4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/lib/affyAtlas.c src/hg/lib/affyAtlas.c
index 8a68bef..d573370 100644
--- src/hg/lib/affyAtlas.c
+++ src/hg/lib/affyAtlas.c
@@ -1,169 +1,169 @@
 /* affyAtlas.c was originally generated by the autoSql program, which also 
  * generated affyAtlas.h and affyAtlas.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. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "affyAtlas.h"
 
 
 void affyAtlasStaticLoad(char **row, struct affyAtlas *ret)
 /* Load a row from affyAtlas table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 ret->annName = row[0];
 ret->probeSet = row[1];
 ret->signal = atof(row[2]);
 strcpy(ret->detection, row[3]);
 ret->pval = atof(row[4]);
 ret->tissue = row[5];
 }
 
 struct affyAtlas *affyAtlasLoad(char **row)
 /* Load a affyAtlas from row fetched with select * from affyAtlas
  * from database.  Dispose of this with affyAtlasFree(). */
 {
 struct affyAtlas *ret;
 
 AllocVar(ret);
 ret->annName = cloneString(row[0]);
 ret->probeSet = cloneString(row[1]);
 ret->signal = atof(row[2]);
 strcpy(ret->detection, row[3]);
 ret->pval = atof(row[4]);
 ret->tissue = cloneString(row[5]);
 return ret;
 }
 
 struct affyAtlas *affyAtlasLoadAll(char *fileName) 
 /* Load all affyAtlas from a tab-separated file.
  * Dispose of this with affyAtlasFreeList(). */
 {
 struct affyAtlas *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[6];
 
 while (lineFileRow(lf, row))
     {
     el = affyAtlasLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct affyAtlas *affyAtlasLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all affyAtlas from table that satisfy the query given.  
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something = 
  * anotherTable.something'.
  * Dispose of this with affyAtlasFreeList(). */
 {
 struct affyAtlas *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = affyAtlasLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void affyAtlasSaveToDb(struct sqlConnection *conn, struct affyAtlas *el, char *tableName, int updateSize)
 /* Save affyAtlas as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
 {
 struct dyString *update = newDyString(updateSize);
 sqlDyStringPrintf(update, "insert into %s values ( '%s','%s',%f,'%s',%f,'%s')", 
 	tableName,  el->annName,  el->probeSet,  el->signal,  el->detection,  el->pval,  el->tissue);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct affyAtlas *affyAtlasCommaIn(char **pS, struct affyAtlas *ret)
 /* Create a affyAtlas out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new affyAtlas */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->annName = sqlStringComma(&s);
 ret->probeSet = sqlStringComma(&s);
 ret->signal = sqlFloatComma(&s);
 sqlFixedStringComma(&s, ret->detection, sizeof(ret->detection));
 ret->pval = sqlFloatComma(&s);
 ret->tissue = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void affyAtlasFree(struct affyAtlas **pEl)
 /* Free a single dynamically allocated affyAtlas such as created
  * with affyAtlasLoad(). */
 {
 struct affyAtlas *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->annName);
 freeMem(el->probeSet);
 freeMem(el->tissue);
 freez(pEl);
 }
 
 void affyAtlasFreeList(struct affyAtlas **pList)
 /* Free a list of dynamically allocated affyAtlas's */
 {
 struct affyAtlas *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     affyAtlasFree(&el);
     }
 *pList = NULL;
 }
 
 void affyAtlasOutput(struct affyAtlas *el, FILE *f, char sep, char lastSep) 
 /* Print out affyAtlas.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->annName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->probeSet);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->signal);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->detection);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->pval);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tissue);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */