533112afe2a2005e80cdb1f82904ea65032d4302
braney
  Sat Oct 2 11:37:34 2021 -0700
split hg/lib into two separate libaries, one only used by the cgis

diff --git src/hg/cgilib/atomDb.c src/hg/cgilib/atomDb.c
new file mode 100644
index 0000000..b390a0e
--- /dev/null
+++ src/hg/cgilib/atomDb.c
@@ -0,0 +1,172 @@
+/* atomDb.c was originally generated by the autoSql program, which also 
+ * generated atomDb.h and atomDb.sql.  This module links the database and
+ * the RAM representation of objects. */
+
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
+#include "common.h"
+#include "linefile.h"
+#include "dystring.h"
+#include "jksql.h"
+#include "atomDb.h"
+
+
+void atomStaticLoad(char **row, struct atom *ret)
+/* Load a row from atom table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->name = row[0];
+ret->instance = sqlUnsigned(row[1]);
+ret->species = row[2];
+ret->chrom = row[3];
+ret->start = sqlUnsigned(row[4]);
+ret->end = sqlUnsigned(row[5]);
+safecpy(ret->strand, sizeof(ret->strand), row[6]);
+ret->fivePrime = row[7];
+ret->threePrime = row[8];
+}
+
+struct atom *atomLoad(char **row)
+/* Load a atom from row fetched with select * from atom
+ * from database.  Dispose of this with atomFree(). */
+{
+struct atom *ret;
+
+AllocVar(ret);
+ret->name = cloneString(row[0]);
+ret->instance = sqlUnsigned(row[1]);
+ret->species = cloneString(row[2]);
+ret->chrom = cloneString(row[3]);
+ret->start = sqlUnsigned(row[4]);
+ret->end = sqlUnsigned(row[5]);
+safecpy(ret->strand, sizeof(ret->strand), row[6]);
+ret->fivePrime = cloneString(row[7]);
+ret->threePrime = cloneString(row[8]);
+return ret;
+}
+
+struct atom *atomLoadAll(char *fileName) 
+/* Load all atom from a whitespace-separated file.
+ * Dispose of this with atomFreeList(). */
+{
+struct atom *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[9];
+
+while (lineFileRow(lf, row))
+    {
+    el = atomLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct atom *atomLoadAllByChar(char *fileName, char chopper) 
+/* Load all atom from a chopper separated file.
+ * Dispose of this with atomFreeList(). */
+{
+struct atom *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[9];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = atomLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct atom *atomCommaIn(char **pS, struct atom *ret)
+/* Create a atom out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new atom */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->name = sqlStringComma(&s);
+ret->instance = sqlUnsignedComma(&s);
+ret->species = sqlStringComma(&s);
+ret->chrom = sqlStringComma(&s);
+ret->start = sqlUnsignedComma(&s);
+ret->end = sqlUnsignedComma(&s);
+sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
+ret->fivePrime = sqlStringComma(&s);
+ret->threePrime = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void atomFree(struct atom **pEl)
+/* Free a single dynamically allocated atom such as created
+ * with atomLoad(). */
+{
+struct atom *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->name);
+freeMem(el->species);
+freeMem(el->chrom);
+freeMem(el->fivePrime);
+freeMem(el->threePrime);
+freez(pEl);
+}
+
+void atomFreeList(struct atom **pList)
+/* Free a list of dynamically allocated atom's */
+{
+struct atom *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    atomFree(&el);
+    }
+*pList = NULL;
+}
+
+void atomOutput(struct atom *el, FILE *f, char sep, char lastSep) 
+/* Print out atom.  Separate fields with sep. Follow last field with lastSep. */
+{
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->name);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->instance);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->species);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->chrom);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->start);
+fputc(sep,f);
+fprintf(f, "%u", el->end);
+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->fivePrime);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->threePrime);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+