8c46bf4f26ab5833f1b9f23e4ec54f62ed60bf00
braney
  Thu May 14 15:48:28 2020 -0700
changes in comment in response to code review

diff --git src/hg/lib/rnaSecStr.c src/hg/lib/rnaSecStr.c
index 426ab31..f73fc00 100644
--- src/hg/lib/rnaSecStr.c
+++ src/hg/lib/rnaSecStr.c
@@ -1,192 +1,192 @@
 /* rnaSecStr.c was originally generated by the autoSql program, which also 
  * generated rnaSecStr.h and rnaSecStr.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 "rnaSecStr.h"
 
 
 struct rnaSecStr *rnaSecStrLoad(char **row)
 /* Load a rnaSecStr from row fetched with select * from rnaSecStr
- * from database.  Dispose of this with rnaSecStrFree(). */
+ * from database. Ignores conf column if present.  Dispose of this with rnaSecStrFree(). */
 {
 struct rnaSecStr *ret;
 
 AllocVar(ret);
 ret->size = sqlUnsigned(row[6]);
 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]);
 strcpy(ret->strand, row[5]);
 ret->secStr = cloneString(row[7]);
 return ret;
 }
 
 struct rnaSecStr *rnaSecStrLoadConf(char **row)
+/* Load a rnaSecStr from row fetched with select * from rnaSecStr
+ * from database. Loads conf column.  Dispose of this with rnaSecStrFree(). */
 {
 struct rnaSecStr *ret;
-/* Load a rnaSecStr from row fetched with select * from rnaSecStr
- * from database.  Dispose of this with rnaSecStrFree(). */
 
 AllocVar(ret);
 ret->size = sqlUnsigned(row[6]);
 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]);
 strcpy(ret->strand, row[5]);
 ret->secStr = cloneString(row[7]);
 {
 int sizeOne;
 sqlDoubleDynamicArray(row[8], &ret->conf, &sizeOne);
 assert(sizeOne == ret->size);
 }
 return ret;
 }
 
 struct rnaSecStr *rnaSecStrLoadAll(char *fileName) 
 /* Load all rnaSecStr from a whitespace-separated file.
  * Dispose of this with rnaSecStrFreeList(). */
 {
 struct rnaSecStr *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[9];
 
 while (lineFileRow(lf, row))
     {
     el = rnaSecStrLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct rnaSecStr *rnaSecStrLoadAllByChar(char *fileName, char chopper) 
 /* Load all rnaSecStr from a chopper separated file.
  * Dispose of this with rnaSecStrFreeList(). */
 {
 struct rnaSecStr *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[9];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = rnaSecStrLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct rnaSecStr *rnaSecStrCommaIn(char **pS, struct rnaSecStr *ret)
 /* Create a rnaSecStr out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new rnaSecStr */
 {
 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->size = sqlUnsignedComma(&s);
 ret->secStr = sqlStringComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->conf, ret->size);
 for (i=0; i<ret->size; ++i)
     {
     ret->conf[i] = sqlDoubleComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 *pS = s;
 return ret;
 }
 
 void rnaSecStrFree(struct rnaSecStr **pEl)
 /* Free a single dynamically allocated rnaSecStr such as created
  * with rnaSecStrLoad(). */
 {
 struct rnaSecStr *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->secStr);
 freeMem(el->conf);
 freez(pEl);
 }
 
 void rnaSecStrFreeList(struct rnaSecStr **pList)
 /* Free a list of dynamically allocated rnaSecStr's */
 {
 struct rnaSecStr *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     rnaSecStrFree(&el);
     }
 *pList = NULL;
 }
 
 void rnaSecStrOutput(struct rnaSecStr *el, FILE *f, char sep, char lastSep) 
 /* Print out rnaSecStr.  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);
 fprintf(f, "%u", el->size);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->secStr);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->size; ++i)
     {
     fprintf(f, "%g", el->conf[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */