src/hg/lib/ensFace.c 1.10

Index: src/hg/lib/ensFace.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/ensFace.c,v
retrieving revision 1.9
retrieving revision 1.10
diff -b -B -U 1000000 -r1.9 -r1.10
--- src/hg/lib/ensFace.c	16 Jan 2009 05:42:15 -0000	1.9
+++ src/hg/lib/ensFace.c	8 May 2009 16:49:15 -0000	1.10
@@ -1,83 +1,108 @@
 /* ensFace - stuff to manage interface to Ensembl web site. */
 
 #include "common.h"
 #include "dystring.h"
 #include "ensFace.h"
 #include "hCommon.h"
+#include "hdb.h"
 
 static char const rcsid[] = "$Id$";
 
 struct stringPair
 /* A pair of strings. */
    {
    char *a;	/* One string. */
    char *b;	/* The other string */
    };
 
 
 char *ensOrgNameFromScientificName(char *scientificName)
 /* Convert from ucsc to Ensembl organism name.
  * This is scientific name, with underscore replacing spaces
  * Caller must free returned string */
 {
     char *p;
     char *res;
     if (scientificName == NULL) 
         return NULL;
     if (sameWord(scientificName, "Takifugu rubripes"))
         {
         /* special case for fugu, whose scientific name
          * has been changed to Takifugu, but not at ensembl */
         return "Fugu_rubripes";
         }
     if (sameWord(scientificName, "Pongo pygmaeus abelii"))
         {
         /* special case for Orangutan, different form of the same
          * scientific name */
         return "Pongo_pygmaeus";
         }
     if (sameWord(scientificName, "Canis lupus familiaris"))
         {
         /* special case for Dog, different form of the same
          * scientific name */
         return "Canis_familiaris";
         }
     if (sameWord(scientificName, "Gorilla gorilla gorilla"))
         {
         /* special case for Dog, different form of the same
          * scientific name */
         return "Gorilla_gorilla";
         }
     /* replace spaces with underscores, assume max two spaces
      * (species and sub-species).  */
     res = cloneString(scientificName);
     if ((p = index(res, ' ')) != NULL)
         *p = '_';
     if ((p = rindex(res, ' ')) != NULL)
         *p = '_';
     return res;
 }
 
+static char *ucscToEnsembl(char *database, char *chrom)
+/* if table UCSC_TO_ENSEMBL exists in the given database, return the
+   Ensembl name for this chrom */
+{
+static char ensemblName[256];
+struct sqlConnection *conn = hAllocConn(database);
+ensemblName[0] = 0;
+if (sqlTableExists(conn, UCSC_TO_ENSEMBL))
+    {
+    char query[256];
+    safef(query, ArraySize(query), "select ensembl from %s where ucsc='%s'",
+	UCSC_TO_ENSEMBL, chrom);
+    (void) sqlQuickQuery(conn,query,ensemblName,ArraySize(ensemblName));
+    }
+return ensemblName;
+}
+
 struct dyString *ensContigViewUrl(
-                            char *ensOrg, char *chrom, int chromSize,
+char *database, char *ensOrg, char *chrom, int chromSize,
                             int winStart, int winEnd, char *archive)
 /* Return a URL that will take you to ensembl's contig view. */
 /* Not using chromSize.  archive is possibly a date reference */
 {
 struct dyString *dy = dyStringNew(0);
 char *chrName;
+char *ensemblName = ucscToEnsembl(database, chrom);
 
-if (startsWith("scaffold", chrom))
+if (isNotEmpty(ensemblName))
+    chrName = ensemblName;
+else if (startsWith("scaffold", chrom))
     chrName = chrom;
 else
     chrName = skipChr(chrom);
-if (archive)
+if (sameWord(database,"hg19"))
+    dyStringPrintf(dy, 
+	   "http://pre.ensembl.org/%s/contigview?chr=%s&start=%d&end=%d",
+		    ensOrg, chrName, winStart, winEnd);
+else if (archive)
     dyStringPrintf(dy, 
 	   "http://%s.archive.ensembl.org/%s/contigview?chr=%s&start=%d&end=%d",
 		    archive, ensOrg, chrName, winStart, winEnd);
 else
     dyStringPrintf(dy, 
                "http://www.ensembl.org/%s/contigview?chr=%s&start=%d&end=%d", ensOrg, chrName, winStart, winEnd);
 return dy;
 }