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/ensFace.c src/hg/lib/ensFace.c
index c2c84b7..c2fc4a8 100644
--- src/hg/lib/ensFace.c
+++ src/hg/lib/ensFace.c
@@ -1,169 +1,172 @@
 /* ensFace - stuff to manage interface to Ensembl web site. */
 
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "dystring.h"
 #include "ensFace.h"
 #include "hCommon.h"
 #include "hdb.h"
 
 
 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";
         }
     if (sameWord(scientificName, "Spermophilus tridecemlineatus"))
         {
         /* special case for squirrel, whose scientific name has been
          * changed from Spermophilusv to Ictidomys at ensembl */
         return "Ictidomys_tridecemlineatus";
         }
 
     /* 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];
     sqlSafef(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];
     sqlSafef(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 (archive)
     if (sameWord(archive,"ncbi36"))
 	{
     dyStringPrintf(dy, 
 	   "http://%s.ensembl.org/%s/contigview?chr=%s&start=%d&end=%d",
 		    archive, ensOrg, chrName, start, end);
 	}
     else
 	{
     dyStringPrintf(dy, 
 	   "http://%s.archive.ensembl.org/%s/contigview?chr=%s&start=%d&end=%d",
 		    archive, ensOrg, chrName, start, end);
 	}
 else
     dyStringPrintf(dy, 
                "http://www.ensembl.org/%s/contigview?chr=%s&start=%d&end=%d", ensOrg, chrName, start, end);
 return dy;
 }
 
 void ensGeneTrackVersion(char *database, char *ensVersionString,
     char *ensDateReference, int stringSize)
 /* check for trackVersion table and find Ensembl version */
 {
 /* see if hgFixed.trackVersion exists */
 boolean trackVersionExists = (sqlDatabaseExists("hgFixed") && hTableExists("hgFixed", "trackVersion"));
 ensVersionString[0] = 0;
 ensDateReference[0] = 0;
 if (trackVersionExists)
     {
     struct sqlConnection *conn = hAllocConn("hgFixed");
     char query[256];
     sqlSafef(query, sizeof(query), "select version,dateReference from hgFixed.trackVersion where db = '%s' and name = 'ensGene' order by updateTime DESC limit 1", database);
     struct sqlResult *sr = sqlGetResult(conn, query);
     char **row;
 
     while ((row = sqlNextRow(sr)) != NULL)
 	{
 	safef(ensVersionString, stringSize, "Ensembl %s", row[0]);
 	safef(ensDateReference, stringSize, "%s", row[1]);
 	}
     sqlFreeResult(&sr);
     hFreeConn(&conn);
     }
 }