c4fe426d0936ce30c7fd65c63dd29a19abb830dc
braney
  Sun Mar 15 15:22:12 2015 -0700
allow using different names for the following tables:  dbDb, defaultDb,
genomeClade, and clade.   This will allow for testing of alternate
versions of these tables on hgwdev.

diff --git src/hg/hgLiftOver/hgLiftOver.c src/hg/hgLiftOver/hgLiftOver.c
index 899cb31..1b97923 100644
--- src/hg/hgLiftOver/hgLiftOver.c
+++ src/hg/hgLiftOver/hgLiftOver.c
@@ -57,31 +57,31 @@
 "document.mainForm.submit();\"";
 
 char *chainStringVal(struct liftOverChain *chain)
 /* keep the last chain in memory in this format */
 {
 char chainS[64];
 safef(chainS, sizeof(chainS), "%s.%s", chain->fromDb, chain->toDb);
 return cloneString(chainS);
 }
 
 void webMain(struct liftOverChain *chain, boolean multiple, boolean keepSettings, int minSizeQ, 
 	     int minChainT, float minBlocks, float minMatch, boolean fudgeThick)
 /* set up page for entering data */
 {
 struct dbDb *dbList;
-char *fromOrg = hArchiveOrganism(chain->fromDb), *toOrg = hArchiveOrganism(chain->toDb);
+char *fromOrg = hOrganism(chain->fromDb), *toOrg = hOrganism(chain->toDb);
 char *chainString = chainStringVal(chain);
 cgiParagraph(
     "This tool converts genome coordinates and genome annotation files "
     "between assemblies.  "
     "The input data can be pasted into the text box, or uploaded from a file.  "
     "If a pair of assemblies cannot be selected from the pull-down menus,"
     " a direct lift between them is unavailable.  "
     "However, a sequential lift may be possible.  "
     "Example: lift from Mouse, May 2004, to Mouse, Feb. 2006, and then from Mouse, "
     "Feb. 2006 to Mouse, July 2007 to achieve a lift from mm5 to mm9.  "
     "");
 
 /* create HMTL form */
 puts("<FORM ACTION=\"../cgi-bin/hgLiftOver\" METHOD=\"POST\" "
        " ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n");
@@ -367,40 +367,40 @@
 score += 10*(maxRank-fromRank);
 score += (maxRank - toRank);
 
 return score;
 }
 
 
 struct liftOverChain *defaultChoices(struct liftOverChain *chainList,
 				     char *cartDb)
 /* Out of a list of liftOverChains and a cart, choose a
  * list to display. */
 {
 char *fromOrg, *fromDb, *toOrg, *toDb, *cartOrg;
 struct liftOverChain *choice = NULL;  
 struct hash *dbRank = hGetDatabaseRank();
-struct hash *dbDbHash = hDbDbAndArchiveHash();
+struct hash *dbDbHash = hDbDbHash();
 double bestScore = -1;
 struct liftOverChain *this = NULL;
 
 /* Get the initial values. */
 fromOrg = cartCgiUsualString(cart, HGLFT_FROMORG_VAR, "0");
 fromDb = cartCgiUsualString(cart, HGLFT_FROMDB_VAR, "0");
 toOrg = cartCgiUsualString(cart, HGLFT_TOORG_VAR, "0");
 toDb = cartCgiUsualString(cart, HGLFT_TODB_VAR, "0");
-cartOrg = hArchiveOrganism(cartDb);
+cartOrg = hOrganism(cartDb);
 
 if (sameWord(fromOrg,"0"))
     fromOrg = NULL;
 if (sameWord(fromDb,"0"))
     fromDb = NULL;
 if (sameWord(toOrg,"0"))
     toOrg = NULL;
 if (sameWord(toDb,"0"))
     toDb = NULL;
 if (sameWord(cartDb,"0"))
     cartDb = NULL;
 
 for (this = chainList; this != NULL; this = this->next)
     {
     double score = scoreLiftOverChain(this, fromOrg, fromDb, toOrg, toDb, cartOrg, cartDb, dbRank, dbDbHash);