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/rikenBest.c src/hg/lib/rikenBest.c
index 3e83a03..aca6a11 100644
--- src/hg/lib/rikenBest.c
+++ src/hg/lib/rikenBest.c
@@ -1,168 +1,171 @@
 /* rikenBest.c was originally generated by the autoSql program, which also 
  * generated rikenBest.h and rikenBest.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 "rikenBest.h"
 
 
 void rikenBestStaticLoad(char **row, struct rikenBest *ret)
 /* Load a row from rikenBest table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->name = row[0];
 ret->orfScore = atof(row[1]);
 strcpy(ret->orfStrand, row[2]);
 ret->intronOrientation = sqlSigned(row[3]);
 ret->position = row[4];
 ret->rikenCount = sqlSigned(row[5]);
 ret->genBankCount = sqlSigned(row[6]);
 ret->refSeqCount = sqlSigned(row[7]);
 ret->clusterId = row[8];
 }
 
 struct rikenBest *rikenBestLoad(char **row)
 /* Load a rikenBest from row fetched with select * from rikenBest
  * from database.  Dispose of this with rikenBestFree(). */
 {
 struct rikenBest *ret;
 
 AllocVar(ret);
 ret->name = cloneString(row[0]);
 ret->orfScore = atof(row[1]);
 strcpy(ret->orfStrand, row[2]);
 ret->intronOrientation = sqlSigned(row[3]);
 ret->position = cloneString(row[4]);
 ret->rikenCount = sqlSigned(row[5]);
 ret->genBankCount = sqlSigned(row[6]);
 ret->refSeqCount = sqlSigned(row[7]);
 ret->clusterId = cloneString(row[8]);
 return ret;
 }
 
 struct rikenBest *rikenBestLoadAll(char *fileName) 
 /* Load all rikenBest from a tab-separated file.
  * Dispose of this with rikenBestFreeList(). */
 {
 struct rikenBest *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[9];
 
 while (lineFileRow(lf, row))
     {
     el = rikenBestLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct rikenBest *rikenBestLoadWhere(struct sqlConnection *conn, char *table, char *where)
 /* Load all rikenBest from table that satisfy where clause. The
  * where clause may be NULL in which case whole table is loaded
  * Dispose of this with rikenBestFreeList(). */
 {
 struct rikenBest *list = NULL, *el;
 struct dyString *query = dyStringNew(256);
 struct sqlResult *sr;
 char **row;
 
 sqlDyStringPrintf(query, "select * from %s", table);
 if (where != NULL)
     dyStringPrintf(query, " where %s", where);
 sr = sqlGetResult(conn, query->string);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = rikenBestLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 dyStringFree(&query);
 return list;
 }
 
 struct rikenBest *rikenBestCommaIn(char **pS, struct rikenBest *ret)
 /* Create a rikenBest out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new rikenBest */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->name = sqlStringComma(&s);
 ret->orfScore = sqlFloatComma(&s);
 sqlFixedStringComma(&s, ret->orfStrand, sizeof(ret->orfStrand));
 ret->intronOrientation = sqlSignedComma(&s);
 ret->position = sqlStringComma(&s);
 ret->rikenCount = sqlSignedComma(&s);
 ret->genBankCount = sqlSignedComma(&s);
 ret->refSeqCount = sqlSignedComma(&s);
 ret->clusterId = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void rikenBestFree(struct rikenBest **pEl)
 /* Free a single dynamically allocated rikenBest such as created
  * with rikenBestLoad(). */
 {
 struct rikenBest *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->name);
 freeMem(el->position);
 freeMem(el->clusterId);
 freez(pEl);
 }
 
 void rikenBestFreeList(struct rikenBest **pList)
 /* Free a list of dynamically allocated rikenBest's */
 {
 struct rikenBest *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     rikenBestFree(&el);
     }
 *pList = NULL;
 }
 
 void rikenBestOutput(struct rikenBest *el, FILE *f, char sep, char lastSep) 
 /* Print out rikenBest.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->orfScore);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->orfStrand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->intronOrientation);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->position);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->rikenCount);
 fputc(sep,f);
 fprintf(f, "%d", el->genBankCount);
 fputc(sep,f);
 fprintf(f, "%d", el->refSeqCount);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->clusterId);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }