src/hg/inc/gbSeq.h 1.1

Index: src/hg/inc/gbSeq.h
===================================================================
RCS file: src/hg/inc/gbSeq.h
diff -N src/hg/inc/gbSeq.h
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/inc/gbSeq.h	4 Jul 2009 07:14:19 -0000	1.1
@@ -0,0 +1,81 @@
+/* gbSeq.h was originally generated by the autoSql program, which also 
+ * generated gbSeq.c and gbSeq.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef GBSEQ_H
+#define GBSEQ_H
+
+#define GBSEQ_NUM_COLS 9
+
+enum gbSeqType
+    {
+    gbSeqEST = 0,
+    gbSeqMRNA = 1,
+    gbSeqPEP = 2,
+    };
+enum gbSeqSrcDb
+    {
+    gbSeqGenBank = 0,
+    gbSeqRefSeq = 1,
+    gbSeqOther = 2,
+    };
+struct gbSeq
+/* Information about sequences contained in files described in gbExtFile */
+    {
+    struct gbSeq *next;  /* Next in singly linked list. */
+    unsigned id;	/* ID/index */
+    char *acc;	/* Accession of sequence */
+    int version;	/* Genbank version */
+    unsigned size;	/* Size of sequence (number of bases) */
+    unsigned gbExtFile;	/* ID/index of file in gbExtFile */
+    long long file_offset;	/* byte offset of sequence in file */
+    unsigned file_size;	/* byte size of sequence in file */
+    enum gbSeqType type;	/* Type of sequence */
+    enum gbSeqSrcDb srcDb;	/* Source database */
+    };
+
+void gbSeqStaticLoad(char **row, struct gbSeq *ret);
+/* Load a row from gbSeq table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+
+struct gbSeq *gbSeqLoad(char **row);
+/* Load a gbSeq from row fetched with select * from gbSeq
+ * from database.  Dispose of this with gbSeqFree(). */
+
+struct gbSeq *gbSeqLoadAll(char *fileName);
+/* Load all gbSeq from whitespace-separated file.
+ * Dispose of this with gbSeqFreeList(). */
+
+struct gbSeq *gbSeqLoadAllByChar(char *fileName, char chopper);
+/* Load all gbSeq from chopper separated file.
+ * Dispose of this with gbSeqFreeList(). */
+
+#define gbSeqLoadAllByTab(a) gbSeqLoadAllByChar(a, '\t');
+/* Load all gbSeq from tab separated file.
+ * Dispose of this with gbSeqFreeList(). */
+
+struct gbSeq *gbSeqCommaIn(char **pS, struct gbSeq *ret);
+/* Create a gbSeq out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new gbSeq */
+
+void gbSeqFree(struct gbSeq **pEl);
+/* Free a single dynamically allocated gbSeq such as created
+ * with gbSeqLoad(). */
+
+void gbSeqFreeList(struct gbSeq **pList);
+/* Free a list of dynamically allocated gbSeq's */
+
+void gbSeqOutput(struct gbSeq *el, FILE *f, char sep, char lastSep);
+/* Print out gbSeq.  Separate fields with sep. Follow last field with lastSep. */
+
+#define gbSeqTabOut(el,f) gbSeqOutput(el,f,'\t','\n');
+/* Print out gbSeq as a line in a tab-separated file. */
+
+#define gbSeqCommaOut(el,f) gbSeqOutput(el,f,',',',');
+/* Print out gbSeq as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+#endif /* GBSEQ_H */
+