src/hg/lib/gbSeq.c 1.1

Index: src/hg/lib/gbSeq.c
===================================================================
RCS file: src/hg/lib/gbSeq.c
diff -N src/hg/lib/gbSeq.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/lib/gbSeq.c	4 Jul 2009 07:14:20 -0000	1.1
@@ -0,0 +1,168 @@
+/* gbSeq.c was originally generated by the autoSql program, which also 
+ * generated gbSeq.h and gbSeq.sql.  This module links the database and
+ * the RAM representation of objects. */
+
+#include "common.h"
+#include "linefile.h"
+#include "dystring.h"
+#include "jksql.h"
+#include "gbSeq.h"
+
+static char const rcsid[] = "$Id$";
+
+/* definitions for type column */
+static char *values_type[] = {"EST", "mRNA", "PEP", NULL};
+static struct hash *valhash_type = NULL;
+
+/* definitions for srcDb column */
+static char *values_srcDb[] = {"GenBank", "RefSeq", "Other", NULL};
+static struct hash *valhash_srcDb = NULL;
+
+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. */
+{
+
+ret->id = sqlUnsigned(row[0]);
+ret->acc = row[1];
+ret->version = sqlSigned(row[2]);
+ret->size = sqlUnsigned(row[3]);
+ret->gbExtFile = sqlUnsigned(row[4]);
+ret->file_offset = sqlLongLong(row[5]);
+ret->file_size = sqlUnsigned(row[6]);
+ret->type = sqlEnumParse(row[7], values_type, &valhash_type);
+ret->srcDb = sqlEnumParse(row[8], values_srcDb, &valhash_srcDb);
+}
+
+struct gbSeq *gbSeqLoad(char **row)
+/* Load a gbSeq from row fetched with select * from gbSeq
+ * from database.  Dispose of this with gbSeqFree(). */
+{
+struct gbSeq *ret;
+
+AllocVar(ret);
+ret->id = sqlUnsigned(row[0]);
+ret->acc = cloneString(row[1]);
+ret->version = sqlSigned(row[2]);
+ret->size = sqlUnsigned(row[3]);
+ret->gbExtFile = sqlUnsigned(row[4]);
+ret->file_offset = sqlLongLong(row[5]);
+ret->file_size = sqlUnsigned(row[6]);
+ret->type = sqlEnumParse(row[7], values_type, &valhash_type);
+ret->srcDb = sqlEnumParse(row[8], values_srcDb, &valhash_srcDb);
+return ret;
+}
+
+struct gbSeq *gbSeqLoadAll(char *fileName) 
+/* Load all gbSeq from a whitespace-separated file.
+ * Dispose of this with gbSeqFreeList(). */
+{
+struct gbSeq *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[9];
+
+while (lineFileRow(lf, row))
+    {
+    el = gbSeqLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gbSeq *gbSeqLoadAllByChar(char *fileName, char chopper) 
+/* Load all gbSeq from a chopper separated file.
+ * Dispose of this with gbSeqFreeList(). */
+{
+struct gbSeq *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[9];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = gbSeqLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+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 */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->id = sqlUnsignedComma(&s);
+ret->acc = sqlStringComma(&s);
+ret->version = sqlSignedComma(&s);
+ret->size = sqlUnsignedComma(&s);
+ret->gbExtFile = sqlUnsignedComma(&s);
+ret->file_offset = sqlLongLongComma(&s);
+ret->file_size = sqlUnsignedComma(&s);
+ret->type = sqlEnumComma(&s, values_type, &valhash_type);
+ret->srcDb = sqlEnumComma(&s, values_srcDb, &valhash_srcDb);
+*pS = s;
+return ret;
+}
+
+void gbSeqFree(struct gbSeq **pEl)
+/* Free a single dynamically allocated gbSeq such as created
+ * with gbSeqLoad(). */
+{
+struct gbSeq *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->acc);
+freez(pEl);
+}
+
+void gbSeqFreeList(struct gbSeq **pList)
+/* Free a list of dynamically allocated gbSeq's */
+{
+struct gbSeq *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    gbSeqFree(&el);
+    }
+*pList = NULL;
+}
+
+void gbSeqOutput(struct gbSeq *el, FILE *f, char sep, char lastSep) 
+/* Print out gbSeq.  Separate fields with sep. Follow last field with lastSep. */
+{
+fprintf(f, "%u", el->id);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->acc);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%d", el->version);
+fputc(sep,f);
+fprintf(f, "%u", el->size);
+fputc(sep,f);
+fprintf(f, "%u", el->gbExtFile);
+fputc(sep,f);
+fprintf(f, "%lld", el->file_offset);
+fputc(sep,f);
+fprintf(f, "%u", el->file_size);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+sqlEnumPrint(f, el->type, values_type);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+sqlEnumPrint(f, el->srcDb, values_srcDb);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+