/* Free a list of dynamically allocated asmAlias's */
+
+void asmAliasOutput(struct asmAlias *el, FILE *f, char sep, char lastSep);
+/* Print out asmAlias.  Separate fields with sep. Follow last field with lastSep. */
+
+#define asmAliasTabOut(el,f) asmAliasOutput(el,f,'\t','\n');
+/* Print out asmAlias as a line in a tab-separated file. */
+
+#define asmAliasCommaOut(el,f) asmAliasOutput(el,f,',',',');
+/* Print out asmAlias as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+char *asmAliasFind(char *alias);
+/* If this assembly is an alias for a db we know about, return it.  Otherwise return what we were sent. */
+
+#endif /* ASMALIAS_H */
+