src/hg/lib/arCOGs.c 1.1

Index: src/hg/lib/arCOGs.c
===================================================================
RCS file: src/hg/lib/arCOGs.c
diff -N src/hg/lib/arCOGs.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/lib/arCOGs.c	14 Oct 2009 20:27:50 -0000	1.1
@@ -0,0 +1,154 @@
+/* arCOGs.c was originally generated by the autoSql program, which also 
+ * generated arCOGs.h and arCOGs.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 "arCOGs.h"
+
+static char const rcsid[] = "$Id$";
+
+void arCOGsStaticLoad(char **row, struct arCOGs *ret)
+/* Load a row from arCOGs table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->chrom = row[0];
+ret->chromStart = sqlUnsigned(row[1]);
+ret->chromEnd = sqlUnsigned(row[2]);
+ret->name = row[3];
+ret->score = sqlUnsigned(row[4]);
+safecpy(ret->strand, sizeof(ret->strand), row[5]);
+ret->gene = row[6];
+}
+
+struct arCOGs *arCOGsLoad(char **row)
+/* Load a arCOGs from row fetched with select * from arCOGs
+ * from database.  Dispose of this with arCOGsFree(). */
+{
+struct arCOGs *ret;
+
+AllocVar(ret);
+ret->chrom = cloneString(row[0]);
+ret->chromStart = sqlUnsigned(row[1]);
+ret->chromEnd = sqlUnsigned(row[2]);
+ret->name = cloneString(row[3]);
+ret->score = sqlUnsigned(row[4]);
+safecpy(ret->strand, sizeof(ret->strand), row[5]);
+ret->gene = cloneString(row[6]);
+return ret;
+}
+
+struct arCOGs *arCOGsLoadAll(char *fileName) 
+/* Load all arCOGs from a whitespace-separated file.
+ * Dispose of this with arCOGsFreeList(). */
+{
+struct arCOGs *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[7];
+
+while (lineFileRow(lf, row))
+    {
+    el = arCOGsLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct arCOGs *arCOGsLoadAllByChar(char *fileName, char chopper) 
+/* Load all arCOGs from a chopper separated file.
+ * Dispose of this with arCOGsFreeList(). */
+{
+struct arCOGs *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[7];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = arCOGsLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct arCOGs *arCOGsCommaIn(char **pS, struct arCOGs *ret)
+/* Create a arCOGs out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new arCOGs */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->chrom = sqlStringComma(&s);
+ret->chromStart = sqlUnsignedComma(&s);
+ret->chromEnd = sqlUnsignedComma(&s);
+ret->name = sqlStringComma(&s);
+ret->score = sqlUnsignedComma(&s);
+sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
+ret->gene = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void arCOGsFree(struct arCOGs **pEl)
+/* Free a single dynamically allocated arCOGs such as created
+ * with arCOGsLoad(). */
+{
+struct arCOGs *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->gene);
+freez(pEl);
+}
+
+void arCOGsFreeList(struct arCOGs **pList)
+/* Free a list of dynamically allocated arCOGs's */
+{
+struct arCOGs *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    arCOGsFree(&el);
+    }
+*pList = NULL;
+}
+
+void arCOGsOutput(struct arCOGs *el, FILE *f, char sep, char lastSep) 
+/* Print out arCOGs.  Separate fields with sep. Follow last field with lastSep. */
+{
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->chrom);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->chromStart);
+fputc(sep,f);
+fprintf(f, "%u", el->chromEnd);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->name);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->score);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->strand);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->gene);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+