src/hg/lib/ensFace.c 1.11

Index: src/hg/lib/ensFace.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/ensFace.c,v
retrieving revision 1.10
retrieving revision 1.11
diff -b -B -U 1000000 -r1.10 -r1.11
--- src/hg/lib/ensFace.c	8 May 2009 16:49:15 -0000	1.10
+++ src/hg/lib/ensFace.c	8 May 2009 17:36:16 -0000	1.11
@@ -1,108 +1,133 @@
 /* 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;
 }
 
+static int liftToEnsembl(char *database, char *chrom)
+/* if table ENSEMBL_LIFT exists in the given database, return the
+   offset for this chrom, else return zero */
+{
+int offset = 0;
+struct sqlConnection *conn = hAllocConn(database);
+
+if (sqlTableExists(conn, ENSEMBL_LIFT))
+    {
+    char query[256];
+    safef(query, ArraySize(query), "select offset from %s where chrom='%s'",
+	ENSEMBL_LIFT, chrom);
+    offset = sqlQuickNum(conn,query); // returns 0 for failed query
+    }
+return offset;
+}
+
 struct dyString *ensContigViewUrl(
 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);
+int ensemblLift = 0;
+int start = winStart;
+int end = winEnd;
 
 if (isNotEmpty(ensemblName))
+    {
     chrName = ensemblName;
+    ensemblLift = liftToEnsembl(database, ensemblName);
+    start += ensemblLift;
+    end += ensemblLift;
+    }
 else if (startsWith("scaffold", chrom))
     chrName = chrom;
 else
     chrName = skipChr(chrom);
 if (sameWord(database,"hg19"))
     dyStringPrintf(dy, 
 	   "http://pre.ensembl.org/%s/contigview?chr=%s&start=%d&end=%d",
-		    ensOrg, chrName, winStart, winEnd);
+		    ensOrg, chrName, start, end);
 else if (archive)
     dyStringPrintf(dy, 
 	   "http://%s.archive.ensembl.org/%s/contigview?chr=%s&start=%d&end=%d",
-		    archive, ensOrg, chrName, winStart, winEnd);
+		    archive, ensOrg, chrName, start, end);
 else
     dyStringPrintf(dy, 
-               "http://www.ensembl.org/%s/contigview?chr=%s&start=%d&end=%d", ensOrg, chrName, winStart, winEnd);
+               "http://www.ensembl.org/%s/contigview?chr=%s&start=%d&end=%d", ensOrg, chrName, start, end);
 return dy;
 }