static void transformToCanonical(struct searchResult *list,
struct sqlConnection *conn)
/* Transform search results to canonical versions. */
{
struct dyString *dy = newDyString(1024);
char *cannon = genomeSetting("canonicalTable");
char *isoform = genomeSetting("isoformTable");
struct sqlResult *sr;
char **row;
struct searchResult *el;
for (el = list; el != NULL; el = el->next)
{
dyStringClear(dy);
sqlDyStringPrintf(dy,
"select %s.transcript,%s.chrom,%s.chromStart,%s.chromEnd,%s.protein ",
cannon, cannon, cannon, cannon, cannon);
sqlDyStringPrintf(dy,
"from %s,%s ",
isoform, cannon);
sqlDyStringPrintf(dy,
"where %s.transcript = '%s' ",
isoform, el->gp.name);
sqlDyStringPrintf(dy,
"and %s.clusterId = %s.clusterId",
isoform, cannon);
sr = sqlGetResult(conn, dy->string);
if ((row = sqlNextRow(sr)) != NULL)
genePosFillFrom5(&el->gp, row);
sqlFreeResult(&sr);
}
dyStringFree(&dy);
}
static struct genePos *genePosFromQuery(struct sqlConnection *conn, char *query, boolean oneOnly)
/* Get all positions from a query that returns 5 columns. */
{
struct sqlResult *sr;
char **row;
struct genePos *gpList = NULL, *gp;
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
AllocVar(gp);
genePosFillFrom5(gp, row);
slAddHead(&gpList, gp);
if (oneOnly)
break;
}
sqlFreeResult(&sr);
return gpList;
}