e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/lib/atomDb.c src/hg/lib/atomDb.c
index 2ee941b..b390a0e 100644
--- src/hg/lib/atomDb.c
+++ src/hg/lib/atomDb.c
@@ -1,169 +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 -------------------------------- */