src/hg/inc/bed12wSeq.h 1.1

Index: src/hg/inc/bed12wSeq.h
===================================================================
RCS file: src/hg/inc/bed12wSeq.h
diff -N src/hg/inc/bed12wSeq.h
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/inc/bed12wSeq.h	24 Sep 2009 21:26:17 -0000	1.1
@@ -0,0 +1,96 @@
+/* bed12wSeq.h was originally generated by the autoSql program, which also 
+ * generated bed12wSeq.c and bed12wSeq.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef BED12WSEQ_H
+#define BED12WSEQ_H
+
+#include "jksql.h"
+#define BED12WSEQ_NUM_COLS 14
+
+struct bed12wSeq
+/* Browser extensible data (12 fields) plus two sequences */
+    {
+    struct bed12wSeq *next;  /* Next in singly linked list. */
+    char *chrom;	/* Chromosome (or contig, scaffold, etc.) */
+    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 - */
+    unsigned thickStart;	/* Start of where display should be thick (start codon) */
+    unsigned thickEnd;	/* End of where display should be thick (stop codon) */
+    unsigned reserved;	/* Used as itemRgb as of 2004-11-22 */
+    int blockCount;	/* Number of blocks */
+    int *blockSizes;	/* Comma separated list of block sizes */
+    int *chromStarts;	/* Start positions relative to chromStart */
+    char *seq1;	/* sequence 1, normally left paired end */
+    char *seq2;	/* sequence 2, normally right paired end */
+    };
+
+struct bed12wSeq *bed12wSeqLoad(char **row);
+/* Load a bed12wSeq from row fetched with select * from bed12wSeq
+ * from database.  Dispose of this with bed12wSeqFree(). */
+
+struct bed12wSeq *bed12wSeqLoadAll(char *fileName);
+/* Load all bed12wSeq from whitespace-separated file.
+ * Dispose of this with bed12wSeqFreeList(). */
+
+struct bed12wSeq *bed12wSeqLoadAllByChar(char *fileName, char chopper);
+/* Load all bed12wSeq from chopper separated file.
+ * Dispose of this with bed12wSeqFreeList(). */
+
+#define bed12wSeqLoadAllByTab(a) bed12wSeqLoadAllByChar(a, '\t');
+/* Load all bed12wSeq from tab separated file.
+ * Dispose of this with bed12wSeqFreeList(). */
+
+struct bed12wSeq *bed12wSeqLoadByQuery(struct sqlConnection *conn, char *query);
+/* Load all bed12wSeq 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 bed12wSeqFreeList(). */
+
+void bed12wSeqSaveToDb(struct sqlConnection *conn, struct bed12wSeq *el, char *tableName, int updateSize);
+/* Save bed12wSeq 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 bed12wSeqSaveToDbEscaped() */
+
+void bed12wSeqSaveToDbEscaped(struct sqlConnection *conn, struct bed12wSeq *el, char *tableName, int updateSize);
+/* Save bed12wSeq 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 bed12wSeqSaveToDb().
+ * For example automatically copies and converts: 
+ * "autosql's features include" --> "autosql\'s features include" 
+ * before inserting into database. */ 
+
+struct bed12wSeq *bed12wSeqCommaIn(char **pS, struct bed12wSeq *ret);
+/* Create a bed12wSeq out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new bed12wSeq */
+
+void bed12wSeqFree(struct bed12wSeq **pEl);
+/* Free a single dynamically allocated bed12wSeq such as created
+ * with bed12wSeqLoad(). */
+
+void bed12wSeqFreeList(struct bed12wSeq **pList);
+/* Free a list of dynamically allocated bed12wSeq's */
+
+void bed12wSeqOutput(struct bed12wSeq *el, FILE *f, char sep, char lastSep);
+/* Print out bed12wSeq.  Separate fields with sep. Follow last field with lastSep. */
+
+#define bed12wSeqTabOut(el,f) bed12wSeqOutput(el,f,'\t','\n');
+/* Print out bed12wSeq as a line in a tab-separated file. */
+
+#define bed12wSeqCommaOut(el,f) bed12wSeqOutput(el,f,',',',');
+/* Print out bed12wSeq as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+#endif /* BED12WSEQ_H */
+