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/taxonNode.c src/hg/lib/taxonNode.c
index d062e07..f500b9d 100644
--- src/hg/lib/taxonNode.c
+++ src/hg/lib/taxonNode.c
@@ -1,218 +1,221 @@
 /* taxonNode.c was originally generated by the autoSql program, which also 
  * generated taxonNode.h and taxonNode.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 "taxonNode.h"
 
 
 void taxonNodeStaticLoad(char **row, struct taxonNode *ret)
 /* Load a row from taxonNode table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->taxon = sqlUnsigned(row[0]);
 ret->parent = sqlUnsigned(row[1]);
 ret->rank = row[2];
 ret->emblcode = row[3];
 ret->division = sqlUnsigned(row[4]);
 ret->inheritedDiv = sqlUnsigned(row[5]);
 ret->geneticCode = sqlUnsigned(row[6]);
 ret->inheritedGC = sqlUnsigned(row[7]);
 ret->mitoGeneticCode = sqlUnsigned(row[8]);
 ret->inheritedMitoGC = sqlUnsigned(row[9]);
 ret->GenBankHidden = sqlUnsigned(row[10]);
 ret->notSequenced = sqlUnsigned(row[11]);
 ret->comments = row[12];
 }
 
 struct taxonNode *taxonNodeLoad(char **row)
 /* Load a taxonNode from row fetched with select * from taxonNode
  * from database.  Dispose of this with taxonNodeFree(). */
 {
 struct taxonNode *ret;
 
 AllocVar(ret);
 ret->taxon = sqlUnsigned(row[0]);
 ret->parent = sqlUnsigned(row[1]);
 ret->rank = cloneString(row[2]);
 ret->emblcode = cloneString(row[3]);
 ret->division = sqlUnsigned(row[4]);
 ret->inheritedDiv = sqlUnsigned(row[5]);
 ret->geneticCode = sqlUnsigned(row[6]);
 ret->inheritedGC = sqlUnsigned(row[7]);
 ret->mitoGeneticCode = sqlUnsigned(row[8]);
 ret->inheritedMitoGC = sqlUnsigned(row[9]);
 ret->GenBankHidden = sqlUnsigned(row[10]);
 ret->notSequenced = sqlUnsigned(row[11]);
 ret->comments = cloneString(row[12]);
 return ret;
 }
 
 struct taxonNode *taxonNodeLoadAll(char *fileName) 
 /* Load all taxonNode from a whitespace-separated file.
  * Dispose of this with taxonNodeFreeList(). */
 {
 struct taxonNode *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[13];
 
 while (lineFileRow(lf, row))
     {
     el = taxonNodeLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct taxonNode *taxonNodeLoadAllByChar(char *fileName, char chopper) 
 /* Load all taxonNode from a chopper separated file.
  * Dispose of this with taxonNodeFreeList(). */
 {
 struct taxonNode *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[13];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = taxonNodeLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct taxonNode *taxonNodeLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all taxonNode 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 taxonNodeFreeList(). */
 {
 struct taxonNode *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = taxonNodeLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void taxonNodeSaveToDb(struct sqlConnection *conn, struct taxonNode *el, char *tableName, int updateSize)
 /* Save taxonNode 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 ( %u,%u,'%s','%s',%u,%u,%u,%u,%u,%u,%u,%u,'%s')", 
 	tableName,  el->taxon,  el->parent,  el->rank,  el->emblcode,  el->division,  el->inheritedDiv,  el->geneticCode,  el->inheritedGC,  el->mitoGeneticCode,  el->inheritedMitoGC,  el->GenBankHidden,  el->notSequenced,  el->comments);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct taxonNode *taxonNodeCommaIn(char **pS, struct taxonNode *ret)
 /* Create a taxonNode out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new taxonNode */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->taxon = sqlUnsignedComma(&s);
 ret->parent = sqlUnsignedComma(&s);
 ret->rank = sqlStringComma(&s);
 ret->emblcode = sqlStringComma(&s);
 ret->division = sqlUnsignedComma(&s);
 ret->inheritedDiv = sqlUnsignedComma(&s);
 ret->geneticCode = sqlUnsignedComma(&s);
 ret->inheritedGC = sqlUnsignedComma(&s);
 ret->mitoGeneticCode = sqlUnsignedComma(&s);
 ret->inheritedMitoGC = sqlUnsignedComma(&s);
 ret->GenBankHidden = sqlUnsignedComma(&s);
 ret->notSequenced = sqlUnsignedComma(&s);
 ret->comments = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void taxonNodeFree(struct taxonNode **pEl)
 /* Free a single dynamically allocated taxonNode such as created
  * with taxonNodeLoad(). */
 {
 struct taxonNode *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->rank);
 freeMem(el->emblcode);
 freeMem(el->comments);
 freez(pEl);
 }
 
 void taxonNodeFreeList(struct taxonNode **pList)
 /* Free a list of dynamically allocated taxonNode's */
 {
 struct taxonNode *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     taxonNodeFree(&el);
     }
 *pList = NULL;
 }
 
 void taxonNodeOutput(struct taxonNode *el, FILE *f, char sep, char lastSep) 
 /* Print out taxonNode.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%u", el->taxon);
 fputc(sep,f);
 fprintf(f, "%u", el->parent);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->rank);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->emblcode);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->division);
 fputc(sep,f);
 fprintf(f, "%u", el->inheritedDiv);
 fputc(sep,f);
 fprintf(f, "%u", el->geneticCode);
 fputc(sep,f);
 fprintf(f, "%u", el->inheritedGC);
 fputc(sep,f);
 fprintf(f, "%u", el->mitoGeneticCode);
 fputc(sep,f);
 fprintf(f, "%u", el->inheritedMitoGC);
 fputc(sep,f);
 fprintf(f, "%u", el->GenBankHidden);
 fputc(sep,f);
 fprintf(f, "%u", el->notSequenced);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->comments);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */