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/rikenCluster.c src/hg/lib/rikenCluster.c
index 6d5f7ad..c5857dd 100644
--- src/hg/lib/rikenCluster.c
+++ src/hg/lib/rikenCluster.c
@@ -1,224 +1,227 @@
 /* rikenCluster.c was originally generated by the autoSql program, which also 
  * generated rikenCluster.h and rikenCluster.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 "rikenCluster.h"
 
 
 struct rikenUcscCluster *rikenUcscClusterLoad(char **row)
 /* Load a rikenUcscCluster from row fetched with select * from rikenUcscCluster
  * from database.  Dispose of this with rikenUcscClusterFree(). */
 {
 struct rikenUcscCluster *ret;
 int sizeOne;
 
 AllocVar(ret);
 ret->refSeqCount = sqlUnsigned(row[6]);
 ret->genBankCount = sqlUnsigned(row[8]);
 ret->rikenCount = sqlUnsigned(row[10]);
 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]);
 strcpy(ret->strand, row[5]);
 sqlStringDynamicArray(row[7], &ret->refSeqs, &sizeOne);
 assert(sizeOne == ret->refSeqCount);
 sqlStringDynamicArray(row[9], &ret->genBanks, &sizeOne);
 assert(sizeOne == ret->genBankCount);
 sqlStringDynamicArray(row[11], &ret->rikens, &sizeOne);
 assert(sizeOne == ret->rikenCount);
 return ret;
 }
 
 struct rikenUcscCluster *rikenUcscClusterLoadAll(char *fileName) 
 /* Load all rikenUcscCluster from a tab-separated file.
  * Dispose of this with rikenUcscClusterFreeList(). */
 {
 struct rikenUcscCluster *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileRow(lf, row))
     {
     el = rikenUcscClusterLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct rikenUcscCluster *rikenUcscClusterLoadWhere(struct sqlConnection *conn, char *table, char *where)
 /* Load all rikenUcscCluster from table that satisfy where clause. The
  * where clause may be NULL in which case whole table is loaded
  * Dispose of this with rikenUcscClusterFreeList(). */
 {
 struct rikenUcscCluster *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 = rikenUcscClusterLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 dyStringFree(&query);
 return list;
 }
 
 struct rikenUcscCluster *rikenUcscClusterCommaIn(char **pS, struct rikenUcscCluster *ret)
 /* Create a rikenUcscCluster out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new rikenUcscCluster */
 {
 char *s = *pS;
 int i;
 
 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);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->refSeqCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->refSeqs, ret->refSeqCount);
 for (i=0; i<ret->refSeqCount; ++i)
     {
     ret->refSeqs[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->genBankCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->genBanks, ret->genBankCount);
 for (i=0; i<ret->genBankCount; ++i)
     {
     ret->genBanks[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->rikenCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->rikens, ret->rikenCount);
 for (i=0; i<ret->rikenCount; ++i)
     {
     ret->rikens[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 *pS = s;
 return ret;
 }
 
 void rikenUcscClusterFree(struct rikenUcscCluster **pEl)
 /* Free a single dynamically allocated rikenUcscCluster such as created
  * with rikenUcscClusterLoad(). */
 {
 struct rikenUcscCluster *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 /* All strings in refSeqs are allocated at once, so only need to free first. */
 if (el->refSeqs != NULL)
     freeMem(el->refSeqs[0]);
 freeMem(el->refSeqs);
 /* All strings in genBanks are allocated at once, so only need to free first. */
 if (el->genBanks != NULL)
     freeMem(el->genBanks[0]);
 freeMem(el->genBanks);
 /* All strings in rikens are allocated at once, so only need to free first. */
 if (el->rikens != NULL)
     freeMem(el->rikens[0]);
 freeMem(el->rikens);
 freez(pEl);
 }
 
 void rikenUcscClusterFreeList(struct rikenUcscCluster **pList)
 /* Free a list of dynamically allocated rikenUcscCluster's */
 {
 struct rikenUcscCluster *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     rikenUcscClusterFree(&el);
     }
 *pList = NULL;
 }
 
 void rikenUcscClusterOutput(struct rikenUcscCluster *el, FILE *f, char sep, char lastSep) 
 /* Print out rikenUcscCluster.  Separate fields with sep. Follow last field with lastSep. */
 {
 int i;
 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);
 fprintf(f, "%u", el->refSeqCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->refSeqCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->refSeqs[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%u", el->genBankCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->genBankCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->genBanks[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%u", el->rikenCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->rikenCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->rikens[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(lastSep,f);
 }