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/taxonXref.c src/hg/lib/taxonXref.c
index b7749f0..93463b3 100644
--- src/hg/lib/taxonXref.c
+++ src/hg/lib/taxonXref.c
@@ -1,173 +1,176 @@
 /* taxonXref.c was originally generated by the autoSql program, which also 
  * generated taxonXref.h and taxonXref.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 "taxonXref.h"
 
 
 void taxonXrefStaticLoad(char **row, struct taxonXref *ret)
 /* Load a row from taxonXref table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->organism = row[0];
 ret->taxon = sqlUnsigned(row[1]);
 ret->name = row[2];
 ret->toGenus = row[3];
 }
 
 struct taxonXref *taxonXrefLoad(char **row)
 /* Load a taxonXref from row fetched with select * from taxonXref
  * from database.  Dispose of this with taxonXrefFree(). */
 {
 struct taxonXref *ret;
 
 AllocVar(ret);
 ret->organism = cloneString(row[0]);
 ret->taxon = sqlUnsigned(row[1]);
 ret->name = cloneString(row[2]);
 ret->toGenus = cloneString(row[3]);
 return ret;
 }
 
 struct taxonXref *taxonXrefLoadAll(char *fileName) 
 /* Load all taxonXref from a whitespace-separated file.
  * Dispose of this with taxonXrefFreeList(). */
 {
 struct taxonXref *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileRow(lf, row))
     {
     el = taxonXrefLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct taxonXref *taxonXrefLoadAllByChar(char *fileName, char chopper) 
 /* Load all taxonXref from a chopper separated file.
  * Dispose of this with taxonXrefFreeList(). */
 {
 struct taxonXref *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = taxonXrefLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct taxonXref *taxonXrefLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all taxonXref 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 taxonXrefFreeList(). */
 {
 struct taxonXref *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = taxonXrefLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void taxonXrefSaveToDb(struct sqlConnection *conn, struct taxonXref *el, char *tableName, int updateSize)
 /* Save taxonXref 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,'%s','%s')", 
 	tableName,  el->organism,  el->taxon,  el->name,  el->toGenus);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct taxonXref *taxonXrefCommaIn(char **pS, struct taxonXref *ret)
 /* Create a taxonXref out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new taxonXref */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->organism = sqlStringComma(&s);
 ret->taxon = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->toGenus = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void taxonXrefFree(struct taxonXref **pEl)
 /* Free a single dynamically allocated taxonXref such as created
  * with taxonXrefLoad(). */
 {
 struct taxonXref *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->organism);
 freeMem(el->name);
 freeMem(el->toGenus);
 freez(pEl);
 }
 
 void taxonXrefFreeList(struct taxonXref **pList)
 /* Free a list of dynamically allocated taxonXref's */
 {
 struct taxonXref *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     taxonXrefFree(&el);
     }
 *pList = NULL;
 }
 
 void taxonXrefOutput(struct taxonXref *el, FILE *f, char sep, char lastSep) 
 /* Print out taxonXref.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->organism);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->taxon);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->toGenus);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */