ae3969602106c0229160648f6ff6c87c3ad0de2d
giardine
  Tue Dec 7 14:13:12 2010 -0800
Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
diff --git src/hg/inc/variome.h src/hg/inc/variome.h
new file mode 100644
index 0000000..4baf96c
--- /dev/null
+++ src/hg/inc/variome.h
@@ -0,0 +1,122 @@
+/* variome.h was originally generated by the autoSql program, which also 
+ * generated variome.c and variome.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef VARIOME_H
+#define VARIOME_H
+
+#ifndef JKSQL_H
+#include "jksql.h"
+#endif
+
+#define VARIOME_NUM_COLS 16
+
+struct variome
+/* variome bed 6+ structure */
+    {
+    struct variome *next;  /* Next in singly linked list. */
+    unsigned short bin;	/* used for efficient position indexing */
+    char *chrom;	/* Reference sequence chromosome or scaffold */
+    unsigned chromStart;	/* Start position in chromosome */
+    unsigned chromEnd;	/* End position in chromosome */
+    char *name;	/* Name of item */
+    unsigned score;	/* Score from 0-1000 */
+    char strand[2];	/* + or - */
+    char *db;	/* database for item */
+    char *owner;	/* creator of item */
+    char *color;	/* rgb color of item (currently unused) */
+    char *class;	/* classification of item (browser group) */
+    char *creationDate;	/* date item created */
+    char *lastModifiedDate;	/* date item last updated */
+    char *descriptionKey;	/* name of wiki description page */
+    unsigned id;	/* auto-increment item ID */
+    char *geneSymbol;	/* knownGene kgXref geneSymbol name */
+    };
+
+void variomeStaticLoad(char **row, struct variome *ret);
+/* Load a row from variome table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+
+struct variome *variomeLoad(char **row);
+/* Load a variome from row fetched with select * from variome
+ * from database.  Dispose of this with variomeFree(). */
+
+struct variome *variomeLoadAll(char *fileName);
+/* Load all variome from whitespace-separated file.
+ * Dispose of this with variomeFreeList(). */
+
+struct variome *variomeLoadAllByChar(char *fileName, char chopper);
+/* Load all variome from chopper separated file.
+ * Dispose of this with variomeFreeList(). */
+
+#define variomeLoadAllByTab(a) variomeLoadAllByChar(a, '\t');
+/* Load all variome from tab separated file.
+ * Dispose of this with variomeFreeList(). */
+
+struct variome *variomeLoadByQuery(struct sqlConnection *conn, char *query);
+/* Load all variome 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 variomeFreeList(). */
+
+void variomeSaveToDb(struct sqlConnection *conn, struct variome *el, char *tableName, int updateSize);
+/* Save variome 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 variomeSaveToDbEscaped() */
+
+void variomeSaveToDbEscaped(struct sqlConnection *conn, struct variome *el, char *tableName, int updateSize);
+/* Save variome 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 variomeSaveToDb().
+ * For example automatically copies and converts: 
+ * "autosql's features include" --> "autosql\'s features include" 
+ * before inserting into database. */ 
+
+struct variome *variomeCommaIn(char **pS, struct variome *ret);
+/* Create a variome out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new variome */
+
+void variomeFree(struct variome **pEl);
+/* Free a single dynamically allocated variome such as created
+ * with variomeLoad(). */
+
+void variomeFreeList(struct variome **pList);
+/* Free a list of dynamically allocated variome's */
+
+void variomeOutput(struct variome *el, FILE *f, char sep, char lastSep);
+/* Print out variome.  Separate fields with sep. Follow last field with lastSep. */
+
+#define variomeTabOut(el,f) variomeOutput(el,f,'\t','\n');
+/* Print out variome as a line in a tab-separated file. */
+
+#define variomeCommaOut(el,f) variomeOutput(el,f,',',',');
+/* Print out variome as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+extern char *variomeClassList[];
+extern int variomeClassCnt;
+extern char *variomeCoorList[];
+
+struct variome *findVariomeItemId(char *db, char *wikiItemId);
+/* given a wikiItemId return the row from the table */
+
+int addVariomeItem(char *db, char *chrom, int start, int end,
+    char *name, int score, char *strand, char *owner, char *class,
+        char *color, char *category, char *geneSymbol, char *wikiKey);
+/* create new Variome row with given parameters */
+
+void updateVariomeLastModifiedDate(char *db, int id);
+/* set lastModifiedDate to now() */
+
+void deleteVariomeItem(char *db, int id);
+/* delete the item with specified id */
+
+#endif /* VARIOME_H */
+