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/sage.c src/hg/lib/sage.c
index be48c07..0aea20f 100644
--- src/hg/lib/sage.c
+++ src/hg/lib/sage.c
@@ -1,212 +1,215 @@
 /* sage.c was originally generated by the autoSql program, which also 
  * generated sage.h and sage.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 "jksql.h"
 #include "sage.h"
 
 
 struct sage *sageLoad(char **row)
 /* Load a sage from row fetched with select * from sage
  * from database.  Dispose of this with sageFree(). */
 {
 struct sage *ret;
 int sizeOne;
 
 AllocVar(ret);
 ret->numTags = sqlSigned(row[4]);
 ret->numExps = sqlSigned(row[6]);
 ret->uni = sqlSigned(row[0]);
 strcpy(ret->gb, row[1]);
 strcpy(ret->gi, row[2]);
 ret->description = cloneString(row[3]);
 sqlStringDynamicArray(row[5], &ret->tags, &sizeOne);
 assert(sizeOne == ret->numTags);
 sqlSignedDynamicArray(row[7], &ret->exps, &sizeOne);
 assert(sizeOne == ret->numExps);
 sqlFloatDynamicArray(row[8], &ret->meds, &sizeOne);
 assert(sizeOne == ret->numExps);
 sqlFloatDynamicArray(row[9], &ret->aves, &sizeOne);
 assert(sizeOne == ret->numExps);
 sqlFloatDynamicArray(row[10], &ret->stdevs, &sizeOne);
 assert(sizeOne == ret->numExps);
 return ret;
 }
 
 struct sage *sageLoadAll(char *fileName) 
 /* Load all sage from a tab-separated file.
  * Dispose of this with sageFreeList(). */
 {
 struct sage *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[11];
 
 while (lineFileRow(lf, row))
     {
     el = sageLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct sage *sageCommaIn(char **pS, struct sage *ret)
 /* Create a sage out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new sage */
 {
 char *s = *pS;
 int i;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->uni = sqlSignedComma(&s);
 sqlFixedStringComma(&s, ret->gb, sizeof(ret->gb));
 sqlFixedStringComma(&s, ret->gi, sizeof(ret->gi));
 ret->description = sqlStringComma(&s);
 ret->numTags = sqlSignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->tags, ret->numTags);
 for (i=0; i<ret->numTags; ++i)
     {
     ret->tags[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->numExps = sqlSignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->exps, ret->numExps);
 for (i=0; i<ret->numExps; ++i)
     {
     ret->exps[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->meds, ret->numExps);
 for (i=0; i<ret->numExps; ++i)
     {
     ret->meds[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->aves, ret->numExps);
 for (i=0; i<ret->numExps; ++i)
     {
     ret->aves[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->stdevs, ret->numExps);
 for (i=0; i<ret->numExps; ++i)
     {
     ret->stdevs[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 *pS = s;
 return ret;
 }
 
 void sageFree(struct sage **pEl)
 /* Free a single dynamically allocated sage such as created
  * with sageLoad(). */
 {
 struct sage *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->description);
 /* All strings in tags are allocated at once, so only need to free first. */
 freeMem(el->tags[0]);
 freeMem(el->tags);
 freeMem(el->exps);
 freeMem(el->meds);
 freeMem(el->aves);
 freeMem(el->stdevs);
 freez(pEl);
 }
 
 void sageFreeList(struct sage **pList)
 /* Free a list of dynamically allocated sage's */
 {
 struct sage *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     sageFree(&el);
     }
 *pList = NULL;
 }
 
 void sageOutput(struct sage *el, FILE *f, char sep, char lastSep) 
 /* Print out sage.  Separate fields with sep. Follow last field with lastSep. */
 {
 int i;
 fprintf(f, "%d", el->uni);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->gb);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->gi);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->description);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->numTags);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->numTags; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->tags[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%d", el->numExps);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->numExps; ++i)
     {
     fprintf(f, "%d", el->exps[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->numExps; ++i)
     {
     fprintf(f, "%f", el->meds[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->numExps; ++i)
     {
     fprintf(f, "%f", el->aves[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->numExps; ++i)
     {
     fprintf(f, "%f", el->stdevs[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(lastSep,f);
 }