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/encode/encodeRna.c src/hg/lib/encode/encodeRna.c
index 68fb588..592c98b 100644
--- src/hg/lib/encode/encodeRna.c
+++ src/hg/lib/encode/encodeRna.c
@@ -1,235 +1,235 @@
 /* encodeRna.c was originally generated by the autoSql program, which also 
  * generated encodeRna.h and encodeRna.sql.  This module links the database and
  * the RAM representation of objects. */
 
 /* Copyright (C) 2013 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 "encode/encodeRna.h"
 
 
 void encodeRnaStaticLoad(char **row, struct encodeRna *ret)
 /* Load a row from encodeRna table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->chrom = row[0];
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = row[3];
 ret->score = sqlUnsigned(row[4]);
 ret->strand = row[5];
 ret->source = row[6];
 ret->type = row[7];
 ret->fullScore = atof(row[8]);
 ret->isPsuedo = sqlUnsigned(row[9]);
 ret->isRmasked = sqlUnsigned(row[10]);
 ret->isTranscribed = sqlUnsigned(row[11]);
 ret->isPrediction = sqlUnsigned(row[12]);
 ret->transcribedIn = row[13];
 }
 
 struct encodeRna *encodeRnaLoad(char **row)
 /* Load a encodeRna from row fetched with select * from encodeRna
  * from database.  Dispose of this with encodeRnaFree(). */
 {
 struct encodeRna *ret;
 
 AllocVar(ret);
 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]);
 ret->strand = cloneString(row[5]);
 ret->source = cloneString(row[6]);
 ret->type = cloneString(row[7]);
 ret->fullScore = atof(row[8]);
 ret->isPsuedo = sqlUnsigned(row[9]);
 ret->isRmasked = sqlUnsigned(row[10]);
 ret->isTranscribed = sqlUnsigned(row[11]);
 ret->isPrediction = sqlUnsigned(row[12]);
 ret->transcribedIn = cloneString(row[13]);
 return ret;
 }
 
 struct encodeRna *encodeRnaLoadAll(char *fileName) 
 /* Load all encodeRna from a whitespace-separated file.
  * Dispose of this with encodeRnaFreeList(). */
 {
 struct encodeRna *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[14];
 
 while (lineFileRow(lf, row))
     {
     el = encodeRnaLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct encodeRna *encodeRnaLoadAllByChar(char *fileName, char chopper) 
 /* Load all encodeRna from a chopper separated file.
  * Dispose of this with encodeRnaFreeList(). */
 {
 struct encodeRna *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[14];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = encodeRnaLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct encodeRna *encodeRnaLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all encodeRna 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 encodeRnaFreeList(). */
 {
 struct encodeRna *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = encodeRnaLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void encodeRnaSaveToDb(struct sqlConnection *conn, struct encodeRna *el, char *tableName, int updateSize)
 /* Save encodeRna 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',%u,%u,'%s',%u,'%s','%s','%s',%g,%u,%u,%u,%u,'%s')", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->source,  el->type,  el->fullScore,  el->isPsuedo,  el->isRmasked,  el->isTranscribed,  el->isPrediction,  el->transcribedIn);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct encodeRna *encodeRnaCommaIn(char **pS, struct encodeRna *ret)
 /* Create a encodeRna out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new encodeRna */
 {
 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);
 ret->strand = sqlStringComma(&s);
 ret->source = sqlStringComma(&s);
 ret->type = sqlStringComma(&s);
 ret->fullScore = sqlFloatComma(&s);
 ret->isPsuedo = sqlUnsignedComma(&s);
 ret->isRmasked = sqlUnsignedComma(&s);
 ret->isTranscribed = sqlUnsignedComma(&s);
 ret->isPrediction = sqlUnsignedComma(&s);
 ret->transcribedIn = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void encodeRnaFree(struct encodeRna **pEl)
 /* Free a single dynamically allocated encodeRna such as created
  * with encodeRnaLoad(). */
 {
 struct encodeRna *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->strand);
 freeMem(el->source);
 freeMem(el->type);
 freeMem(el->transcribedIn);
 freez(pEl);
 }
 
 void encodeRnaFreeList(struct encodeRna **pList)
 /* Free a list of dynamically allocated encodeRna's */
 {
 struct encodeRna *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     encodeRnaFree(&el);
     }
 *pList = NULL;
 }
 
 void encodeRnaOutput(struct encodeRna *el, FILE *f, char sep, char lastSep) 
 /* Print out encodeRna.  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);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->source);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->type);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->fullScore);
 fputc(sep,f);
 fprintf(f, "%u", el->isPsuedo);
 fputc(sep,f);
 fprintf(f, "%u", el->isRmasked);
 fputc(sep,f);
 fprintf(f, "%u", el->isTranscribed);
 fputc(sep,f);
 fprintf(f, "%u", el->isPrediction);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->transcribedIn);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */