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/itemAttr.c src/hg/lib/itemAttr.c
index 78a16c2..121f06a 100644
--- src/hg/lib/itemAttr.c
+++ src/hg/lib/itemAttr.c
@@ -1,223 +1,226 @@
 /* itemAttr.c was originally generated by the autoSql program, which also 
  * generated itemAttr.h and itemAttr.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 "itemAttr.h"
 #include "hdb.h"
 
 
 void itemAttrStaticLoad(char **row, struct itemAttr *ret)
 /* Load a row from itemAttr table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->name = row[0];
 ret->chrom = row[1];
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->colorR = sqlUnsigned(row[4]);
 ret->colorG = sqlUnsigned(row[5]);
 ret->colorB = sqlUnsigned(row[6]);
 }
 
 struct itemAttr *itemAttrLoad(char **row)
 /* Load a itemAttr from row fetched with select * from itemAttr
  * from database.  Dispose of this with itemAttrFree(). */
 {
 struct itemAttr *ret;
 
 AllocVar(ret);
 ret->name = cloneString(row[0]);
 ret->chrom = cloneString(row[1]);
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->colorR = sqlUnsigned(row[4]);
 ret->colorG = sqlUnsigned(row[5]);
 ret->colorB = sqlUnsigned(row[6]);
 return ret;
 }
 
 struct itemAttr *itemAttrLoadAll(char *fileName) 
 /* Load all itemAttr from a whitespace-separated file.
  * Dispose of this with itemAttrFreeList(). */
 {
 struct itemAttr *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileRow(lf, row))
     {
     el = itemAttrLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct itemAttr *itemAttrLoadAllByChar(char *fileName, char chopper) 
 /* Load all itemAttr from a chopper separated file.
  * Dispose of this with itemAttrFreeList(). */
 {
 struct itemAttr *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = itemAttrLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct itemAttr *itemAttrCommaIn(char **pS, struct itemAttr *ret)
 /* Create a itemAttr out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new itemAttr */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->name = sqlStringComma(&s);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->colorR = sqlUnsignedComma(&s);
 ret->colorG = sqlUnsignedComma(&s);
 ret->colorB = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void itemAttrFree(struct itemAttr **pEl)
 /* Free a single dynamically allocated itemAttr such as created
  * with itemAttrLoad(). */
 {
 struct itemAttr *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->name);
 freeMem(el->chrom);
 freez(pEl);
 }
 
 void itemAttrFreeList(struct itemAttr **pList)
 /* Free a list of dynamically allocated itemAttr's */
 {
 struct itemAttr *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     itemAttrFree(&el);
     }
 *pList = NULL;
 }
 
 void itemAttrOutput(struct itemAttr *el, FILE *f, char sep, char lastSep) 
 /* Print out itemAttr.  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);
 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);
 fprintf(f, "%u", el->colorR);
 fputc(sep,f);
 fprintf(f, "%u", el->colorG);
 fputc(sep,f);
 fprintf(f, "%u", el->colorB);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 
 struct itemAttrTbl
 /* object holding itemAttr from a range query */
 {
     char *table;
     struct hash *nameMap;  /* hash of items, indexed by name, multiple
                             * entries per name allowed. */
 };
 
 struct itemAttrTbl *itemAttrTblNew(char *table)
 /* Create a new itemAttr object. This saves the table name, but
  * doesn't load the data. */
 {
 struct itemAttrTbl *iat;
 AllocVar(iat);
 iat->table = cloneString(table);
 return iat;    
 }
 
 void itemAttrTblLoad(struct itemAttrTbl *iat,
                      struct sqlConnection *conn,
                      char *chrom, int start, int end)
 /* load itemAttrs for the specified chrom range */
 {
 int rowOffset;
 struct sqlResult *result;
 char **row;
 
 if (iat->nameMap == NULL)
     iat->nameMap = hashNew(18);
 
 result = hRangeQuery(conn, iat->table, chrom, start, end,
                      NULL, &rowOffset);
 
 while ((row = sqlNextRow(result)) != NULL)
     {
     struct itemAttr* ia = itemAttrLoad(row+rowOffset);
     hashAdd(iat->nameMap, ia->name, ia);
     }
 sqlFreeResult(&result);
 }
 
 struct itemAttr *itemAttrTblGet(struct itemAttrTbl *iat, char* name,
                                 char *chrom, int chromStart, int chromEnd)
 /* lookup an itemAttr by name and location */
 {
 struct hashEl *hel = hashLookup(iat->nameMap, name);
 
 /* search for matching location */
 while (hel != NULL)
     {
     struct itemAttr* ia = hel->val;
     if ((ia->chromStart == chromStart) && (ia->chromEnd == chromEnd)
         && sameString(ia->chrom, chrom))
         return ia;
     hel = hashLookupNext(hel);
     }
 return NULL; /* not found */
 }
 
 void itemAttrTblFree(struct itemAttrTbl **iatPtr)
 /* free an itemAttrTbl */
 {
 struct itemAttrTbl *iat = *iatPtr;
 if (iat != NULL)
     {
     struct hashCookie cookie = hashFirst(iat->nameMap);
     struct hashEl *hel;
     while((hel = hashNext(&cookie)) != NULL)
         itemAttrFree((struct itemAttr**)&hel->val);
     hashFree(&iat->nameMap);
     freez(iatPtr);
     }
 }