cd53a755e4e7dfbbfdeeef59b03c8261146d2a82
baertsch
  Sun May 15 03:16:54 2011 -0700
add ucscRetroOrtho table and code for ucscRetro child table
diff --git src/hg/inc/ucscRetroOrtho.h src/hg/inc/ucscRetroOrtho.h
new file mode 100644
index 0000000..ef3c654
--- /dev/null
+++ src/hg/inc/ucscRetroOrtho.h
@@ -0,0 +1,89 @@
+/* ucscRetroOrtho.h was originally generated by the autoSql program, which also 
+ * generated ucscRetroOrtho.c and ucscRetroOrtho.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef UCSCRETROORTHO_H
+#define UCSCRETROORTHO_H
+
+#include "jksql.h"
+#define UCSCRETROORTHO_NUM_COLS 3
+
+struct ucscRetroOrtho
+/* Orthlogy of retrogenes based on chains/nets with other species. */
+    {
+    struct ucscRetroOrtho *next;  /* Next in singly linked list. */
+    char *name;	/* Unique name of retrogene  */
+    char *db;	/* database of other species */
+    int overlap;	/* percent of retro that breaks net relative to other species */
+    };
+
+void ucscRetroOrthoStaticLoad(char **row, struct ucscRetroOrtho *ret);
+/* Load a row from ucscRetroOrtho table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+
+struct ucscRetroOrtho *ucscRetroOrthoLoadByQuery(struct sqlConnection *conn, char *query);
+/* Load all ucscRetroOrtho 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 ucscRetroOrthoFreeList(). */
+
+void ucscRetroOrthoSaveToDb(struct sqlConnection *conn, struct ucscRetroOrtho *el, char *tableName, int updateSize);
+/* Save ucscRetroOrtho 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. Note that strings must be escaped to allow insertion into the database.
+ * For example "autosql's features include" --> "autosql\'s features include" 
+ * If worried about this use ucscRetroOrthoSaveToDbEscaped() */
+
+void ucscRetroOrthoSaveToDbEscaped(struct sqlConnection *conn, struct ucscRetroOrtho *el, char *tableName, int updateSize);
+/* Save ucscRetroOrtho 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. Automatically 
+ * escapes all simple strings (not arrays of string) but may be slower than ucscRetroOrthoSaveToDb().
+ * For example automatically copies and converts: 
+ * "autosql's features include" --> "autosql\'s features include" 
+ * before inserting into database. */ 
+
+struct ucscRetroOrtho *ucscRetroOrthoLoad(char **row);
+/* Load a ucscRetroOrtho from row fetched with select * from ucscRetroOrtho
+ * from database.  Dispose of this with ucscRetroOrthoFree(). */
+
+struct ucscRetroOrtho *ucscRetroOrthoLoadAll(char *fileName);
+/* Load all ucscRetroOrtho from whitespace-separated file.
+ * Dispose of this with ucscRetroOrthoFreeList(). */
+
+struct ucscRetroOrtho *ucscRetroOrthoLoadAllByChar(char *fileName, char chopper);
+/* Load all ucscRetroOrtho from chopper separated file.
+ * Dispose of this with ucscRetroOrthoFreeList(). */
+
+#define ucscRetroOrthoLoadAllByTab(a) ucscRetroOrthoLoadAllByChar(a, '\t');
+/* Load all ucscRetroOrtho from tab separated file.
+ * Dispose of this with ucscRetroOrthoFreeList(). */
+
+struct ucscRetroOrtho *ucscRetroOrthoCommaIn(char **pS, struct ucscRetroOrtho *ret);
+/* Create a ucscRetroOrtho out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new ucscRetroOrtho */
+
+void ucscRetroOrthoFree(struct ucscRetroOrtho **pEl);
+/* Free a single dynamically allocated ucscRetroOrtho such as created
+ * with ucscRetroOrthoLoad(). */
+
+void ucscRetroOrthoFreeList(struct ucscRetroOrtho **pList);
+/* Free a list of dynamically allocated ucscRetroOrtho's */
+
+void ucscRetroOrthoOutput(struct ucscRetroOrtho *el, FILE *f, char sep, char lastSep);
+/* Print out ucscRetroOrtho.  Separate fields with sep. Follow last field with lastSep. */
+
+#define ucscRetroOrthoTabOut(el,f) ucscRetroOrthoOutput(el,f,'\t','\n');
+/* Print out ucscRetroOrtho as a line in a tab-separated file. */
+
+#define ucscRetroOrthoCommaOut(el,f) ucscRetroOrthoOutput(el,f,',',',');
+/* Print out ucscRetroOrtho as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+#endif /* UCSCRETROORTHO_H */
+